Query psy284
Match_columns 139
No_of_seqs 149 out of 1059
Neff 9.5
Searched_HMMs 46136
Date Fri Aug 16 18:14:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy284.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/284hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 6.5E-23 1.4E-27 151.3 1.6 99 36-139 332-436 (468)
2 KOG1044|consensus 99.9 1.4E-22 3E-27 154.2 3.2 123 9-138 101-226 (670)
3 KOG1701|consensus 99.8 2.8E-22 6.2E-27 147.9 -3.1 95 37-138 273-368 (468)
4 KOG4577|consensus 99.8 3.3E-22 7.1E-27 141.2 -3.2 101 34-139 29-129 (383)
5 KOG2272|consensus 99.8 3.7E-20 8E-25 128.8 -0.9 97 35-138 192-288 (332)
6 KOG2272|consensus 99.7 6.5E-20 1.4E-24 127.6 -2.0 96 37-138 11-107 (332)
7 KOG1703|consensus 99.6 4.4E-17 9.6E-22 126.1 1.0 98 36-138 361-458 (479)
8 KOG1703|consensus 99.6 1.4E-15 3.1E-20 117.7 3.3 97 36-138 301-397 (479)
9 PF00412 LIM: LIM domain; Int 99.5 2.4E-14 5.2E-19 80.4 4.7 57 41-99 1-58 (58)
10 KOG1044|consensus 99.3 4.7E-12 1E-16 97.3 4.8 92 31-139 9-100 (670)
11 KOG1700|consensus 99.2 5E-12 1.1E-16 87.6 0.3 99 37-138 6-143 (200)
12 smart00132 LIM Zinc-binding do 99.0 3.2E-10 6.9E-15 58.2 2.9 36 104-139 1-36 (39)
13 PF00412 LIM: LIM domain; Int 99.0 3E-10 6.4E-15 63.6 2.8 35 105-139 1-35 (58)
14 smart00132 LIM Zinc-binding do 98.6 2.6E-08 5.6E-13 50.9 2.5 36 40-75 1-37 (39)
15 KOG4577|consensus 98.3 2E-07 4.3E-12 66.9 0.8 64 38-101 92-156 (383)
16 KOG0490|consensus 98.0 3.4E-07 7.4E-12 64.8 -2.7 91 44-138 2-94 (235)
17 KOG1700|consensus 97.8 3.8E-06 8.3E-11 58.4 0.2 65 33-99 103-167 (200)
18 KOG1702|consensus 97.6 6.9E-06 1.5E-10 56.5 -1.9 59 38-98 4-62 (264)
19 PF08394 Arc_trans_TRASH: Arch 93.4 0.06 1.3E-06 27.0 1.6 29 105-133 1-29 (37)
20 PF10367 Vps39_2: Vacuolar sor 91.8 0.13 2.9E-06 31.7 2.0 29 104-132 80-108 (109)
21 PF14446 Prok-RING_1: Prokaryo 89.5 0.25 5.3E-06 27.0 1.4 28 104-131 7-36 (54)
22 PF09943 DUF2175: Uncharacteri 87.3 0.25 5.4E-06 30.5 0.6 29 104-132 4-32 (101)
23 PF07754 DUF1610: Domain of un 87.1 0.43 9.3E-06 21.5 1.2 15 105-119 1-15 (24)
24 PF13920 zf-C3HC4_3: Zinc fing 86.9 1.5 3.2E-05 23.2 3.5 44 67-113 4-48 (50)
25 PF09943 DUF2175: Uncharacteri 84.5 0.35 7.7E-06 29.9 0.3 31 40-70 4-35 (101)
26 PF10367 Vps39_2: Vacuolar sor 83.5 0.94 2E-05 27.8 2.0 32 36-67 76-108 (109)
27 smart00504 Ubox Modified RING 83.2 2.1 4.6E-05 23.4 3.2 46 66-114 2-47 (63)
28 KOG0320|consensus 82.0 1.2 2.5E-05 30.5 2.0 52 62-114 128-179 (187)
29 KOG1813|consensus 81.3 0.79 1.7E-05 33.8 1.1 46 66-114 242-287 (313)
30 PF10235 Cript: Microtubule-as 80.5 1 2.2E-05 27.3 1.2 43 60-114 39-81 (90)
31 PF11781 RRN7: RNA polymerase 77.8 1.3 2.9E-05 22.0 1.0 23 66-94 9-31 (36)
32 PF13923 zf-C3HC4_2: Zinc fing 77.2 2.8 6.2E-05 20.8 2.2 39 68-108 1-39 (39)
33 PF14835 zf-RING_6: zf-RING of 77.2 1.9 4.1E-05 24.4 1.6 48 66-117 8-55 (65)
34 COG5152 Uncharacterized conser 77.1 1.2 2.6E-05 31.0 0.9 48 64-114 195-242 (259)
35 PF10083 DUF2321: Uncharacteri 76.2 2.8 6.1E-05 28.0 2.4 50 85-138 25-76 (158)
36 PF14634 zf-RING_5: zinc-RING 75.6 5.2 0.00011 20.4 3.0 43 68-110 2-44 (44)
37 KOG3579|consensus 74.3 3.4 7.4E-05 30.5 2.7 36 34-69 264-299 (352)
38 PF14471 DUF4428: Domain of un 73.5 3.9 8.4E-05 22.0 2.2 30 67-98 1-30 (51)
39 PF14570 zf-RING_4: RING/Ubox 71.3 5.8 0.00013 21.1 2.5 24 88-111 22-46 (48)
40 COG4847 Uncharacterized protei 69.3 2.1 4.5E-05 26.1 0.5 29 104-132 8-36 (103)
41 PRK14890 putative Zn-ribbon RN 69.0 3.9 8.5E-05 22.7 1.6 13 104-116 9-21 (59)
42 PF06677 Auto_anti-p27: Sjogre 67.2 3.2 6.9E-05 21.3 0.9 22 67-94 19-40 (41)
43 PF12156 ATPase-cat_bd: Putati 66.5 4.6 0.0001 24.3 1.7 30 104-136 2-32 (88)
44 PF06906 DUF1272: Protein of u 66.3 15 0.00034 20.1 3.5 46 67-114 7-53 (57)
45 COG1645 Uncharacterized Zn-fin 66.2 3.2 6.8E-05 27.0 1.0 22 67-95 30-51 (131)
46 COG0068 HypF Hydrogenase matur 66.1 3.5 7.6E-05 34.2 1.4 84 35-138 98-181 (750)
47 cd00162 RING RING-finger (Real 66.1 9.6 0.00021 18.6 2.7 26 86-111 18-44 (45)
48 PF00645 zf-PARP: Poly(ADP-rib 65.7 3.1 6.8E-05 24.4 0.9 31 37-67 6-47 (82)
49 PF01258 zf-dskA_traR: Prokary 64.6 1.2 2.6E-05 21.9 -0.9 28 68-97 6-33 (36)
50 PF12773 DZR: Double zinc ribb 62.9 3.2 6.9E-05 21.8 0.5 9 104-112 31-39 (50)
51 PF10886 DUF2685: Protein of u 60.4 7.5 0.00016 21.2 1.6 26 39-64 2-27 (54)
52 PF11571 Med27: Mediator compl 59.1 3.9 8.5E-05 24.7 0.4 17 94-112 48-64 (90)
53 COG2888 Predicted Zn-ribbon RN 57.2 9.3 0.0002 21.3 1.7 17 104-120 11-27 (61)
54 COG2191 Formylmethanofuran deh 55.5 3.4 7.5E-05 28.9 -0.3 31 66-98 173-203 (206)
55 PF03854 zf-P11: P-11 zinc fin 52.6 9.5 0.00021 20.2 1.2 32 83-114 16-47 (50)
56 PRK00420 hypothetical protein; 52.5 7.1 0.00015 24.7 0.8 9 67-75 25-33 (112)
57 PF13639 zf-RING_2: Ring finge 49.9 14 0.0003 18.6 1.6 7 88-94 23-29 (44)
58 PF06827 zf-FPG_IleRS: Zinc fi 49.4 4.4 9.5E-05 18.9 -0.4 11 104-114 3-13 (30)
59 PF07191 zinc-ribbons_6: zinc- 47.6 13 0.00027 21.5 1.3 9 105-113 53-61 (70)
60 COG3813 Uncharacterized protei 46.4 34 0.00073 19.9 2.9 44 68-113 8-52 (84)
61 PF13248 zf-ribbon_3: zinc-rib 45.3 15 0.00032 16.5 1.1 9 40-48 4-12 (26)
62 PF06750 DiS_P_DiS: Bacterial 44.9 9.3 0.0002 23.2 0.5 36 38-75 33-68 (92)
63 PRK14559 putative protein seri 44.0 13 0.00028 30.8 1.3 13 39-51 2-14 (645)
64 KOG3002|consensus 43.8 22 0.00048 26.5 2.4 44 66-114 49-92 (299)
65 PF12674 Zn_ribbon_2: Putative 43.7 13 0.00027 22.1 0.9 30 68-97 3-35 (81)
66 PF13240 zinc_ribbon_2: zinc-r 43.5 6.1 0.00013 17.4 -0.4 6 107-112 4-9 (23)
67 PF07503 zf-HYPF: HypF finger; 42.0 10 0.00022 18.7 0.3 30 41-75 2-31 (35)
68 PRK00807 50S ribosomal protein 41.9 17 0.00037 19.6 1.2 25 104-128 3-29 (52)
69 COG4306 Uncharacterized protei 41.3 30 0.00066 22.4 2.4 46 89-138 29-76 (160)
70 PLN03208 E3 ubiquitin-protein 40.6 63 0.0014 22.5 4.1 11 104-114 70-80 (193)
71 TIGR00143 hypF [NiFe] hydrogen 40.1 9.6 0.00021 31.9 0.0 36 35-75 65-100 (711)
72 PF04570 DUF581: Protein of un 40.1 25 0.00053 19.5 1.6 29 67-95 18-47 (58)
73 KOG2932|consensus 39.9 13 0.00029 27.9 0.7 44 67-114 92-135 (389)
74 PF06689 zf-C4_ClpX: ClpX C4-t 38.9 55 0.0012 16.5 2.8 30 67-96 3-32 (41)
75 KOG0978|consensus 37.8 10 0.00022 31.5 -0.1 48 66-116 644-692 (698)
76 PF14569 zf-UDP: Zinc-binding 36.2 54 0.0012 19.3 2.7 23 88-111 36-60 (80)
77 TIGR00599 rad18 DNA repair pro 36.2 34 0.00074 26.6 2.4 45 66-113 27-71 (397)
78 KOG2114|consensus 35.7 18 0.00038 30.9 0.9 10 123-132 860-869 (933)
79 PF14255 Cys_rich_CPXG: Cystei 35.5 17 0.00036 19.7 0.5 28 40-67 2-29 (52)
80 smart00291 ZnF_ZZ Zinc-binding 35.4 46 0.00099 16.9 2.2 9 89-97 28-36 (44)
81 PF02069 Metallothio_Pro: Prok 34.8 22 0.00047 19.3 0.9 28 67-96 9-37 (52)
82 cd02249 ZZ Zinc finger, ZZ typ 34.6 51 0.0011 16.9 2.3 7 90-96 25-31 (46)
83 PF00096 zf-C2H2: Zinc finger, 34.2 10 0.00022 16.0 -0.4 8 131-138 1-8 (23)
84 KOG3497|consensus 33.5 14 0.0003 20.6 -0.0 14 38-51 4-17 (69)
85 KOG4739|consensus 33.4 40 0.00086 24.3 2.2 31 82-114 19-49 (233)
86 COG2174 RPL34A Ribosomal prote 32.9 15 0.00032 22.3 0.0 20 95-114 27-46 (93)
87 smart00746 TRASH metallochaper 32.4 48 0.0011 14.7 2.0 23 105-127 1-25 (39)
88 TIGR00570 cdk7 CDK-activating 31.8 68 0.0015 24.1 3.3 29 86-114 26-55 (309)
89 KOG2034|consensus 31.8 18 0.00038 31.0 0.3 30 102-131 817-846 (911)
90 PF01194 RNA_pol_N: RNA polyme 31.7 26 0.00057 19.5 0.9 14 38-51 4-17 (60)
91 PF00097 zf-C3HC4: Zinc finger 30.4 61 0.0013 15.7 2.2 17 83-99 14-30 (41)
92 PHA02610 uvsY.-2 hypothetical 30.4 41 0.00089 18.1 1.5 25 39-63 2-26 (53)
93 cd02336 ZZ_RSC8 Zinc finger, Z 29.8 39 0.00084 17.6 1.3 29 67-97 2-32 (45)
94 PF04810 zf-Sec23_Sec24: Sec23 29.8 37 0.00081 16.9 1.2 31 38-73 2-32 (40)
95 PF00320 GATA: GATA zinc finge 29.6 73 0.0016 15.4 2.3 16 81-96 12-28 (36)
96 PF12677 DUF3797: Domain of un 29.5 42 0.00092 17.8 1.4 27 104-130 15-42 (49)
97 PLN00032 DNA-directed RNA poly 29.4 16 0.00035 21.1 -0.2 14 38-51 4-17 (71)
98 PF00569 ZZ: Zinc finger, ZZ t 29.3 58 0.0013 16.7 2.0 10 88-97 28-37 (46)
99 cd00472 Ribosomal_L24e_L24 Rib 28.5 41 0.0009 18.3 1.3 25 103-127 4-30 (54)
100 COG1644 RPB10 DNA-directed RNA 28.4 19 0.00041 20.2 -0.0 14 38-51 4-17 (63)
101 smart00547 ZnF_RBZ Zinc finger 28.3 15 0.00032 16.2 -0.4 7 104-110 18-24 (26)
102 PF07649 C1_3: C1-like domain; 28.0 37 0.00081 15.6 1.0 9 67-75 2-10 (30)
103 COG0266 Nei Formamidopyrimidin 27.6 35 0.00076 25.1 1.2 25 104-130 247-271 (273)
104 PF01927 Mut7-C: Mut7-C RNAse 27.5 26 0.00056 23.0 0.5 35 104-138 93-132 (147)
105 KOG2893|consensus 27.5 22 0.00047 25.8 0.1 36 38-76 10-45 (341)
106 PF02591 DUF164: Putative zinc 26.6 16 0.00034 19.7 -0.5 13 39-51 23-35 (56)
107 PF00130 C1_1: Phorbol esters/ 26.1 41 0.0009 17.5 1.1 13 37-49 10-22 (53)
108 PF13894 zf-C2H2_4: C2H2-type 26.0 22 0.00047 14.6 -0.1 8 131-138 1-8 (24)
109 smart00214 VWC von Willebrand 25.4 52 0.0011 17.8 1.4 18 117-134 5-23 (59)
110 smart00184 RING Ring finger. E 25.4 31 0.00066 15.8 0.4 15 117-131 11-25 (39)
111 PF13834 DUF4193: Domain of un 25.4 18 0.00039 22.3 -0.5 29 65-94 70-98 (99)
112 PLN02638 cellulose synthase A 25.3 79 0.0017 28.0 3.0 15 36-50 15-29 (1079)
113 PRK04016 DNA-directed RNA poly 25.2 26 0.00056 19.7 0.1 13 38-50 4-16 (62)
114 COG4357 Zinc finger domain con 24.8 7.6 0.00017 23.8 -2.1 17 59-75 56-72 (105)
115 PF07975 C1_4: TFIIH C1-like d 23.8 27 0.00059 18.8 0.1 10 105-114 2-11 (51)
