Query psy10849
Match_columns 267
No_of_seqs 369 out of 2173
Neff 7.6
Searched_HMMs 46136
Date Fri Aug 16 20:00:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10849.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10849hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4577|consensus 100.0 5.2E-35 1.1E-39 253.3 12.0 149 1-163 74-229 (383)
2 KOG0484|consensus 99.8 3.1E-21 6.7E-26 144.1 2.5 60 104-163 14-79 (125)
3 KOG0489|consensus 99.8 4.4E-19 9.5E-24 157.7 3.9 62 105-166 157-224 (261)
4 KOG0850|consensus 99.7 7.8E-17 1.7E-21 136.8 8.7 69 97-165 112-186 (245)
5 KOG2251|consensus 99.7 3.9E-17 8.4E-22 138.0 6.6 63 101-163 31-99 (228)
6 KOG0494|consensus 99.7 1.2E-17 2.7E-22 143.5 2.7 62 103-164 136-204 (332)
7 KOG0490|consensus 99.7 2.2E-17 4.7E-22 143.9 1.6 113 25-161 2-120 (235)
8 KOG0488|consensus 99.7 3E-17 6.5E-22 148.7 2.5 62 102-163 167-234 (309)
9 KOG0843|consensus 99.7 4.1E-17 8.9E-22 133.6 2.9 58 106-163 101-164 (197)
10 KOG0487|consensus 99.6 6.7E-17 1.5E-21 144.5 2.9 60 105-164 233-298 (308)
11 KOG0492|consensus 99.6 1.7E-16 3.6E-21 132.7 4.0 62 102-163 139-206 (246)
12 KOG0485|consensus 99.6 5.4E-16 1.2E-20 130.4 5.1 58 106-163 103-166 (268)
13 KOG0842|consensus 99.6 1.4E-15 3.1E-20 136.0 7.2 65 100-164 146-216 (307)
14 KOG0848|consensus 99.6 1E-15 2.3E-20 132.3 2.1 55 109-163 201-261 (317)
15 KOG0844|consensus 99.5 4.2E-15 9.1E-20 130.7 3.5 65 104-168 178-248 (408)
16 KOG0493|consensus 99.5 7.9E-15 1.7E-19 126.4 3.2 57 107-163 246-308 (342)
17 KOG0486|consensus 99.5 6.1E-15 1.3E-19 130.3 2.5 59 105-163 110-174 (351)
18 KOG0490|consensus 99.5 2.1E-14 4.5E-19 125.1 4.0 160 1-161 39-213 (235)
19 KOG1701|consensus 99.5 2.3E-15 5E-20 137.7 -2.1 77 2-82 318-395 (468)
20 PF00412 LIM: LIM domain; Int 99.5 1.1E-13 2.4E-18 95.0 5.9 58 22-80 1-58 (58)
21 PF00046 Homeobox: Homeobox do 99.4 4.6E-14 1E-18 96.6 0.9 51 108-158 1-57 (57)
22 TIGR01565 homeo_ZF_HD homeobox 99.4 3.8E-13 8.3E-18 92.0 4.1 46 108-153 2-57 (58)
23 COG5576 Homeodomain-containing 99.4 3.1E-13 6.8E-18 110.9 4.2 64 100-163 44-113 (156)
24 KOG4577|consensus 99.4 8E-15 1.7E-19 128.0 -6.4 158 13-173 27-199 (383)
25 KOG0491|consensus 99.4 5.9E-14 1.3E-18 113.5 -1.3 57 108-164 101-163 (194)
26 KOG1701|consensus 99.3 1.7E-12 3.7E-17 119.1 4.1 79 3-81 378-464 (468)
27 KOG0847|consensus 99.2 5.1E-12 1.1E-16 106.7 3.4 54 108-161 168-227 (288)
28 smart00389 HOX Homeodomain. DN 99.2 5.8E-12 1.3E-16 85.6 1.8 50 108-157 1-56 (56)
29 KOG0483|consensus 99.1 1.2E-11 2.5E-16 105.1 1.1 54 110-163 53-112 (198)
30 cd00086 homeodomain Homeodomai 99.1 1.8E-11 4E-16 83.8 1.8 52 108-159 1-58 (59)