116 smart00531 TFIIE Transcription 23.6 22 0.00047 23.4 -0.4 37 37-76 98-134 (147)
117 PRK12775 putative trifunctiona 23.6 62 0.0013 28.4 2.2 32 104-138 798-829 (1006)
118 PF05502 Dynactin_p62: Dynacti 23.5 46 0.001 26.6 1.3 37 39-76 27-63 (483)
119 PF04945 YHS: YHS domain; Int 23.4 28 0.0006 17.9 0.1 23 106-128 4-27 (47)
120 PRK11595 DNA utilization prote 23.4 93 0.002 22.0 2.8 10 39-48 6-15 (227)
121 TIGR00595 priA primosomal prot 23.4 34 0.00075 27.4 0.6 38 67-111 224-262 (505)
122 PRK14873 primosome assembly pr 22.7 38 0.00083 28.2 0.7 38 67-111 394-431 (665)
123 cd02341 ZZ_ZZZ3 Zinc finger, Z 22.4 1E+02 0.0022 16.2 2.1 9 89-97 27-35 (48)
124 PRK00398 rpoP DNA-directed RNA 22.0 41 0.00088 17.2 0.5 10 66-75 22-31 (46)
125 PLN03123 poly [ADP-ribose] pol 21.9 60 0.0013 28.5 1.7 29 104-132 19-57 (981)
126 cd02340 ZZ_NBR1_like Zinc fing 21.8 49 0.0011 16.9 0.8 11 104-114 2-12 (43)
127 PF14445 Prok-RING_2: Prokaryo 21.5 12 0.00027 20.0 -1.5 24 87-113 29-52 (57)
128 KOG3039|consensus 21.5 3.4E+02 0.0074 20.0 5.6 84 33-116 178-273 (303)
129 KOG3476|consensus 21.4 28 0.00061 20.9 -0.2 37 67-115 56-92 (100)
130 PF08271 TF_Zn_Ribbon: TFIIB z 21.0 47 0.001 16.7 0.6 10 66-75 20-29 (43)
131 COG4068 Uncharacterized protei 20.9 56 0.0012 18.1 0.9 13 104-116 10-22 (64)
132 PLN02195 cellulose synthase A 20.7 1.1E+02 0.0024 26.8 3.0 53 37-113 5-59 (977)
No 1
>KOG1701|consensus
Probab=99.86 E-value=6.5e-23 Score=151.30 Aligned_cols=99 Identities=27% Similarity=0.674 Sum_probs=87.9
Q ss_pred CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeE-eeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY-TKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
.+..+|..|++.|.+. ++.++++.||+.||+|..|.+.|+ +..|. ..++++||..||+++|++ +|+.|+++|++
T Consensus 332 ~tlekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ld--gipFtvd~~n~v~Cv~dfh~kfAP--rCs~C~~PI~P 406 (468)
T KOG1701|consen 332 DTLEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLD--GIPFTVDSQNNVYCVPDFHKKFAP--RCSVCGNPILP 406 (468)
T ss_pred HHHHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccC--CccccccCCCceeeehhhhhhcCc--chhhccCCccC
Confidence 4567899999999998 789999999999999999999994 44555 578899999999999999 99999999988
Q ss_pred Cce-----EEEeCCccccccccccccCCCC
Q psy284 115 FEM-----VMRARNNVYHLECFACQQCNHR 139 (139)
Q Consensus 115 ~~~-----~~~~~~~~~H~~Cf~C~~C~~~ 139 (139)
.+. .|+++++.||.+||+|+.|+.+
T Consensus 407 ~~G~~etvRvvamdr~fHv~CY~CEDCg~~ 436 (468)
T KOG1701|consen 407 RDGKDETVRVVAMDRDFHVNCYKCEDCGLL 436 (468)
T ss_pred CCCCcceEEEEEccccccccceehhhcCcc
Confidence 542 6789999999999999999863
No 2
>KOG1044|consensus
Probab=99.86 E-value=1.4e-22 Score=154.15 Aligned_cols=123 Identities=31% Similarity=0.706 Sum_probs=111.5
Q ss_pred cCccccccccccc---ccCCCCCCCCCCCCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEee
Q psy284 9 HLKINRMSMDVKT---QQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTK 85 (139)
Q Consensus 9 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~ 85 (139)
-..+++++++++. |+.+.+.+..+....+...|++|++.|.....+.++++.||..||+|..|+..|. ..|+.+
T Consensus 101 f~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~---gey~sk 177 (670)
T KOG1044|consen 101 FKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN---GEYMSK 177 (670)
T ss_pred CCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhccccc---ceeecc
Confidence 4567888888877 7777777777888888999999999999987788999999999999999999884 569999
Q ss_pred CCccccHhhHHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284 86 ANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 86 ~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
++.+||+.||...||. +|..|.+.|.| .++.|.|++|||.|-+|++|++
T Consensus 178 dg~pyce~dy~~~fgv--kc~~c~~fisg--kvLqag~kh~HPtCARCsRCgq 226 (670)
T KOG1044|consen 178 DGVPYCEKDYQAKFGV--KCEECEKFISG--KVLQAGDKHFHPTCARCSRCGQ 226 (670)
T ss_pred CCCcchhhhhhhhcCe--ehHHhhhhhhh--hhhhccCcccCcchhhhhhhcc
Confidence 9999999999999999 99999999988 8999999999999999999985
No 3
>KOG1701|consensus
Probab=99.82 E-value=2.8e-22 Score=147.92 Aligned_cols=95 Identities=27% Similarity=0.645 Sum_probs=86.0
Q ss_pred CCCcccccccccccc-eeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284 37 GPQECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF 115 (139)
Q Consensus 37 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~ 115 (139)
...+|.+|++.|.++ ..+.++++.||..||+|..|.+.| .++.||..++++||+.||.... ++|..|+++|++
T Consensus 273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L--~Gq~FY~v~~k~~CE~cyq~tl---ekC~~Cg~~I~d- 346 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQL--AGQSFYQVDGKPYCEGCYQDTL---EKCNKCGEPIMD- 346 (468)
T ss_pred hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhh--ccccccccCCcccchHHHHHHH---HHHhhhhhHHHH-
Confidence 344999999999985 447899999999999999999999 6789999999999999998754 389999999965
Q ss_pred ceEEEeCCccccccccccccCCC
Q psy284 116 EMVMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 116 ~~~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
.+++|.|+.||+.||+|..|++
T Consensus 347 -~iLrA~GkayHp~CF~Cv~C~r 368 (468)
T KOG1701|consen 347 -RILRALGKAYHPGCFTCVVCAR 368 (468)
T ss_pred -HHHHhcccccCCCceEEEEecc
Confidence 9999999999999999999986
No 4
>KOG4577|consensus
Probab=99.82 E-value=3.3e-22 Score=141.21 Aligned_cols=101 Identities=42% Similarity=0.950 Sum_probs=92.8
Q ss_pred CCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCC
Q psy284 34 NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIP 113 (139)
Q Consensus 34 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~ 113 (139)
.....++|++|.+.|.+.+++.++++.||..|++|+.|..+|+ ..++.+++.+||+++|.++||. +|..|+..|.
T Consensus 29 ~~~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~---drCFsR~~s~yCkedFfKrfGT--KCsaC~~GIp 103 (383)
T KOG4577|consen 29 SNVEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLA---DRCFSREGSVYCKEDFFKRFGT--KCSACQEGIP 103 (383)
T ss_pred cccccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHH---HHHhhcCCceeehHHHHHHhCC--cchhhcCCCC
Confidence 3446889999999999999999999999999999999999995 4689999999999999999999 9999999999
Q ss_pred CCceEEEeCCccccccccccccCCCC
Q psy284 114 AFEMVMRARNNVYHLECFACQQCNHR 139 (139)
Q Consensus 114 ~~~~~~~~~~~~~H~~Cf~C~~C~~~ 139 (139)
+...+..|.+..||.+||.|..|+++
T Consensus 104 PtqVVRkAqd~VYHl~CF~C~iC~R~ 129 (383)
T KOG4577|consen 104 PTQVVRKAQDFVYHLHCFACFICKRQ 129 (383)
T ss_pred hHHHHHHhhcceeehhhhhhHhhhcc
Confidence 96556679999999999999999875
No 5
>KOG2272|consensus
Probab=99.76 E-value=3.7e-20 Score=128.82 Aligned_cols=97 Identities=32% Similarity=0.789 Sum_probs=90.8
Q ss_pred CCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
..+.++|+.|.++|.+. +|.++++.||.+.|+|..|.+++ .+.+.|.+.|..||+.+|.++||. .|..|+..|.|
T Consensus 192 ~mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPF--lGHrHYEkkGlaYCe~h~~qLfG~--~CF~C~~~i~G 266 (332)
T KOG2272|consen 192 KMGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPF--LGHRHYEKKGLAYCETHYHQLFGN--LCFICNRVIGG 266 (332)
T ss_pred ccCCcccccccCchHHH-HHHHhccccchhheeehhcCCcc--cchhhhhhcCchhHHHHHHHHhhh--hheecCCccCc
Confidence 36788999999999986 68899999999999999999998 778899999999999999999999 99999999977
Q ss_pred CceEEEeCCccccccccccccCCC
Q psy284 115 FEMVMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 115 ~~~~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
.++.++++.|.++||.|+.|++
T Consensus 267 --~vv~al~KawCv~cf~Cs~Cdk 288 (332)
T KOG2272|consen 267 --DVVSALNKAWCVECFSCSTCDK 288 (332)
T ss_pred --cHHHHhhhhhcccccccccccc
Confidence 7999999999999999999986
No 6
>KOG2272|consensus
Probab=99.74 E-value=6.5e-20 Score=127.60 Aligned_cols=96 Identities=27% Similarity=0.662 Sum_probs=86.9
Q ss_pred CCCcccccccccccce-eeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284 37 GPQECAGCGKHITDRF-LLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF 115 (139)
Q Consensus 37 ~~~~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~ 115 (139)
....|.+|.......+ ++..++..||..||.|..|-.++ ++..||..+++.||+.++..+|+| .|..|++.|.|
T Consensus 11 ~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf--~~g~~~efEgRkYCEhDF~~LfaP--cC~kC~EFiiG- 85 (332)
T KOG2272|consen 11 ANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPF--PDGIFYEFEGRKYCEHDFHVLFAP--CCGKCGEFIIG- 85 (332)
T ss_pred HHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcC--CCceeEEecCcccccccchhhhch--hhcccccchhh-
Confidence 3557999998887753 45678899999999999999999 678899999999999999999999 99999999988
Q ss_pred ceEEEeCCccccccccccccCCC
Q psy284 116 EMVMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 116 ~~~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
++|.+++..|||.||+|..|++
T Consensus 86 -rVikamnnSwHp~CF~Cd~Cn~ 107 (332)
T KOG2272|consen 86 -RVIKAMNNSWHPACFRCDLCNK 107 (332)
T ss_pred -HHHHhhccccCcccchhHHHHH
Confidence 8999999999999999999875
No 7
>KOG1703|consensus
Probab=99.63 E-value=4.4e-17 Score=126.11 Aligned_cols=98 Identities=26% Similarity=0.582 Sum_probs=89.0
Q ss_pred CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284 36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF 115 (139)
Q Consensus 36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~ 115 (139)
...+.|.+|+.+|.+. .|.+++..||++||.|..|...+ ....++..++.+||..||..++.+ +|..|.++|...