31 KOG1703|consensus 99.1 2E-11 4.4E-16 117.5 1.1 77 3-82 347-423 (479)
32 KOG0849|consensus 99.1 1.2E-10 2.7E-15 107.8 6.1 61 102-162 171-237 (354)
33 KOG2272|consensus 99.0 4E-11 8.6E-16 103.4 -0.9 75 2-78 237-311 (332)
34 KOG3802|consensus 99.0 8E-10 1.7E-14 101.4 7.1 56 106-161 293-354 (398)
35 KOG2272|consensus 99.0 7.2E-11 1.6E-15 101.8 -0.3 77 4-83 180-256 (332)
36 KOG1044|consensus 99.0 9.8E-11 2.1E-15 111.1 0.3 74 2-77 175-248 (670)
37 KOG1703|consensus 98.7 4.5E-09 9.8E-14 101.3 0.7 75 1-76 404-478 (479)
38 KOG1168|consensus 98.6 2E-08 4.3E-13 88.4 2.2 57 107-163 309-371 (385)
39 smart00132 LIM Zinc-binding do 98.5 7E-08 1.5E-12 60.1 2.9 38 21-58 1-38 (39)
40 KOG1044|consensus 98.4 9.5E-08 2.1E-12 91.1 2.0 59 21-82 135-193 (670)
41 KOG1700|consensus 98.0 1E-06 2.2E-11 75.5 -0.4 58 21-80 110-167 (200)
42 KOG0775|consensus 97.6 0.0002 4.3E-09 63.1 6.9 58 104-161 164-236 (304)
43 KOG1146|consensus 97.5 5.4E-05 1.2E-09 78.7 3.3 57 107-163 903-965 (1406)
44 KOG1702|consensus 97.2 2.2E-05 4.9E-10 66.3 -3.6 60 21-82 6-65 (264)
45 KOG0774|consensus 97.1 0.0013 2.8E-08 57.6 6.9 57 107-163 188-253 (334)
46 KOG2252|consensus 97.1 0.00024 5.1E-09 68.2 1.7 52 105-156 418-475 (558)
47 KOG1700|consensus 97.0 0.00015 3.3E-09 62.2 0.2 62 19-82 7-68 (200)
48 PF05920 Homeobox_KN: Homeobox 95.9 0.00077 1.7E-08 42.6 -1.9 28 128-155 7-40 (40)
49 PF08394 Arc_trans_TRASH: Arch 92.5 0.058 1.3E-06 33.4 0.9 33 22-57 1-33 (37)
50 KOG3623|consensus 91.7 0.27 5.8E-06 49.3 4.9 46 119-164 568-619 (1007)
51 PF10367 Vps39_2: Vacuolar sor 82.1 1.2 2.6E-05 33.4 2.5 29 20-48 79-107 (109)
52 PF11569 Homez: Homeodomain le 79.9 0.26 5.6E-06 33.4 -1.6 37 119-155 10-52 (56)
53 PF14446 Prok-RING_1: Prokaryo 76.1 1.9 4.1E-05 29.0 1.7 31 18-48 4-36 (54)
54 PF09943 DUF2175: Uncharacteri 75.6 0.91 2E-05 34.5 0.0 33 49-81 4-36 (101)
55 PF00412 LIM: LIM domain; Int 75.3 1.6 3.4E-05 28.9 1.2 38 4-48 17-54 (58)
56 KOG0773|consensus 72.8 4.1 9E-05 37.5 3.7 54 107-160 239-301 (342)
57 PF14471 DUF4428: Domain of un 72.8 2.9 6.3E-05 27.7 2.0 30 49-79 1-30 (51)
58 COG1645 Uncharacterized Zn-fin 64.9 3.6 7.9E-05 32.8 1.3 24 49-78 30-53 (131)
59 PF04218 CENP-B_N: CENP-B N-te 64.4 3.3 7.1E-05 27.5 0.9 46 108-153 1-47 (53)
60 PF11571 Med27: Mediator compl 62.1 1.9 4E-05 32.1 -0.8 16 14-29 49-64 (90)
61 PF09943 DUF2175: Uncharacteri 61.0 6 0.00013 30.1 1.8 32 21-52 4-35 (101)
62 PF13240 zinc_ribbon_2: zinc-r 59.9 6.2 0.00014 21.6 1.3 10 22-31 2-11 (23)
63 COG4847 Uncharacterized protei 59.7 5.4 0.00012 29.9 1.4 29 48-76 7-35 (103)
64 PF00645 zf-PARP: Poly(ADP-rib 57.7 5.3 0.00011 28.8 1.0 15 21-35 9-23 (82)