T Consensus 361 ~~~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~--~~~~~~~~~~~pyce~~~~~~~~~--~~~~~~~p~~~~ 435 (479)
T KOG1703|consen 361 PFRPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPL--KNSSFFESDGEPYCEDHYKKLFTT--KCDYCKKPVEFG 435 (479)
T ss_pred hhCccccccCCchHHh-HhhhccCeechhceeeecccCCC--CCCcccccCCccchhhhHhhhccc--cchhccchhHhh
Confidence 5567999999999997 57777999999999999998888 567899999999999999999998 999999998765
Q ss_pred ceEEEeCCccccccccccccCCC
Q psy284 116 EMVMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 116 ~~~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
+..+.+++..||..||+|+.|.+
T Consensus 436 ~~~ie~~~~~~h~~~F~c~~c~~ 458 (479)
T KOG1703|consen 436 SRQIEADGSPFHGDCFRCANCMK 458 (479)
T ss_pred hhHhhccCccccccceehhhhhc
Confidence 68899999999999999999975
No 8
>KOG1703|consensus
Probab=99.56 E-value=1.4e-15 Score=117.75 Aligned_cols=97 Identities=24% Similarity=0.502 Sum_probs=87.0
Q ss_pred CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284 36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF 115 (139)
Q Consensus 36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~ 115 (139)
...++|..|...|.+...+.+++..||..+|.|..|...+. ...+...++++||..||.+.+.+ .|.+|+++|.+
T Consensus 301 ~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~--~~~~~~~~g~~~c~~~~~~~~~p--~C~~C~~~i~~- 375 (479)
T KOG1703|consen 301 VTRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVIL--DGGPRELDGKILCHECFHAPFRP--NCKRCLLPILE- 375 (479)
T ss_pred cccccccccccCcccceeEeeccccccccceeecccccccc--CCCccccCCCccHHHHHHHhhCc--cccccCCchHH-
Confidence 44589999999999944788999999999999999999985 34568899999999999999999 99999999976
Q ss_pred ceEEEeCCccccccccccccCCC
Q psy284 116 EMVMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 116 ~~~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
.+|.+.++.||++||.|..|++
T Consensus 376 -~~v~a~~~~wH~~cf~C~~C~~ 397 (479)
T KOG1703|consen 376 -EGVCALGRLWHPECFVCADCGK 397 (479)
T ss_pred -hHhhhccCeechhceeeecccC
Confidence 8899999999999999999954
No 9
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.51 E-value=2.4e-14 Score=80.42 Aligned_cols=57 Identities=37% Similarity=0.831 Sum_probs=50.3
Q ss_pred ccccccccccceee-eecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHh
Q psy284 41 CAGCGKHITDRFLL-KALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99 (139)
Q Consensus 41 C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~ 99 (139)
|.+|+++|.+...+ .++++.||++||+|..|+..|. +..++..++++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLN--DGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTT--TSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccC--CCeeEeECCEEECHHHHhhhC
Confidence 78999999986554 6999999999999999999995 345899999999999999875
No 10
>KOG1044|consensus
Probab=99.27 E-value=4.7e-12 Score=97.34 Aligned_cols=92 Identities=27% Similarity=0.677 Sum_probs=72.7
Q ss_pred CCCCCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCC
Q psy284 31 VPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSK 110 (139)
Q Consensus 31 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~ 110 (139)
++........|..|.+.-... ++.+.++.||..||+|..|++.|++. .|+.+++. +++++ ..|..
T Consensus 9 s~~~~~~~i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~--gff~k~~~--------~~ygt----~~c~~ 73 (670)
T KOG1044|consen 9 SPQTGKQGIKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEG--GFFTKPEN--------RLYGT----DDCRA 73 (670)
T ss_pred CccccccceehhhhCCccccc-eeEeeccccceeeeeccccCCCcccc--cceecccc--------eeecc----cchhh
Confidence 344455567899999988886 78999999999999999999999743 36665554 33332 55777
Q ss_pred CCCCCceEEEeCCccccccccccccCCCC
Q psy284 111 VIPAFEMVMRARNNVYHLECFACQQCNHR 139 (139)
Q Consensus 111 ~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 139 (139)
.|.+ .+|.++|+.||++||.|+.|+++
T Consensus 74 ~~~g--evvsa~gktyh~~cf~cs~ck~p 100 (670)
T KOG1044|consen 74 FVEG--EVVSTLGKTYHPKCFSCSTCKSP 100 (670)
T ss_pred hccc--eeEecccceeccccceecccCCC
Confidence 7766 89999999999999999999763
No 11
>KOG1700|consensus
Probab=99.16 E-value=5e-12 Score=87.65 Aligned_cols=99 Identities=26% Similarity=0.591 Sum_probs=81.9
Q ss_pred CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCc-------------
Q psy284 37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTG------------- 103 (139)
Q Consensus 37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~------------- 103 (139)
....|..|++.++..+.+...+..||+.||.|..|...|. ...+..+++.+||+.+|...+++.+
T Consensus 6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~--~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (200)
T KOG1700|consen 6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLT--LSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGL 83 (200)
T ss_pred ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccc--cccccccccccccccchHhhhCcccccccccccccCCC
Confidence 3458999999999976677889999999999999999994 4567889999999997766554422
Q ss_pred --------------------------cccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284 104 --------------------------YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 104 --------------------------~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
.|..|++.+.+.| .+...+..||..||+|+.|+.
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E-k~~~~~~~~hk~cfrc~~~~~ 143 (200)
T KOG1700|consen 84 GKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE-KVTGNGLEFHKSCFRCTHCGK 143 (200)
T ss_pred CcccccccccccccchhHHhhhccccccccccceeeehH-HHhhhhhhhhhhheeeccccc
Confidence 1999999998754 556789999999999999975
No 12
>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=99.00 E-value=3.2e-10 Score=58.17 Aligned_cols=36 Identities=44% Similarity=0.929 Sum_probs=32.3
Q ss_pred cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284 104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139 (139)
Q Consensus 104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 139 (139)
+|.+|+++|.+.+..+.+.++.||++||+|..|+++
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 36 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKP 36 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCc
Confidence 588999999886678899999999999999999864
No 13
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.00 E-value=3e-10 Score=63.58 Aligned_cols=35 Identities=40% Similarity=0.921 Sum_probs=31.7
Q ss_pred ccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139 (139)
Q Consensus 105 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 139 (139)
|..|+++|.+.+.++.+.++.||++||+|+.|+++
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 35 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKP 35 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCB
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCc
Confidence 78999999987777789999999999999999863
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=98.63 E-value=2.6e-08 Score=50.87 Aligned_cols=36 Identities=47% Similarity=1.104 Sum_probs=32.3
Q ss_pred cccccccccccc-eeeeecCccccccCcccccCCCCc
Q psy284 40 ECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRL 75 (139)
Q Consensus 40 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l 75 (139)
+|.+|++.|.+. ..+.+.+..||..||+|..|+..|
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcC
Confidence 588999999986 567889999999999999999887
No 15
>KOG4577|consensus
Probab=98.29 E-value=2e-07 Score=66.91 Aligned_cols=64 Identities=23% Similarity=0.489 Sum_probs=51.2
Q ss_pred CCcccccccccccceee-eecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284 38 PQECAGCGKHITDRFLL-KALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS 101 (139)
Q Consensus 38 ~~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~ 101 (139)
..+|..|+..|-+..++ .+.+..||..||.|..|.+.|..++..|...+.++.|+++|+..-..
T Consensus 92 GTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k 156 (383)
T KOG4577|consen 92 GTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQK 156 (383)
T ss_pred CCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhc
Confidence 45899999999886544 56788999999999999999985444444688999999999865433
No 16
>KOG0490|consensus
Probab=98.01 E-value=3.4e-07 Score=64.75 Aligned_cols=91 Identities=47% Similarity=0.998 Sum_probs=74.7
Q ss_pred cccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHH--HhCCCccccccCCCCCCCceEEEe
Q psy284 44 CGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR--LFGSTGYCAACSKVIPAFEMVMRA 121 (139)
Q Consensus 44 C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~--~~~~~~~C~~C~~~I~~~~~~~~~ 121 (139)
|+..|.+.+.+.+.+..||..|..|..|...+..... .+..++..||..+|.+ .+.. +|.+|.+.|...|.+..+
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~g~~~~~~d~~~~~~~~~--rr~rt~~~~~ql~~ler~ 78 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDT-CFSKDGSIYCKRDYQREFKFSK--RCARCKFTISQLDELERA 78 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCC-cccCCCcccccccchhhhhccc--cccCCCCCcCHHHHHHHh
Confidence 6677788766677799999999999999999963334 4444999999999998 6666 999999999877778888
Q ss_pred CCccccccccccccCCC
Q psy284 122 RNNVYHLECFACQQCNH 138 (139)
Q Consensus 122 ~~~~~H~~Cf~C~~C~~ 138 (139)
..+. |.-||.|..|..
T Consensus 79 f~~~-h~Pd~~~r~~la 94 (235)
T KOG0490|consen 79 FEKV-HLPCFACRECLA 94 (235)
T ss_pred hcCC-CcCccchHHHHh
Confidence 8888 999999988753
No 17
>KOG1700|consensus
Probab=97.85 E-value=3.8e-06 Score=58.41 Aligned_cols=65 Identities=22% Similarity=0.517 Sum_probs=54.8
Q ss_pred CCCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHh
Q psy284 33 NNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99 (139)
Q Consensus 33 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~ 99 (139)
........|..|++.+++.+.+...+..||..||+|..|+..|. ...+....+.+||...+..++
T Consensus 103 ~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls--~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 103 VFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLS--PKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred hhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccC--CcchhhcCCccccchhhheee
Confidence 45566789999999999987788899999999999999999995 456788889999987766544
No 18
>KOG1702|consensus
Probab=97.56 E-value=6.9e-06 Score=56.47 Aligned_cols=59 Identities=25% Similarity=0.523 Sum_probs=50.0
Q ss_pred CCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHH
Q psy284 38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98 (139)
Q Consensus 38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~ 98 (139)
...|..|++.+++.+.+.-+++.||..||+|..|+..|++ ..+-..+.++||..+|.+.
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnm--KnyKgy~kkpycn~hYpkq 62 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNM--KNYKGYDKKPYCNPHYPKQ 62 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhh--hhccccccCCCcCcccccc
Confidence 3457789999999777888999999999999999999963 4566789999999999653
No 19
>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=93.43 E-value=0.06 Score=27.03 Aligned_cols=29 Identities=31% Similarity=0.677 Sum_probs=22.5
Q ss_pred ccccCCCCCCCceEEEeCCcccccccccc
Q psy284 105 CAACSKVIPAFEMVMRARNNVYHLECFAC 133 (139)
Q Consensus 105 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C 133 (139)
|.-|++.|.+.-.++...++.||--|-+|
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 67899999986568889999999544443
No 20
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=91.83 E-value=0.13 Score=31.67 Aligned_cols=29 Identities=24% Similarity=0.504 Sum_probs=22.7
Q ss_pred cccccCCCCCCCceEEEeCCccccccccc
Q psy284 104 YCAACSKVIPAFEMVMRARNNVYHLECFA 132 (139)
Q Consensus 104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~ 132 (139)
.|..|+++|...-.++...|..+|..|+.
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 79999999977545666777889988863
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=89.49 E-value=0.25 Score=26.98 Aligned_cols=28 Identities=21% Similarity=0.548 Sum_probs=22.1
Q ss_pred cccccCCCCCCCceEEE--eCCcccccccc
Q psy284 104 YCAACSKVIPAFEMVMR--ARNNVYHLECF 131 (139)
Q Consensus 104 ~C~~C~~~I~~~~~~~~--~~~~~~H~~Cf 131 (139)
+|..|+++|.+++.++. .=+..||.+|+
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 89999999976555555 45688999998
No 22
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=87.31 E-value=0.25 Score=30.53 Aligned_cols=29 Identities=28% Similarity=0.521 Sum_probs=22.2
Q ss_pred cccccCCCCCCCceEEEeCCccccccccc
Q psy284 104 YCAACSKVIPAFEMVMRARNNVYHLECFA 132 (139)
Q Consensus 104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~ 132 (139)
+|..|+++|...+..-...+..-|..||+
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~ 32 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFR 32 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHH
Confidence 79999999987544444566888988886
No 23
>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=87.13 E-value=0.43 Score=21.53 Aligned_cols=15 Identities=27% Similarity=0.705 Sum_probs=9.7
Q ss_pred ccccCCCCCCCceEE
Q psy284 105 CAACSKVIPAFEMVM 119 (139)
Q Consensus 105 C~~C~~~I~~~~~~~ 119 (139)
|..|+..|.+.+..+
T Consensus 1 C~sC~~~i~~r~~~v 15 (24)
T PF07754_consen 1 CTSCGRPIAPREQAV 15 (24)
T ss_pred CccCCCcccCcccCc
Confidence 667888887754333
No 24
>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=86.90 E-value=1.5 Score=23.18 Aligned_cols=44 Identities=18% Similarity=0.394 Sum_probs=29.3
Q ss_pred ccccCCCCcccCCCeeEeeCCcc-ccHhhHHHHhCCCccccccCCCCC
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLI-LCKRDYLRLFGSTGYCAACSKVIP 113 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~-~C~~cy~~~~~~~~~C~~C~~~I~ 113 (139)
.|..|..... ...+..=+.. +|..|+.+.+....+|..|.++|.
T Consensus 4 ~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4555655542 3455667777 999999877544449999999985
No 25
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=84.54 E-value=0.35 Score=29.86 Aligned_cols=31 Identities=26% Similarity=0.420 Sum_probs=23.4
Q ss_pred cccccccccccceeeee-cCccccccCccccc
Q psy284 40 ECAGCGKHITDRFLLKA-LDMYWHEDCLKCGC 70 (139)
Q Consensus 40 ~C~~C~~~i~~~~~~~~-~~~~~H~~Cf~C~~ 70 (139)
.|..|+++|+.++...+ .+...|..||+=..
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 69999999998766554 44678999998443
No 26
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=83.55 E-value=0.94 Score=27.77 Aligned_cols=32 Identities=25% Similarity=0.589 Sum_probs=21.4
Q ss_pred CCCCcccccccccccc-eeeeecCccccccCcc
Q psy284 36 QGPQECAGCGKHITDR-FLLKALDMYWHEDCLK 67 (139)
Q Consensus 36 ~~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~ 67 (139)
.....|..|++.|... ..+.-.+..+|..|++
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4456799999988875 3334456677877753
No 27
>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=83.20 E-value=2.1 Score=23.43 Aligned_cols=46 Identities=9% Similarity=0.048 Sum_probs=33.1
Q ss_pred cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
|.|..|...+. ..+....|..||..+..+.+.....|..|++++..
T Consensus 2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 56777877774 23566778999999977655434489999988854
No 28
>KOG0320|consensus
Probab=81.99 E-value=1.2 Score=30.51 Aligned_cols=52 Identities=25% Similarity=0.446 Sum_probs=37.8
Q ss_pred cccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 62 HEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 62 H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
-..+++|..|-....+. ..+..+-|.+||..|-........+|..|++.|.-
T Consensus 128 ~~~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred cccccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 34578998887776422 22446889999999987665444599999998864
No 29
>KOG1813|consensus
Probab=81.27 E-value=0.79 Score=33.76 Aligned_cols=46 Identities=22% Similarity=0.388 Sum_probs=36.8
Q ss_pred cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
|.|..|..... ..+...-+..+|..|..+.|...++|..|++.+.+
T Consensus 242 f~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred ccccccccccc---cchhhcCCceeehhhhccccccCCcceeccccccc
Confidence 77888887773 34566778899999999888665699999999976
No 30
>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=80.52 E-value=1 Score=27.33 Aligned_cols=43 Identities=23% Similarity=0.505 Sum_probs=29.5
Q ss_pred cccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 60 YWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 60 ~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
.|-..--.|..|...+. ..+..||..|..+ ++.|+-|++.|.+
T Consensus 39 Py~~~~~~C~~CK~~v~--------q~g~~YCq~CAYk----kGiCamCGKki~d 81 (90)
T PF10235_consen 39 PYAPYSSKCKICKTKVH--------QPGAKYCQTCAYK----KGICAMCGKKILD 81 (90)
T ss_pred cccccCccccccccccc--------cCCCccChhhhcc----cCcccccCCeecc
Confidence 34443346777876663 2256799999655 4599999999965
No 31
>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=77.77 E-value=1.3 Score=21.97 Aligned_cols=23 Identities=26% Similarity=0.668 Sum_probs=15.4
Q ss_pred cccccCCCCcccCCCeeEeeCCccccHhh
Q psy284 66 LKCGCCDCRLGEVGSTLYTKANLILCKRD 94 (139)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c 94 (139)
+.|..|+.. .+...+|..||..|
T Consensus 9 ~~C~~C~~~------~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 9 EPCPVCGSR------WFYSDDGFYYCDRC 31 (36)
T ss_pred CcCCCCCCe------EeEccCCEEEhhhC
Confidence 346667643 36778888888666
No 32
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=77.23 E-value=2.8 Score=20.76 Aligned_cols=39 Identities=21% Similarity=0.432 Sum_probs=20.9
Q ss_pred cccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCcccccc
Q psy284 68 CGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAAC 108 (139)
Q Consensus 68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C 108 (139)
|..|...+ ........-|..||..|..+.+....+|..|
T Consensus 1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 34455555 2222456778888988877655432355443
No 33
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=77.18 E-value=1.9 Score=24.44 Aligned_cols=48 Identities=23% Similarity=0.388 Sum_probs=21.4
Q ss_pred cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCCce
Q psy284 66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEM 117 (139)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~ 117 (139)
++|+.|...|.+ .-....-...||..|-...++. .|..|+.|...+|.
T Consensus 8 LrCs~C~~~l~~--pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~ 55 (65)
T PF14835_consen 8 LRCSICFDILKE--PVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDI 55 (65)
T ss_dssp TS-SSS-S--SS---B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS-
T ss_pred cCCcHHHHHhcC--CceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHH
Confidence 567777776642 1123455577888887777777 89999988765443
No 34
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=77.14 E-value=1.2 Score=31.04 Aligned_cols=48 Identities=21% Similarity=0.404 Sum_probs=37.8
Q ss_pred cCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 64 DCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 64 ~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
.=|.|..|..... ......-|..||..|+.+.|.....|..|++...|
T Consensus 195 IPF~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 195 IPFLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred Cceeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 3488999987774 33566778899999999988655599999998776
No 35
>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=76.20 E-value=2.8 Score=28.00 Aligned_cols=50 Identities=16% Similarity=0.293 Sum_probs=32.9
Q ss_pred eCCccccHhhHHHHhCCCccccccCCCCCCCce--EEEeCCccccccccccccCCC
Q psy284 85 KANLILCKRDYLRLFGSTGYCAACSKVIPAFEM--VMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 85 ~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~--~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
....-||..|-.+... .|..|+.+|.|..- .+...+..|++=- -|..|++
T Consensus 25 ~~~~~fC~kCG~~tI~---~Cp~C~~~IrG~y~v~gv~~~g~~~~~Ps-YC~~CGk 76 (158)
T PF10083_consen 25 ELREKFCSKCGAKTIT---SCPNCSTPIRGDYHVEGVFGLGGHYEAPS-YCHNCGK 76 (158)
T ss_pred hHHHHHHHHhhHHHHH---HCcCCCCCCCCceecCCeeeeCCCCCCCh-hHHhCCC
Confidence 3446799999877764 79999999988421 1223456777422 3666765
No 36
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=75.64 E-value=5.2 Score=20.43 Aligned_cols=43 Identities=26% Similarity=0.510 Sum_probs=23.7
Q ss_pred cccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCC
Q psy284 68 CGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSK 110 (139)
Q Consensus 68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~ 110 (139)
|..|..........+...=+..+|..|..+..+....|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 3344444421223444566778888888776622226777753
No 37
>KOG3579|consensus
Probab=74.34 E-value=3.4 Score=30.45 Aligned_cols=36 Identities=19% Similarity=0.529 Sum_probs=28.6
Q ss_pred CCCCCCcccccccccccceeeeecCccccccCcccc
Q psy284 34 NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCG 69 (139)
Q Consensus 34 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~ 69 (139)
.....-.|..|.+.+.|...+..-.-.-|+.||-|+
T Consensus 264 A~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCS 299 (352)
T KOG3579|consen 264 APSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCS 299 (352)
T ss_pred CCCCceeehhhhhhhccCceeecCCCcccceecccC
Confidence 445556889999999998667777778899999875
No 38
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=73.45 E-value=3.9 Score=21.98 Aligned_cols=30 Identities=27% Similarity=0.573 Sum_probs=21.6
Q ss_pred ccccCCCCcccCCCeeEeeCCccccHhhHHHH
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~ 98 (139)
.|..|+..++... .+-..++ ..|.+|+.+.
T Consensus 1 ~C~iCg~kigl~~-~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFK-RFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCcccccccccc-ceeccCc-cchHHHHHHh
Confidence 4778888887432 3556777 7899999775
No 39
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=71.34 E-value=5.8 Score=21.09 Aligned_cols=24 Identities=21% Similarity=0.656 Sum_probs=12.2
Q ss_pred ccccHhhHHHHhC-CCccccccCCC
Q psy284 88 LILCKRDYLRLFG-STGYCAACSKV 111 (139)
Q Consensus 88 ~~~C~~cy~~~~~-~~~~C~~C~~~ 111 (139)
--.|..||.+... ..++|.+|.++
T Consensus 22 f~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 22 FQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp ----HHHHHHHTTSS-SB-TTT--B
T ss_pred CcHHHHHHHHHHhccCCCCCCCCCC
Confidence 3468999987763 35599999875
No 40
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=69.25 E-value=2.1 Score=26.14 Aligned_cols=29 Identities=24% Similarity=0.447 Sum_probs=19.7
Q ss_pred cccccCCCCCCCceEEEeCCccccccccc
Q psy284 104 YCAACSKVIPAFEMVMRARNNVYHLECFA 132 (139)
Q Consensus 104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~ 132 (139)
+|..|+++|.-.+..-......-|-+||.
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~ 36 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLA 36 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHH
Confidence 78889988865333333456778888875
No 41
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=69.00 E-value=3.9 Score=22.69 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=8.2
Q ss_pred cccccCCCCCCCc
Q psy284 104 YCAACSKVIPAFE 116 (139)
Q Consensus 104 ~C~~C~~~I~~~~ 116 (139)
.|.+|+..|.+.+
T Consensus 9 ~CtSCg~~i~~~~ 21 (59)
T PRK14890 9 KCTSCGIEIAPRE 21 (59)
T ss_pred cccCCCCcccCCC
Confidence 5667776666544
No 42
>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=67.16 E-value=3.2 Score=21.29 Aligned_cols=22 Identities=27% Similarity=0.517 Sum_probs=13.4
Q ss_pred ccccCCCCcccCCCeeEeeCCccccHhh
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILCKRD 94 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c 94 (139)
.|..|+.+| +..++++.||..|
T Consensus 19 ~Cp~C~~PL------~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPL------MRDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCee------EEecCCCEECCCC
Confidence 455666565 3356777777654
No 43
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=66.46 E-value=4.6 Score=24.27 Aligned_cols=30 Identities=20% Similarity=0.559 Sum_probs=16.8
Q ss_pred cccccCCCCCCC-ceEEEeCCccccccccccccC
Q psy284 104 YCAACSKVIPAF-EMVMRARNNVYHLECFACQQC 136 (139)
Q Consensus 104 ~C~~C~~~I~~~-~~~~~~~~~~~H~~Cf~C~~C 136 (139)
.|.+|+.+|... ...+...|..-+ |.|..|
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~---FCC~GC 32 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERP---FCCPGC 32 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccc---cccHHH
Confidence 578888888532 234445554433 555554
No 44
>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=66.32 E-value=15 Score=20.12 Aligned_cols=46 Identities=17% Similarity=0.446 Sum_probs=28.8
Q ss_pred ccccCCCCcccCC-CeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 67 KCGCCDCRLGEVG-STLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 67 ~C~~C~~~l~~~~-~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
.|..|++.|.... ..+.-.-.--||..|....+.. .|.-|+..+..
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~--~CPNCgGelv~ 53 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNG--VCPNCGGELVR 53 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcC--cCcCCCCcccc
Confidence 3556677665221 1233233356889998888765 89999986643
No 45
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=66.15 E-value=3.2 Score=26.99 Aligned_cols=22 Identities=23% Similarity=0.517 Sum_probs=15.8
Q ss_pred ccccCCCCcccCCCeeEeeCCccccHhhH
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILCKRDY 95 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy 95 (139)
.|..|+.+| |.++|.+||..|-
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 466677777 3388888887774
No 46
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=66.07 E-value=3.5 Score=34.17 Aligned_cols=84 Identities=19% Similarity=0.336 Sum_probs=47.2
Q ss_pred CCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
.+....|..|.+.|.+. .++.|+----.|..|+-++. +-+.-+|=.......--+ .|..|.+
T Consensus 98 ~pD~a~C~~Cl~Ei~dp-----~~rrY~YPF~~CT~CGPRfT-------Ii~alPYDR~nTsM~~F~--lC~~C~~---- 159 (750)
T COG0068 98 PPDAATCEDCLEEIFDP-----NSRRYLYPFINCTNCGPRFT-------IIEALPYDRENTSMADFP--LCPFCDK---- 159 (750)
T ss_pred CCchhhhHHHHHHhcCC-----CCcceeccccccCCCCccee-------eeccCCCCcccCccccCc--CCHHHHH----
Confidence 44566899999988885 35667766667888886553 222222221111111112 4555543
Q ss_pred CceEEEeCCccccccccccccCCC
Q psy284 115 FEMVMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 115 ~~~~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
.+-...++.||..=..|..|+.