65 COG4847 Uncharacterized protei 57.4 3.6 7.7E-05 30.9 0.1 36 21-56 8-43 (103)
66 PF06677 Auto_anti-p27: Sjogre 56.3 6.3 0.00014 24.9 1.1 21 50-75 20-40 (41)
67 PF11781 RRN7: RNA polymerase 55.1 7.7 0.00017 23.7 1.3 23 49-76 10-32 (36)
68 KOG3755|consensus 52.2 2.2 4.7E-05 42.1 -2.3 23 140-162 738-760 (769)
69 PF10083 DUF2321: Uncharacteri 50.6 6.3 0.00014 32.3 0.5 51 7-59 28-80 (158)
70 PRK00420 hypothetical protein; 49.5 8.6 0.00019 29.9 1.1 23 49-76 25-47 (112)
71 PF10367 Vps39_2: Vacuolar sor 48.8 11 0.00023 28.1 1.5 29 48-77 79-108 (109)
72 smart00504 Ubox Modified RING 45.1 24 0.00052 23.5 2.7 33 48-82 2-34 (63)
73 PF07754 DUF1610: Domain of un 44.3 17 0.00038 20.2 1.5 12 22-33 1-12 (24)
74 PF04570 DUF581: Protein of un 43.1 21 0.00046 24.3 2.1 26 49-74 18-44 (58)
75 PF13248 zf-ribbon_3: zinc-rib 40.4 22 0.00048 19.8 1.6 10 21-30 4-13 (26)
76 KOG3623|consensus 39.3 69 0.0015 32.9 5.8 55 107-161 626-686 (1007)
77 COG2191 Formylmethanofuran deh 39.2 9.9 0.00022 32.6 -0.0 31 48-79 173-203 (206)
78 TIGR00270 conserved hypothetic 35.4 1.1E+02 0.0025 24.9 5.7 30 50-82 3-35 (154)
79 PF01258 zf-dskA_traR: Prokary 34.3 7.5 0.00016 23.5 -1.1 28 50-78 6-33 (36)
80 PF05502 Dynactin_p62: Dynacti 33.8 25 0.00055 34.2 1.9 51 6-58 4-63 (483)
81 PF06827 zf-FPG_IleRS: Zinc fi 33.8 46 0.00099 19.0 2.3 12 19-30 1-12 (30)
82 KOG0320|consensus 32.3 26 0.00057 29.5 1.4 38 45-82 129-166 (187)
83 PRK00807 50S ribosomal protein 32.1 41 0.00089 22.3 2.1 24 21-44 3-28 (52)
84 PRK14559 putative protein seri 32.0 35 0.00076 34.6 2.5 26 5-30 13-38 (645)
85 cd02249 ZZ Zinc finger, ZZ typ 31.3 35 0.00077 21.7 1.7 10 69-78 23-32 (46)
86 PF06689 zf-C4_ClpX: ClpX C4-t 28.8 91 0.002 19.4 3.2 33 49-81 3-36 (41)
87 PF14634 zf-RING_5: zinc-RING 28.6 22 0.00047 22.3 0.3 21 6-26 21-43 (44)
88 PF08880 QLQ: QLQ; InterPro: 28.0 52 0.0011 20.2 1.9 13 113-125 2-14 (37)
89 PF10235 Cript: Microtubule-as 27.5 34 0.00074 25.5 1.2 23 6-30 58-80 (90)
90 smart00291 ZnF_ZZ Zinc-binding 26.9 51 0.0011 20.7 1.8 9 70-78 28-36 (44)
91 KOG1146|consensus 24.9 25 0.00054 38.1 0.1 58 104-161 441-504 (1406)
92 PF04810 zf-Sec23_Sec24: Sec23 24.5 64 0.0014 19.9 1.9 30 20-55 3-32 (40)
93 PRK14890 putative Zn-ribbon RN 23.9 57 0.0012 22.3 1.6 28 19-56 7-34 (59)
94 KOG2893|consensus 23.6 42 0.00092 29.6 1.2 63 20-91 11-73 (341)
95 PF12674 Zn_ribbon_2: Putative 22.7 40 0.00087 24.5 0.8 30 49-78 2-35 (81)
96 KOG0956|consensus 22.6 8.7E+02 0.019 25.1 10.2 15 16-30 114-128 (900)
97 PRK04136 rpl40e 50S ribosomal 22.6 48 0.001 21.7 1.0 22 6-27 13-36 (48)