T Consensus 160 --EY~dP~nRRfHAQp~aCp~CGP 181 (750)
T COG0068 160 --EYKDPLNRRFHAQPIACPKCGP 181 (750)
T ss_pred --HhcCccccccccccccCcccCC
Confidence 2333556777777677777763
No 47
>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=66.07 E-value=9.6 Score=18.56 Aligned_cols=26 Identities=15% Similarity=0.438 Sum_probs=13.6
Q ss_pred CCccccHhhHHHHhCC-CccccccCCC
Q psy284 86 ANLILCKRDYLRLFGS-TGYCAACSKV 111 (139)
Q Consensus 86 ~~~~~C~~cy~~~~~~-~~~C~~C~~~ 111 (139)
-+..||..|....+.. ...|..|...
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 4555666665443321 2257777654
No 48
>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=65.71 E-value=3.1 Score=24.37 Aligned_cols=31 Identities=32% Similarity=0.715 Sum_probs=18.9
Q ss_pred CCCccccccccccccee-e----eec------CccccccCcc
Q psy284 37 GPQECAGCGKHITDRFL-L----KAL------DMYWHEDCLK 67 (139)
Q Consensus 37 ~~~~C~~C~~~i~~~~~-~----~~~------~~~~H~~Cf~ 67 (139)
+-..|..|++.|..+.+ + ... ...||..||.
T Consensus 6 ~Ra~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~ 47 (82)
T PF00645_consen 6 GRAKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFF 47 (82)
T ss_dssp STEBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHH
T ss_pred CCccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccc
Confidence 34589999999976422 1 111 1467888876
No 49
>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=64.63 E-value=1.2 Score=21.90 Aligned_cols=28 Identities=21% Similarity=0.326 Sum_probs=13.0
Q ss_pred cccCCCCcccCCCeeEeeCCccccHhhHHH
Q psy284 68 CGCCDCRLGEVGSTLYTKANLILCKRDYLR 97 (139)
Q Consensus 68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~ 97 (139)
|..|+..+ +..+.....+..+|..|...
T Consensus 6 C~~CGe~I--~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPI--PEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBE--EHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChH--HHHHHHhCCCcEECHHHhCc
Confidence 45555555 22334444555666666543
No 50
>PF12773 DZR: Double zinc ribbon
Probab=62.93 E-value=3.2 Score=21.79 Aligned_cols=9 Identities=22% Similarity=0.652 Sum_probs=4.5
Q ss_pred cccccCCCC
Q psy284 104 YCAACSKVI 112 (139)
Q Consensus 104 ~C~~C~~~I 112 (139)
.|..|+..+
T Consensus 31 ~C~~Cg~~~ 39 (50)
T PF12773_consen 31 ICPNCGAEN 39 (50)
T ss_pred CCcCCcCCC
Confidence 455555544
No 51
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=60.42 E-value=7.5 Score=21.16 Aligned_cols=26 Identities=19% Similarity=0.356 Sum_probs=17.7
Q ss_pred CcccccccccccceeeeecCcccccc
Q psy284 39 QECAGCGKHITDRFLLKALDMYWHED 64 (139)
Q Consensus 39 ~~C~~C~~~i~~~~~~~~~~~~~H~~ 64 (139)
.+|..|+.+|.++..+...+...|+.
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~g 27 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHPG 27 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCcH
Confidence 46888888888865555555566654
No 52
>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=59.12 E-value=3.9 Score=24.66 Aligned_cols=17 Identities=35% Similarity=0.913 Sum_probs=13.6
Q ss_pred hHHHHhCCCccccccCCCC
Q psy284 94 DYLRLFGSTGYCAACSKVI 112 (139)
Q Consensus 94 cy~~~~~~~~~C~~C~~~I 112 (139)
-|..+|.. .|..|++.+
T Consensus 48 sY~~lfs~--pC~~C~klL 64 (90)
T PF11571_consen 48 SYRNLFST--PCKKCGKLL 64 (90)
T ss_pred HHhhhccc--hhhHHHhHh
Confidence 35667777 899999988
No 53
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=57.22 E-value=9.3 Score=21.25 Aligned_cols=17 Identities=24% Similarity=0.620 Sum_probs=11.0
Q ss_pred cccccCCCCCCCceEEE
Q psy284 104 YCAACSKVIPAFEMVMR 120 (139)
Q Consensus 104 ~C~~C~~~I~~~~~~~~ 120 (139)
.|.+|+..|.+.|..+.
T Consensus 11 ~CtSCg~~i~p~e~~v~ 27 (61)
T COG2888 11 VCTSCGREIAPGETAVK 27 (61)
T ss_pred eeccCCCEeccCCceeE
Confidence 78888877755455443
No 54
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=55.51 E-value=3.4 Score=28.85 Aligned_cols=31 Identities=13% Similarity=0.238 Sum_probs=22.1
Q ss_pred cccccCCCCcccCCCeeEeeCCccccHhhHHHH
Q psy284 66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98 (139)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~ 98 (139)
-+|..|+... ........+|+++|..||.+.
T Consensus 173 v~C~kCGE~~--~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELF--MEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCccc--ccchhhhcCCceecccccccc
Confidence 4677787776 444556778888898888643
No 55
>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=52.62 E-value=9.5 Score=20.24 Aligned_cols=32 Identities=19% Similarity=0.463 Sum_probs=20.3
Q ss_pred EeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 83 YTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 83 ~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
..=.+..+|..|.....+....|..|+++++.
T Consensus 16 i~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 16 IKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp EE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred eeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence 33445678888888777766699999998864
No 56
>PRK00420 hypothetical protein; Validated
Probab=52.47 E-value=7.1 Score=24.70 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=4.2
Q ss_pred ccccCCCCc
Q psy284 67 KCGCCDCRL 75 (139)
Q Consensus 67 ~C~~C~~~l 75 (139)
.|..|+.+|
T Consensus 25 ~CP~Cg~pL 33 (112)
T PRK00420 25 HCPVCGLPL 33 (112)
T ss_pred CCCCCCCcc
Confidence 344455444
No 57
>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=49.95 E-value=14 Score=18.62 Aligned_cols=7 Identities=0% Similarity=0.059 Sum_probs=2.8
Q ss_pred ccccHhh
Q psy284 88 LILCKRD 94 (139)
Q Consensus 88 ~~~C~~c 94 (139)
..|+..|
T Consensus 23 H~fh~~C 29 (44)
T PF13639_consen 23 HVFHRSC 29 (44)
T ss_dssp EEEEHHH
T ss_pred CeeCHHH
Confidence 3344444
No 58
>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=49.39 E-value=4.4 Score=18.90 Aligned_cols=11 Identities=27% Similarity=0.612 Sum_probs=5.9
Q ss_pred cccccCCCCCC
Q psy284 104 YCAACSKVIPA 114 (139)
Q Consensus 104 ~C~~C~~~I~~ 114 (139)
+|..|...|..
T Consensus 3 ~C~rC~~~~~~ 13 (30)
T PF06827_consen 3 KCPRCWNYIED 13 (30)
T ss_dssp B-TTT--BBEE
T ss_pred cCccCCCcceE
Confidence 78889888743
No 59
>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=47.64 E-value=13 Score=21.49 Aligned_cols=9 Identities=33% Similarity=0.992 Sum_probs=2.8
Q ss_pred ccccCCCCC
Q psy284 105 CAACSKVIP 113 (139)
Q Consensus 105 C~~C~~~I~ 113 (139)
|..|+..|.
T Consensus 53 C~~c~gLiS 61 (70)
T PF07191_consen 53 CNHCHGLIS 61 (70)
T ss_dssp -TTTT-EE-
T ss_pred eccCCceee
Confidence 444444443
No 60
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.42 E-value=34 Score=19.87 Aligned_cols=44 Identities=18% Similarity=0.418 Sum_probs=26.4
Q ss_pred cccCCCCccc-CCCeeEeeCCccccHhhHHHHhCCCccccccCCCCC
Q psy284 68 CGCCDCRLGE-VGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIP 113 (139)
Q Consensus 68 C~~C~~~l~~-~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~ 113 (139)
|..|++.|.- .+....-.-.--||.+|...++.. .|..|+..+.
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~g--~CPnCGGelv 52 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENRLHG--LCPNCGGELV 52 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHhhcC--cCCCCCchhh
Confidence 4556666641 111122222345788898888776 8999987654
No 61
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=45.27 E-value=15 Score=16.53 Aligned_cols=9 Identities=44% Similarity=1.125 Sum_probs=4.1
Q ss_pred ccccccccc
Q psy284 40 ECAGCGKHI 48 (139)
Q Consensus 40 ~C~~C~~~i 48 (139)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 344454433
No 62
>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=44.86 E-value=9.3 Score=23.17 Aligned_cols=36 Identities=19% Similarity=0.469 Sum_probs=17.1
Q ss_pred CCcccccccccccceeeeecCccccccCcccccCCCCc
Q psy284 38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRL 75 (139)
Q Consensus 38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l 75 (139)
...|..|++.+.-.+.+-+.+-.+.. -+|..|+.++
T Consensus 33 rS~C~~C~~~L~~~~lIPi~S~l~lr--GrCr~C~~~I 68 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIPILSYLLLR--GRCRYCGAPI 68 (92)
T ss_pred CCcCcCCCCcCcccccchHHHHHHhC--CCCcccCCCC
Confidence 34666666666554444433322222 2444455554
No 63
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=44.01 E-value=13 Score=30.84 Aligned_cols=13 Identities=15% Similarity=0.358 Sum_probs=8.5
Q ss_pred Ccccccccccccc
Q psy284 39 QECAGCGKHITDR 51 (139)
Q Consensus 39 ~~C~~C~~~i~~~ 51 (139)
.+|..|+..+.+.
T Consensus 2 ~~Cp~Cg~~n~~~ 14 (645)
T PRK14559 2 LICPQCQFENPNN 14 (645)
T ss_pred CcCCCCCCcCCCC
Confidence 3677887766553
No 64
>KOG3002|consensus
Probab=43.80 E-value=22 Score=26.54 Aligned_cols=44 Identities=18% Similarity=0.357 Sum_probs=30.3
Q ss_pred cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
+.|..|...| ....+.-.+|.+.|..|-.++.. +|..|..+|..
T Consensus 49 leCPvC~~~l--~~Pi~QC~nGHlaCssC~~~~~~---~CP~Cr~~~g~ 92 (299)
T KOG3002|consen 49 LDCPVCFNPL--SPPIFQCDNGHLACSSCRTKVSN---KCPTCRLPIGN 92 (299)
T ss_pred ccCchhhccC--cccceecCCCcEehhhhhhhhcc---cCCcccccccc
Confidence 5666777777 33456677888888888654332 78888888853
No 65
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=43.67 E-value=13 Score=22.08 Aligned_cols=30 Identities=17% Similarity=0.287 Sum_probs=15.7
Q ss_pred cccCCCCcccCC---CeeEeeCCccccHhhHHH
Q psy284 68 CGCCDCRLGEVG---STLYTKANLILCKRDYLR 97 (139)
Q Consensus 68 C~~C~~~l~~~~---~~~~~~~~~~~C~~cy~~ 97 (139)
|..|+.+|.... ..-....+.-||.-||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 667777775211 111122334588888753
No 66
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=43.47 E-value=6.1 Score=17.41 Aligned_cols=6 Identities=33% Similarity=0.739 Sum_probs=2.2
Q ss_pred ccCCCC
Q psy284 107 ACSKVI 112 (139)
Q Consensus 107 ~C~~~I 112 (139)
.|+..|
T Consensus 4 ~CG~~~ 9 (23)
T PF13240_consen 4 NCGAEI 9 (23)
T ss_pred ccCCCC
Confidence 333333
No 67
>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=42.03 E-value=10 Score=18.66 Aligned_cols=30 Identities=27% Similarity=0.569 Sum_probs=17.3
Q ss_pred ccccccccccceeeeecCccccccCcccccCCCCc
Q psy284 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRL 75 (139)
Q Consensus 41 C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l 75 (139)
|..|.+.+.+. .++.||-.-..|..|+-++
T Consensus 2 C~~C~~Ey~~p-----~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 2 CDDCLKEYFDP-----SNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp -HHHHHHHCST-----TSTTTT-TT--BTTCC-SC
T ss_pred CHHHHHHHcCC-----CCCcccCcCccCCCCCCCE
Confidence 55666555443 4788898888899998665
No 68
>PRK00807 50S ribosomal protein L24e; Validated
Probab=41.91 E-value=17 Score=19.56 Aligned_cols=25 Identities=16% Similarity=0.307 Sum_probs=17.6
Q ss_pred cccccCCCCCCCce--EEEeCCccccc
Q psy284 104 YCAACSKVIPAFEM--VMRARNNVYHL 128 (139)
Q Consensus 104 ~C~~C~~~I~~~~~--~~~~~~~~~H~ 128 (139)
.|.-|+..|.+... ++..+|+.|.-
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~~F 29 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTILYF 29 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEEEE
Confidence 68888888885333 35677888873
No 69
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.27 E-value=30 Score=22.38 Aligned_cols=46 Identities=20% Similarity=0.372 Sum_probs=24.8
Q ss_pred cccHhhHHHHhCCCccccccCCCCCCCce--EEEeCCccccccccccccCCC
Q psy284 89 ILCKRDYLRLFGSTGYCAACSKVIPAFEM--VMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 89 ~~C~~cy~~~~~~~~~C~~C~~~I~~~~~--~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
.||..|-..... .|..|+.+|.|..- .+.-+|..|-+--| |..|++
T Consensus 29 afcskcgeati~---qcp~csasirgd~~vegvlglg~dye~psf-chncgs 76 (160)
T COG4306 29 AFCSKCGEATIT---QCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGS 76 (160)
T ss_pred HHHhhhchHHHh---cCCccCCcccccceeeeeeccCCCCCCcch-hhcCCC
Confidence 456666544332 57888888877321 22245566655433 555554
No 70
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=40.55 E-value=63 Score=22.55 Aligned_cols=11 Identities=18% Similarity=0.670 Sum_probs=9.6
Q ss_pred cccccCCCCCC
Q psy284 104 YCAACSKVIPA 114 (139)
Q Consensus 104 ~C~~C~~~I~~ 114 (139)
.|..|...|..