98 PF12156 ATPase-cat_bd: Putati 22.4 65 0.0014 23.6 1.9 10 21-30 2-11 (88)
99 COG2888 Predicted Zn-ribbon RN 22.1 48 0.001 22.7 1.0 18 19-36 9-26 (61)
100 PF12773 DZR: Double zinc ribb 22.1 71 0.0015 20.3 1.8 10 49-58 31-40 (50)
101 PF10764 Gin: Inhibitor of sig 21.9 84 0.0018 20.3 2.1 29 49-80 1-29 (46)
102 PRK12495 hypothetical protein; 21.8 39 0.00084 29.4 0.7 26 46-77 41-66 (226)
103 PF04502 DUF572: Family of unk 21.5 57 0.0012 30.0 1.7 15 18-32 39-53 (324)
104 PF13834 DUF4193: Domain of un 21.2 31 0.00067 26.1 -0.1 29 47-75 70-98 (99)
105 PF00569 ZZ: Zinc finger, ZZ t 20.8 74 0.0016 20.2 1.7 10 69-78 28-37 (46)
No 1
>KOG4577|consensus
Probab=100.00 E-value=5.2e-35 Score=253.35 Aligned_cols=149 Identities=32% Similarity=0.597 Sum_probs=132.1
Q ss_pred CcccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEee-CCeecchhhHHHH
Q psy10849 1 STSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILR-SGQLFCRQDFEKE 79 (267)
Q Consensus 1 ~~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~-~~~lyC~~cy~k~ 79 (267)
||.|+|.+||+++|.++|+.+|..|...|.+...|-+|.+.+||..||.|.+|++.|.+|++|++. +.++.|+.+|+..
T Consensus 74 CFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~A 153 (383)
T KOG4577|consen 74 CFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETA 153 (383)
T ss_pred HhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHH
Confidence 899999999999999999999999999999886666789999999999999999999999999987 6899999999874
Q ss_pred HhhhcCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhh
Q psy10849 80 MYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQR 153 (267)
Q Consensus 80 f~~~~~~~~~~~~~~~~~~~~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrR 153 (267)
-.. .... -++....||+||.+|..||+.|+.+|...+.|.+.+||+ |..|+|||||||||
T Consensus 154 k~k-------~~~~-------l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRR 219 (383)
T KOG4577|consen 154 KQK-------HCNE-------LEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRR 219 (383)
T ss_pred Hhc-------cccc-------cccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhh
Confidence 321 1111 133455799999999999999999999999999999999 89999999999999
Q ss_pred hhhhhhhhhc
Q psy10849 154 RQFKSSFEIS 163 (267)
Q Consensus 154 ak~k~~~~~~ 163 (267)
||.||.++.+
T Consensus 220 AKEKRLKKDA 229 (383)
T KOG4577|consen 220 AKEKRLKKDA 229 (383)
T ss_pred HHHHhhhhhc
Confidence 9999988776
No 2
>KOG0484|consensus
Probab=99.82 E-value=3.1e-21 Score=144.09 Aligned_cols=60 Identities=22% Similarity=0.278 Sum_probs=57.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
++|+||.||.||..||.+||+.|..++|||+.+||+ |+|.+|||||||||||+||+.+..