T Consensus 70 ~CPvCR~~Is~ 80 (193)
T PLN03208 70 KCPVCKSDVSE 80 (193)
T ss_pred cCCCCCCcCCh
Confidence 79999999975
No 71
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=40.14 E-value=9.6 Score=31.89 Aligned_cols=36 Identities=19% Similarity=0.478 Sum_probs=25.8
Q ss_pred CCCCCcccccccccccceeeeecCccccccCcccccCCCCc
Q psy284 35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRL 75 (139)
Q Consensus 35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l 75 (139)
......|..|.+.+.+. .++.|+---..|..|+-+.
T Consensus 65 ppD~a~C~~Cl~E~~dp-----~~Rry~YpF~nCt~CGPr~ 100 (711)
T TIGR00143 65 PADVATCSDCLEEMLDK-----NDRRYLYPFISCTHCGPRF 100 (711)
T ss_pred CCchhhHHHHHHHhcCC-----CcccccCCcccccCCCCCe
Confidence 34466899999988775 2566766666788887654
No 72
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=40.14 E-value=25 Score=19.49 Aligned_cols=29 Identities=14% Similarity=0.267 Sum_probs=18.5
Q ss_pred ccccCCCCcccCCCeeEeeCCccccH-hhH
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILCK-RDY 95 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C~-~cy 95 (139)
.|..|++.|......|..+..+.+|. .|-
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR 47 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECR 47 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHH
Confidence 45668888874344455677788884 553
No 73
>KOG2932|consensus
Probab=39.87 E-value=13 Score=27.87 Aligned_cols=44 Identities=14% Similarity=0.283 Sum_probs=28.8
Q ss_pred ccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
-|..|+.++.. ..-.+.-+..||.+|...--.+ .|..|...|.-
T Consensus 92 fCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~~~dK--~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 92 FCDRCDFPIAI--YGRMIPCKHVFCLECARSDSDK--ICPLCDDRVQR 135 (389)
T ss_pred eecccCCccee--eecccccchhhhhhhhhcCccc--cCcCcccHHHH
Confidence 46678877731 2223556778898886543334 89999987743
No 74
>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=38.91 E-value=55 Score=16.48 Aligned_cols=30 Identities=20% Similarity=0.418 Sum_probs=13.7
Q ss_pred ccccCCCCcccCCCeeEeeCCccccHhhHH
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILCKRDYL 96 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~ 96 (139)
+|+-|+++-.+.+..+...++...|..|-.
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 466666665533333333335666776654
No 75
>KOG0978|consensus
Probab=37.81 E-value=10 Score=31.55 Aligned_cols=48 Identities=23% Similarity=0.542 Sum_probs=31.1
Q ss_pred cccccCCCCcccCCCeeEeeCCccccHhhHHHHhC-CCccccccCCCCCCCc
Q psy284 66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG-STGYCAACSKVIPAFE 116 (139)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~-~~~~C~~C~~~I~~~~ 116 (139)
++|..|+..+- ......-+..||..|-..+|. .+.+|..|+.+..+.|
T Consensus 644 LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 644 LKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 57777775552 234456667788888665543 2237999998876644
No 76
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=36.16 E-value=54 Score=19.33 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=9.7
Q ss_pred ccccHhhHH--HHhCCCccccccCCC
Q psy284 88 LILCKRDYL--RLFGSTGYCAACSKV 111 (139)
Q Consensus 88 ~~~C~~cy~--~~~~~~~~C~~C~~~ 111 (139)
-+.|+.||. ++-+.+ .|.+|+.+
T Consensus 36 fPvCr~CyEYErkeg~q-~CpqCkt~ 60 (80)
T PF14569_consen 36 FPVCRPCYEYERKEGNQ-VCPQCKTR 60 (80)
T ss_dssp ----HHHHHHHHHTS-S-B-TTT--B
T ss_pred CccchhHHHHHhhcCcc-cccccCCC
Confidence 345888864 455532 68888853
No 77
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.15 E-value=34 Score=26.64 Aligned_cols=45 Identities=18% Similarity=0.368 Sum_probs=22.0
Q ss_pred cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCC
Q psy284 66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIP 113 (139)
Q Consensus 66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~ 113 (139)
+.|..|...+. ......-+..||..|....+.....|..|...+.
T Consensus 27 l~C~IC~d~~~---~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 27 LRCHICKDFFD---VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred cCCCcCchhhh---CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 44555544442 1122344555666665544433335777776653
No 78
>KOG2114|consensus
Probab=35.69 E-value=18 Score=30.89 Aligned_cols=10 Identities=30% Similarity=0.889 Sum_probs=5.0
Q ss_pred Cccccccccc
Q psy284 123 NNVYHLECFA 132 (139)
Q Consensus 123 ~~~~H~~Cf~ 132 (139)
++.||.+||.
T Consensus 860 gHsyHqhC~e 869 (933)
T KOG2114|consen 860 GHSYHQHCLE 869 (933)
T ss_pred ccHHHHHhhc
Confidence 4555555544
No 79
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.53 E-value=17 Score=19.66 Aligned_cols=28 Identities=32% Similarity=0.451 Sum_probs=13.7
Q ss_pred cccccccccccceeeeecCccccccCcc
Q psy284 40 ECAGCGKHITDRFLLKALDMYWHEDCLK 67 (139)
Q Consensus 40 ~C~~C~~~i~~~~~~~~~~~~~H~~Cf~ 67 (139)
.|+.|++.+.-.-=....++.|-.+|-.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~v 29 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQV 29 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhh
Confidence 4677777654420022234555555544
No 80
>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=35.42 E-value=46 Score=16.93 Aligned_cols=9 Identities=22% Similarity=0.608 Sum_probs=5.5
Q ss_pred cccHhhHHH
Q psy284 89 ILCKRDYLR 97 (139)
Q Consensus 89 ~~C~~cy~~ 97 (139)
-+|..||..
T Consensus 28 dlC~~Cf~~ 36 (44)
T smart00291 28 DLCQSCFAK 36 (44)
T ss_pred cchHHHHhC
Confidence 357777654
No 81
>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=34.78 E-value=22 Score=19.25 Aligned_cols=28 Identities=18% Similarity=0.417 Sum_probs=13.8
Q ss_pred ccccCCCCcccCCCeeEeeCCcccc-HhhHH
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILC-KRDYL 96 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C-~~cy~ 96 (139)
.|..|...+. ...-+.++++.|| ..|..
T Consensus 9 aC~~C~C~V~--~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVS--EEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B---TTTSEESSS-EESSHHHHH
T ss_pred cCCCCEeEEC--chHhHHhCCEeeecHHHhc
Confidence 4556666664 2345778899999 45543
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=34.58 E-value=51 Score=16.88 Aligned_cols=7 Identities=43% Similarity=0.894 Sum_probs=3.4
Q ss_pred ccHhhHH
Q psy284 90 LCKRDYL 96 (139)
Q Consensus 90 ~C~~cy~ 96 (139)
+|..||.
T Consensus 25 LC~~Cf~ 31 (46)
T cd02249 25 LCSSCYA 31 (46)
T ss_pred CHHHHHC
Confidence 4555543
No 83
>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=34.23 E-value=10 Score=16.01 Aligned_cols=8 Identities=25% Similarity=1.107 Sum_probs=4.6
Q ss_pred cccccCCC
Q psy284 131 FACQQCNH 138 (139)
Q Consensus 131 f~C~~C~~ 138 (139)
|.|..|++
T Consensus 1 y~C~~C~~ 8 (23)
T PF00096_consen 1 YKCPICGK 8 (23)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 45666654
No 84
>KOG3497|consensus
Probab=33.51 E-value=14 Score=20.64 Aligned_cols=14 Identities=50% Similarity=1.042 Sum_probs=11.0
Q ss_pred CCcccccccccccc
Q psy284 38 PQECAGCGKHITDR 51 (139)
Q Consensus 38 ~~~C~~C~~~i~~~ 51 (139)
+.+|+.|++.|.+.
T Consensus 4 PiRCFtCGKvig~K 17 (69)
T KOG3497|consen 4 PIRCFTCGKVIGDK 17 (69)
T ss_pred eeEeeecccccccc
Confidence 35799999988874
No 85
>KOG4739|consensus
Probab=33.43 E-value=40 Score=24.26 Aligned_cols=31 Identities=19% Similarity=0.362 Sum_probs=23.6
Q ss_pred eEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284 82 LYTKANLILCKRDYLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 82 ~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~ 114 (139)
|..--..++|..|...-.+. .|..|+++|..
T Consensus 19 ~LTaC~HvfC~~C~k~~~~~--~C~lCkk~ir~ 49 (233)
T KOG4739|consen 19 FLTACRHVFCEPCLKASSPD--VCPLCKKSIRI 49 (233)
T ss_pred eeeechhhhhhhhcccCCcc--ccccccceeee
Confidence 33466778899998776666 89999998744
No 86
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=32.86 E-value=15 Score=22.29 Aligned_cols=20 Identities=20% Similarity=0.426 Sum_probs=14.6
Q ss_pred HHHHhCCCccccccCCCCCC
Q psy284 95 YLRLFGSTGYCAACSKVIPA 114 (139)
Q Consensus 95 y~~~~~~~~~C~~C~~~I~~ 114 (139)
|+++.....+|+.|+.++.|
T Consensus 27 ~~kK~~~~p~C~~cg~pL~G 46 (93)
T COG2174 27 YEKKKPTIPKCAICGRPLGG 46 (93)
T ss_pred eeeccCCCCcccccCCccCC
Confidence 44555555599999999866
No 87
>smart00746 TRASH metallochaperone-like domain.
Probab=32.38 E-value=48 Score=14.68 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=13.1
Q ss_pred ccccCCCCC-CC-ceEEEeCCcccc
Q psy284 105 CAACSKVIP-AF-EMVMRARNNVYH 127 (139)
Q Consensus 105 C~~C~~~I~-~~-~~~~~~~~~~~H 127 (139)
|..|+..|. .. ...+...++.||
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~ 25 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFY 25 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEE
Confidence 566777775 22 223346666665
No 88
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.81 E-value=68 Score=24.14 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=19.5
Q ss_pred CCccccHhhHHHHhC-CCccccccCCCCCC
Q psy284 86 ANLILCKRDYLRLFG-STGYCAACSKVIPA 114 (139)
Q Consensus 86 ~~~~~C~~cy~~~~~-~~~~C~~C~~~I~~ 114 (139)
-|..+|..|..+.|. ..+.|..|+.++..
T Consensus 26 CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 26 CGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 455667777766552 22379999988865
No 89
>KOG2034|consensus
Probab=31.77 E-value=18 Score=30.96 Aligned_cols=30 Identities=13% Similarity=0.456 Sum_probs=24.4
Q ss_pred CccccccCCCCCCCceEEEeCCcccccccc
Q psy284 102 TGYCAACSKVIPAFEMVMRARNNVYHLECF 131 (139)
Q Consensus 102 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf 131 (139)
...|..|.++|...-+++..-|+.||.+|.
T Consensus 817 ~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl 846 (911)
T KOG2034|consen 817 QDSCDHCGRPLLIKPFYVFPCGHCFHRDCL 846 (911)
T ss_pred ccchHHhcchhhcCcceeeeccchHHHHHH
Confidence 347999999998766788888999998874
No 90
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=31.69 E-value=26 Score=19.54 Aligned_cols=14 Identities=43% Similarity=0.992 Sum_probs=9.5
Q ss_pred CCcccccccccccc
Q psy284 38 PQECAGCGKHITDR 51 (139)
Q Consensus 38 ~~~C~~C~~~i~~~ 51 (139)
+.+|+.||++|.+.
T Consensus 4 PVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 4 PVRCFTCGKVIGNK 17 (60)
T ss_dssp SSS-STTTSBTCGH
T ss_pred ceecCCCCCChhHh
Confidence 45788888888763
No 91
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=30.45 E-value=61 Score=15.70 Aligned_cols=17 Identities=6% Similarity=0.194 Sum_probs=10.4
Q ss_pred EeeCCccccHhhHHHHh
Q psy284 83 YTKANLILCKRDYLRLF 99 (139)
Q Consensus 83 ~~~~~~~~C~~cy~~~~ 99 (139)
...=+..||..|..+.+
T Consensus 14 ~~~C~H~fC~~C~~~~~ 30 (41)
T PF00097_consen 14 LLPCGHSFCRDCLRKWL 30 (41)
T ss_dssp ETTTSEEEEHHHHHHHH
T ss_pred EecCCCcchHHHHHHHH
Confidence 44556667777765543
No 92
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=30.43 E-value=41 Score=18.12 Aligned_cols=25 Identities=16% Similarity=0.309 Sum_probs=15.4
Q ss_pred CcccccccccccceeeeecCccccc
Q psy284 39 QECAGCGKHITDRFLLKALDMYWHE 63 (139)
Q Consensus 39 ~~C~~C~~~i~~~~~~~~~~~~~H~ 63 (139)
.+|..|+.+|..+..+.......|+
T Consensus 2 ~iCvvCK~Pi~~al~v~T~~Gpvh~ 26 (53)
T PHA02610 2 KICVVCKQPIEKALVVETEKGPVHP 26 (53)
T ss_pred ceeeeeCCchhhceEEecCCCCCCC
Confidence 3677888888666445444445554
No 93
>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=29.81 E-value=39 Score=17.58 Aligned_cols=29 Identities=17% Similarity=0.274 Sum_probs=15.6
Q ss_pred ccccCCCCcccCCCeeEe--eCCccccHhhHHH
Q psy284 67 KCGCCDCRLGEVGSTLYT--KANLILCKRDYLR 97 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~--~~~~~~C~~cy~~ 97 (139)
.|..|+..+. .-+|.- ..+..+|..||.+
T Consensus 2 ~C~~Cg~D~t--~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCT--RVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccC--ceEEEecCCCccccChHHHhC
Confidence 3556666662 222221 2235678888875
No 94
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=29.80 E-value=37 Score=16.95 Aligned_cols=31 Identities=16% Similarity=0.381 Sum_probs=14.3
Q ss_pred CCcccccccccccceeeeecCccccccCcccccCCC
Q psy284 38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDC 73 (139)
Q Consensus 38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~ 73 (139)
+.+|..|+..|.+--.+...++. ++|..|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~-----w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKT-----WICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTE-----EEETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCE-----EECcCCCC
Confidence 46888998888774234333444 46777764
No 95
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=29.65 E-value=73 Score=15.45 Aligned_cols=16 Identities=19% Similarity=-0.039 Sum_probs=10.3
Q ss_pred eeEeeCCcc-ccHhhHH
Q psy284 81 TLYTKANLI-LCKRDYL 96 (139)
Q Consensus 81 ~~~~~~~~~-~C~~cy~ 96 (139)
.....++.. +|..|..
T Consensus 12 WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 12 WRRGPNGNRTLCNACGL 28 (36)
T ss_dssp EEEETTSEE-EEHHHHH
T ss_pred hhcCCCCCCHHHHHHHH
Confidence 334455666 8999964
No 96
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=29.48 E-value=42 Score=17.84 Aligned_cols=27 Identities=15% Similarity=0.391 Sum_probs=21.0
Q ss_pred cccccCCCCCCC-ceEEEeCCccccccc
Q psy284 104 YCAACSKVIPAF-EMVMRARNNVYHLEC 130 (139)
Q Consensus 104 ~C~~C~~~I~~~-~~~~~~~~~~~H~~C 130 (139)
.|..|+.-..+. |..+.+.+..|+..|
T Consensus 15 ~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 15 KCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred cCcccCCcEeecCcceEEEeccceeeee
Confidence 788998877664 457788889998876
No 97
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=29.43 E-value=16 Score=21.08 Aligned_cols=14 Identities=43% Similarity=0.992 Sum_probs=10.9
Q ss_pred CCcccccccccccc
Q psy284 38 PQECAGCGKHITDR 51 (139)
Q Consensus 38 ~~~C~~C~~~i~~~ 51 (139)
+.+|+.||+.|.+.
T Consensus 4 PVRCFTCGkvig~~ 17 (71)
T PLN00032 4 PVRCFTCGKVIGNK 17 (71)
T ss_pred ceeecCCCCCcHHH
Confidence 45899999988763
No 98
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=29.28 E-value=58 Score=16.74 Aligned_cols=10 Identities=20% Similarity=0.504 Sum_probs=6.7
Q ss_pred ccccHhhHHH
Q psy284 88 LILCKRDYLR 97 (139)
Q Consensus 88 ~~~C~~cy~~ 97 (139)
--+|..||.+
T Consensus 28 ~dLC~~C~~~ 37 (46)
T PF00569_consen 28 YDLCEDCFSK 37 (46)
T ss_dssp -EEEHHHHHH
T ss_pred CchhhHHHhC
Confidence 3468888876
No 99
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=28.55 E-value=41 Score=18.26 Aligned_cols=25 Identities=24% Similarity=0.416 Sum_probs=18.0
Q ss_pred ccccccCCCCCCCc--eEEEeCCcccc
Q psy284 103 GYCAACSKVIPAFE--MVMRARNNVYH 127 (139)
Q Consensus 103 ~~C~~C~~~I~~~~--~~~~~~~~~~H 127 (139)
+.|.-|+..|.+.. .+|..+|+.|+
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 37888999998743 36667777776
No 100
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=28.36 E-value=19 Score=20.20 Aligned_cols=14 Identities=43% Similarity=0.985 Sum_probs=10.8
Q ss_pred CCcccccccccccc
Q psy284 38 PQECAGCGKHITDR 51 (139)
Q Consensus 38 ~~~C~~C~~~i~~~ 51 (139)
+.+|+.||++|.+.
T Consensus 4 PiRCFsCGkvi~~~ 17 (63)
T COG1644 4 PVRCFSCGKVIGHK 17 (63)
T ss_pred ceEeecCCCCHHHH
Confidence 45799999988763
No 101
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=28.29 E-value=15 Score=16.23 Aligned_cols=7 Identities=43% Similarity=0.999 Sum_probs=3.9
Q ss_pred cccccCC
Q psy284 104 YCAACSK 110 (139)
Q Consensus 104 ~C~~C~~ 110 (139)
.|..|+.
T Consensus 18 ~C~~C~~ 24 (26)
T smart00547 18 KCFACGA 24 (26)
T ss_pred cccccCC
Confidence 5555554
No 102
>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=27.96 E-value=37 Score=15.61 Aligned_cols=9 Identities=22% Similarity=0.944 Sum_probs=2.1
Q ss_pred ccccCCCCc
Q psy284 67 KCGCCDCRL 75 (139)
Q Consensus 67 ~C~~C~~~l 75 (139)
.|..|+..+
T Consensus 2 ~C~~C~~~~ 10 (30)
T PF07649_consen 2 RCDACGKPI 10 (30)
T ss_dssp --TTTS---
T ss_pred cCCcCCCcC
Confidence 455555544
No 103
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=27.57 E-value=35 Score=25.15 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=15.7
Q ss_pred cccccCCCCCCCceEEEeCCccccccc
Q psy284 104 YCAACSKVIPAFEMVMRARNNVYHLEC 130 (139)
Q Consensus 104 ~C~~C~~~I~~~~~~~~~~~~~~H~~C 130 (139)
-|..|+.+|.- .++.-.+..|.|.|
T Consensus 247 pC~~CGt~I~k--~~~~gR~t~~CP~C 271 (273)
T COG0266 247 PCRRCGTPIEK--IKLGGRSTFYCPVC 271 (273)
T ss_pred CCCccCCEeEE--EEEcCCcCEeCCCC
Confidence 69999999943 34444444454444
No 104
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=27.51 E-value=26 Score=23.02 Aligned_cols=35 Identities=17% Similarity=0.361 Sum_probs=18.2
Q ss_pred cccccCCCCCCCce--E---EEeCCccccccccccccCCC
Q psy284 104 YCAACSKVIPAFEM--V---MRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 104 ~C~~C~~~I~~~~~--~---~~~~~~~~H~~Cf~C~~C~~ 138 (139)
+|..|+.++..-+. + +-..-...+.+-+.|..|++
T Consensus 93 RC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~k 132 (147)
T PF01927_consen 93 RCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGK 132 (147)
T ss_pred ccCCCCcEeeechhhccccccCccccccCCeEEECCCCCC
Confidence 68888876643111 1 11222333445666888875
No 105
>KOG2893|consensus
Probab=27.50 E-value=22 Score=25.76 Aligned_cols=36 Identities=22% Similarity=0.379 Sum_probs=23.6
Q ss_pred CCcccccccccccceeeeecCccccccCcccccCCCCcc
Q psy284 38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76 (139)
Q Consensus 38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 76 (139)
.+-|-.|+..+.+..++.. .-....|+|..|.+.|-
T Consensus 10 kpwcwycnrefddekiliq---hqkakhfkchichkkl~ 45 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQ---HQKAKHFKCHICHKKLF 45 (341)
T ss_pred Cceeeecccccchhhhhhh---hhhhccceeeeehhhhc
Confidence 4578889888877633221 11234689999988884
No 106
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=26.64 E-value=16 Score=19.72 Aligned_cols=13 Identities=23% Similarity=0.792 Sum_probs=8.6
Q ss_pred Ccccccccccccc
Q psy284 39 QECAGCGKHITDR 51 (139)
Q Consensus 39 ~~C~~C~~~i~~~ 51 (139)
..|.+|+-.|.+.
T Consensus 23 ~~C~gC~~~l~~~ 35 (56)
T PF02591_consen 23 GTCSGCHMELPPQ 35 (56)
T ss_pred CccCCCCEEcCHH
Confidence 3677777766664
No 107
>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=26.14 E-value=41 Score=17.51 Aligned_cols=13 Identities=46% Similarity=0.856 Sum_probs=9.0
Q ss_pred CCCcccccccccc
Q psy284 37 GPQECAGCGKHIT 49 (139)
Q Consensus 37 ~~~~C~~C~~~i~ 49 (139)
.+..|..|++.|.
T Consensus 10 ~~~~C~~C~~~i~ 22 (53)
T PF00130_consen 10 KPTYCDVCGKFIW 22 (53)
T ss_dssp STEB-TTSSSBEC
T ss_pred CCCCCcccCcccC
Confidence 4558999998883
No 108
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=26.02 E-value=22 Score=14.64 Aligned_cols=8 Identities=38% Similarity=1.194 Sum_probs=3.3
Q ss_pred cccccCCC
Q psy284 131 FACQQCNH 138 (139)
Q Consensus 131 f~C~~C~~ 138 (139)
|.|..|++
T Consensus 1 ~~C~~C~~ 8 (24)
T PF13894_consen 1 FQCPICGK 8 (24)
T ss_dssp EE-SSTS-
T ss_pred CCCcCCCC
Confidence 45566653
No 109
>smart00214 VWC von Willebrand factor (vWF) type C domain.
Probab=25.38 E-value=52 Score=17.79 Aligned_cols=18 Identities=11% Similarity=0.368 Sum_probs=13.2
Q ss_pred eEEEeCCcccccc-ccccc
Q psy284 117 MVMRARNNVYHLE-CFACQ 134 (139)
Q Consensus 117 ~~~~~~~~~~H~~-Cf~C~ 134 (139)
..+...|..|+++ |..|.
T Consensus 5 g~~y~~G~~W~~~~C~~C~ 23 (59)
T smart00214 5 GEVYNDGETWKPDPCQICT 23 (59)
T ss_pred CEEeCCCCEECCCCCeECC
Confidence 4566788999997 76663
No 110
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=25.37 E-value=31 Score=15.84 Aligned_cols=15 Identities=13% Similarity=0.321 Sum_probs=7.6
Q ss_pred eEEEeCCcccccccc
Q psy284 117 MVMRARNNVYHLECF 131 (139)
Q Consensus 117 ~~~~~~~~~~H~~Cf 131 (139)
.++..=++.||.+|+
T Consensus 11 ~~~~~C~H~~c~~C~ 25 (39)
T smart00184 11 PVVLPCGHTFCRSCI 25 (39)
T ss_pred cEEecCCChHHHHHH
Confidence 344445555655554
No 111
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=25.35 E-value=18 Score=22.30 Aligned_cols=29 Identities=14% Similarity=0.210 Sum_probs=16.2
Q ss_pred CcccccCCCCcccCCCeeEeeCCccccHhh
Q psy284 65 CLKCGCCDCRLGEVGSTLYTKANLILCKRD 94 (139)
Q Consensus 65 Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c 94 (139)
=|+|..|..--. .++.-...++.++|..|
T Consensus 70 EFTCssCFLV~H-RSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHH-RSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEec-hhhhccccCCCEecccc
Confidence 377777753221 12222356788888776
No 112
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.27 E-value=79 Score=28.03 Aligned_cols=15 Identities=33% Similarity=0.753 Sum_probs=10.4
Q ss_pred CCCCccccccccccc
Q psy284 36 QGPQECAGCGKHITD 50 (139)
Q Consensus 36 ~~~~~C~~C~~~i~~ 50 (139)
....+|.-|+..|.-
T Consensus 15 ~~~qiCqICGD~vg~ 29 (1079)
T PLN02638 15 GGGQVCQICGDNVGK 29 (1079)
T ss_pred cCCceeeecccccCc
Confidence 345588889877654
No 113
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=25.17 E-value=26 Score=19.70 Aligned_cols=13 Identities=46% Similarity=1.055 Sum_probs=10.1
Q ss_pred CCccccccccccc
Q psy284 38 PQECAGCGKHITD 50 (139)
Q Consensus 38 ~~~C~~C~~~i~~ 50 (139)
+.+|+.||+.|.+
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 4578888888876
No 114
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=24.84 E-value=7.6 Score=23.80 Aligned_cols=17 Identities=24% Similarity=0.600 Sum_probs=8.4
Q ss_pred ccccccCcccccCCCCc
Q psy284 59 MYWHEDCLKCGCCDCRL 75 (139)
Q Consensus 59 ~~~H~~Cf~C~~C~~~l 75 (139)
..+++.+..|..|...|
T Consensus 56 ~~~~~~~iiCGvC~~~L 72 (105)
T COG4357 56 QEFNPKAIICGVCRKLL 72 (105)
T ss_pred hhcCCccEEhhhhhhhh
Confidence 34444555555555444
No 115
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=23.84 E-value=27 Score=18.75 Aligned_cols=10 Identities=40% Similarity=1.035 Sum_probs=5.3
Q ss_pred ccccCCCCCC
Q psy284 105 CAACSKVIPA 114 (139)
Q Consensus 105 C~~C~~~I~~ 114 (139)
|.+|.+++..
T Consensus 2 CfgC~~~~~~ 11 (51)
T PF07975_consen 2 CFGCQKPFPD 11 (51)
T ss_dssp ETTTTEE-TT
T ss_pred CccCCCCCCC
Confidence 5566666644
No 116
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.60 E-value=22 Score=23.42 Aligned_cols=37 Identities=24% Similarity=0.406 Sum_probs=20.5
Q ss_pred CCCcccccccccccceeeeecCccccccCcccccCCCCcc
Q psy284 37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76 (139)
Q Consensus 37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 76 (139)
....|+.|+..+...+.+...+. ..-|.|..|+..|.
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 35578888766554332322221 22378888877763
No 117
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=23.59 E-value=62 Score=28.44 Aligned_cols=32 Identities=16% Similarity=0.514 Sum_probs=25.7
Q ss_pred cccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284 104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH 138 (139)
Q Consensus 104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~ 138 (139)
.|..|++|+.+.|.++-..+.... |+|..|++
T Consensus 798 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ 829 (1006)
T PRK12775 798 TCPKCHRPLEGDEEYVCCATSELQ---WRCDDCGK 829 (1006)
T ss_pred cCcccCCCCCCCceeEEecCccee---eehhhhcc
Confidence 599999999998889888887776 46666654
No 118
>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=23.49 E-value=46 Score=26.62 Aligned_cols=37 Identities=16% Similarity=0.386 Sum_probs=24.0
Q ss_pred CcccccccccccceeeeecCccccccCcccccCCCCcc
Q psy284 39 QECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76 (139)
Q Consensus 39 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 76 (139)
..|..|-..+...+ +...+..-...||.|..|...|.
T Consensus 27 ~yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 27 YYCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred eECccccccCChhh-heeccceeccccccCCCCCCcce
Confidence 35666665555443 33344555668999999998885
No 119
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=23.44 E-value=28 Score=17.94 Aligned_cols=23 Identities=13% Similarity=0.368 Sum_probs=12.9
Q ss_pred cccCCCCCC-CceEEEeCCccccc
Q psy284 106 AACSKVIPA-FEMVMRARNNVYHL 128 (139)
Q Consensus 106 ~~C~~~I~~-~~~~~~~~~~~~H~ 128 (139)
..|+..|.+ ....+...|+.||-
T Consensus 4 Pvcg~~v~~~~~~~~~y~G~~Y~F 27 (47)
T PF04945_consen 4 PVCGMKVPGNAAYSVEYNGRTYYF 27 (47)
T ss_dssp -GGG-BE-----EEEEETTEEEEE
T ss_pred CCCCCEEccCccEEEEECCEEEEE
Confidence 457777722 23577789999983
No 120
>PRK11595 DNA utilization protein GntX; Provisional
Probab=23.44 E-value=93 Score=21.95 Aligned_cols=10 Identities=20% Similarity=0.351 Sum_probs=5.1
Q ss_pred Cccccccccc
Q psy284 39 QECAGCGKHI 48 (139)
Q Consensus 39 ~~C~~C~~~i 48 (139)
++|..|+..+
T Consensus 6 ~~C~~C~~~~ 15 (227)
T PRK11595 6 GLCWLCRMPL 15 (227)
T ss_pred CcCccCCCcc
Confidence 3455555544
No 121
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.42 E-value=34 Score=27.40 Aligned_cols=38 Identities=24% Similarity=0.425 Sum_probs=24.3
Q ss_pred ccccCCCCcccCCCeeEeeCCccccHhhHH-HHhCCCccccccCCC
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILCKRDYL-RLFGSTGYCAACSKV 111 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~-~~~~~~~~C~~C~~~ 111 (139)
+|..|+..| .|+...+.+.|..|-. ..+.. .|..|+..
T Consensus 224 ~C~~C~~~l-----~~h~~~~~l~Ch~Cg~~~~~~~--~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSL-----TYHKKEGKLRCHYCGYQEPIPK--TCPQCGSE 262 (505)
T ss_pred CCCCCCCce-----EEecCCCeEEcCCCcCcCCCCC--CCCCCCCC
Confidence 444555444 3556677888988854 33444 89999863
No 122
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.67 E-value=38 Score=28.25 Aligned_cols=38 Identities=18% Similarity=0.292 Sum_probs=23.7
Q ss_pred ccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCC
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKV 111 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~ 111 (139)
+|..|+.+| .|+...+.+.|.-|-...... .|..|+..
T Consensus 394 ~C~~C~~~L-----~~h~~~~~l~Ch~CG~~~~p~--~Cp~Cgs~ 431 (665)
T PRK14873 394 RCRHCTGPL-----GLPSAGGTPRCRWCGRAAPDW--RCPRCGSD 431 (665)
T ss_pred ECCCCCCce-----eEecCCCeeECCCCcCCCcCc--cCCCCcCC
Confidence 444555455 234445678898886544433 89999874
No 123
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=22.37 E-value=1e+02 Score=16.21 Aligned_cols=9 Identities=22% Similarity=0.486 Sum_probs=5.3
Q ss_pred cccHhhHHH
Q psy284 89 ILCKRDYLR 97 (139)
Q Consensus 89 ~~C~~cy~~ 97 (139)
-+|..||..
T Consensus 27 DlC~~C~~~ 35 (48)
T cd02341 27 DLCQDCVVK 35 (48)
T ss_pred ccCHHHHhC
Confidence 356677654
No 124
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.02 E-value=41 Score=17.25 Aligned_cols=10 Identities=30% Similarity=1.082 Sum_probs=6.0
Q ss_pred cccccCCCCc
Q psy284 66 LKCGCCDCRL 75 (139)
Q Consensus 66 f~C~~C~~~l 75 (139)
++|..|+..+
T Consensus 22 ~~Cp~CG~~~ 31 (46)
T PRK00398 22 VRCPYCGYRI 31 (46)
T ss_pred eECCCCCCeE
Confidence 5666666554
No 125
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=21.89 E-value=60 Score=28.51 Aligned_cols=29 Identities=21% Similarity=0.356 Sum_probs=18.9
Q ss_pred cccccCCCCCCCceEEE-------eC---Cccccccccc
Q psy284 104 YCAACSKVIPAFEMVMR-------AR---NNVYHLECFA 132 (139)
Q Consensus 104 ~C~~C~~~I~~~~~~~~-------~~---~~~~H~~Cf~ 132 (139)
.|.+|++.|.-.+..|. +. ..-||..||.
T Consensus 19 ~Ck~C~~~I~K~~lRi~~~v~~~~~dg~~~~W~H~~Cf~ 57 (981)
T PLN03123 19 SCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCIL 57 (981)
T ss_pred cccccCCcccCCCeEEEEeecccccCCCCCeeecccccc
Confidence 79999999976443321 11 2467889985
No 126
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=21.82 E-value=49 Score=16.89 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=9.4
Q ss_pred cccccCCCCCC
Q psy284 104 YCAACSKVIPA 114 (139)
Q Consensus 104 ~C~~C~~~I~~ 114 (139)
.|.+|+++|.|
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 68999998877
No 127
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=21.54 E-value=12 Score=20.03 Aligned_cols=24 Identities=17% Similarity=0.451 Sum_probs=16.1
Q ss_pred CccccHhhHHHHhCCCccccccCCCCC
Q psy284 87 NLILCKRDYLRLFGSTGYCAACSKVIP 113 (139)
Q Consensus 87 ~~~~C~~cy~~~~~~~~~C~~C~~~I~ 113 (139)
|+--|..|+...|. .|..|+..|.
T Consensus 29 GRWaC~sCW~deYY---~CksC~Gii~ 52 (57)
T PF14445_consen 29 GRWACNSCWQDEYY---TCKSCNGIIN 52 (57)
T ss_pred chhhhhhhhhhhHh---HHHhhhchhh
Confidence 44457778766654 5888887663
No 128
>KOG3039|consensus
Probab=21.47 E-value=3.4e+02 Score=19.98 Aligned_cols=84 Identities=13% Similarity=0.133 Sum_probs=56.5
Q ss_pred CCCCCCCccccccccccccee--ee--ecC-------ccccccCcccccCCCCcc-cCCCeeEeeCCccccHhhHHHHhC
Q psy284 33 NNAQGPQECAGCGKHITDRFL--LK--ALD-------MYWHEDCLKCGCCDCRLG-EVGSTLYTKANLILCKRDYLRLFG 100 (139)
Q Consensus 33 ~~~~~~~~C~~C~~~i~~~~~--~~--~~~-------~~~H~~Cf~C~~C~~~l~-~~~~~~~~~~~~~~C~~cy~~~~~ 100 (139)
..++....|..=+++|.-..+ +. .++ ..-|..-|.|..+...|. ...-.+....|..++..|.++++.
T Consensus 178 ekP~~~v~CP~s~kplklkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir 257 (303)
T KOG3039|consen 178 EKPSTTVVCPVSGKPLKLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR 257 (303)
T ss_pred cCCCceeeccCCCCccchhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc
Confidence 345666788888888654222 11 111 134556788999988875 222334457888999999999887
Q ss_pred CCccccccCCCCCCCc
Q psy284 101 STGYCAACSKVIPAFE 116 (139)
Q Consensus 101 ~~~~C~~C~~~I~~~~ 116 (139)
....|..|.+++...+
T Consensus 258 ~D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 258 KDMVDPVTDKPLKDRD 273 (303)
T ss_pred ccccccCCCCcCcccc
Confidence 7678999999997643
No 129
>KOG3476|consensus
Probab=21.36 E-value=28 Score=20.91 Aligned_cols=37 Identities=27% Similarity=0.543 Sum_probs=26.0
Q ss_pred ccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284 67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF 115 (139)
Q Consensus 67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~ 115 (139)
.|..|...+- ..|.-||..|..+ ++.|+-|++.|...
T Consensus 56 kC~iCk~~vH--------Q~GshYC~tCAY~----KgiCAMCGKki~nT 92 (100)
T KOG3476|consen 56 KCRICKQLVH--------QPGSHYCQTCAYK----KGICAMCGKKILNT 92 (100)
T ss_pred hhHHHHHHhc--------CCcchhHhHhhhh----hhHHHHhhhHhhcc
Confidence 5667765553 3345689999665 34899999999764
No 130
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.01 E-value=47 Score=16.73 Aligned_cols=10 Identities=40% Similarity=0.750 Sum_probs=4.2
Q ss_pred cccccCCCCc
Q psy284 66 LKCGCCDCRL 75 (139)
Q Consensus 66 f~C~~C~~~l 75 (139)
+.|..|+.-|
T Consensus 20 ~vC~~CG~Vl 29 (43)
T PF08271_consen 20 LVCPNCGLVL 29 (43)
T ss_dssp EEETTT-BBE
T ss_pred EECCCCCCEe
Confidence 3455554444
No 131
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=20.93 E-value=56 Score=18.13 Aligned_cols=13 Identities=46% Similarity=0.915 Sum_probs=10.0
Q ss_pred cccccCCCCCCCc
Q psy284 104 YCAACSKVIPAFE 116 (139)
Q Consensus 104 ~C~~C~~~I~~~~ 116 (139)
.|-.|+++|...|
T Consensus 10 HC~VCg~aIp~de 22 (64)
T COG4068 10 HCVVCGKAIPPDE 22 (64)
T ss_pred cccccCCcCCCcc
Confidence 6888888887743
No 132
>PLN02195 cellulose synthase A
Probab=20.66 E-value=1.1e+02 Score=26.83 Aligned_cols=53 Identities=25% Similarity=0.486 Sum_probs=29.7
Q ss_pred CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHH--HHhCCCccccccCCCCC
Q psy284 37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYL--RLFGSTGYCAACSKVIP 113 (139)
Q Consensus 37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~--~~~~~~~~C~~C~~~I~ 113 (139)
..+.|..|+..|.-. .+|..| -.|..|+ -+.|+.||+ ++-|.+ .|.+|+..-.
T Consensus 5 ~~~~c~~cgd~~~~~----~~g~~f----vaC~eC~---------------~pvCrpCyeyer~eg~q-~CpqCkt~Yk 59 (977)
T PLN02195 5 GAPICATCGEEVGVD----SNGEAF----VACHECS---------------YPLCKACLEYEIKEGRK-VCLRCGGPYD 59 (977)
T ss_pred CCccceecccccCcC----CCCCeE----EEeccCC---------------CccccchhhhhhhcCCc-cCCccCCccc
Confidence 345788887766543 234433 2333443 234788864 555532 7889987554
Done!