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 678999999999999999999999999999999999 999999999999999999987655
No 3
>KOG0489|consensus
Probab=99.75 E-value=4.4e-19 Score=157.74 Aligned_cols=62 Identities=23% Similarity=0.211 Sum_probs=56.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhccCC
Q psy10849 105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISSMP 166 (267)
Q Consensus 105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~~~ 166 (267)
.+.||.||.||..||.+||++|+.|+|.++..|.+ |+|||||||||||||||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 34799999999999999999999999999999998 999999999999999999977665543
No 4
>KOG0850|consensus
Probab=99.69 E-value=7.8e-17 Score=136.78 Aligned_cols=69 Identities=22% Similarity=0.255 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhccC
Q psy10849 97 NCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISSM 165 (267)
Q Consensus 97 ~~~~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~~ 165 (267)
+.+++...+|.|+.||+|+.-||..|.+.|++++|....+|.+ |+..||||||||||.|+||+++..+.
T Consensus 112 e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~ 186 (245)
T KOG0850|consen 112 ERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG 186 (245)
T ss_pred eeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence 4566777788899999999999999999999999999888888 99999999999999999999885543
No 5
>KOG2251|consensus
Probab=99.69 E-value=3.9e-17 Score=138.03 Aligned_cols=63 Identities=17% Similarity=0.202 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 101 RDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 101 ~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
..+.||.||.||+||..||.+||+.|.+++|||+.+||+ |.|.+|||||.|||||+|++++.+
T Consensus 31 ~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 31 SSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred CccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 367889999999999999999999999999999999999 999999999999999999987754
No 6
>KOG0494|consensus
Probab=99.68 E-value=1.2e-17 Score=143.52 Aligned_cols=62 Identities=19% Similarity=0.256 Sum_probs=54.5
Q ss_pred CCCCCCCC-CCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849 103 GRRGPKRP-RTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS 164 (267)
Q Consensus 103 ~~~~~kr~-Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~ 164 (267)
++++.||. ||.||..|+.+||+.|.+.+|||...||. |+|-+||||||||||||||.++...
T Consensus 136 kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 136 KKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 34444554 99999999999999999999999999987 9999999999999999999876654
No 7
>KOG0490|consensus
Probab=99.66 E-value=2.2e-17 Score=143.89 Aligned_cols=113 Identities=20% Similarity=0.498 Sum_probs=94.1
Q ss_pred CCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhhhcCCCCCCCcccCCCCCCCCCC
Q psy10849 25 CGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGR 104 (267)
Q Consensus 25 C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~~~~~~~~~~~~~~~~~~~~~~~ 104 (267)
|+..|.+. ..+.+.+..||..|..|..|...+..+...+..++..||..+|.+ ..+
T Consensus 2 ~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~-----------------------~~~ 57 (235)
T KOG0490|consen 2 CGRQILDR-YLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQR-----------------------EFK 57 (235)
T ss_pred CCccccch-HHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchh-----------------------hhh
Confidence 66777654 455667899999999999999999533444444899999888755 123
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849 105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE 161 (267)
Q Consensus 105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~ 161 (267)
.+.||.||.|+..|+.+|++.|+.++||+...|+. ++|.+|||||||||+||+++.+
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 45689999999999999999999999999999887 8999999999999999999764
No 8
>KOG0488|consensus
Probab=99.65 E-value=3e-17 Score=148.69 Aligned_cols=62 Identities=13% Similarity=0.110 Sum_probs=56.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
+..+|.|+.||+||+.||.+||+.|++..|.+..+|.+ |+..|||+||||||+||||+....
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence 34578888999999999999999999999999998887 999999999999999999987653
No 9
>KOG0843|consensus
Probab=99.65 E-value=4.1e-17 Score=133.64 Aligned_cols=58 Identities=22% Similarity=0.206 Sum_probs=54.5
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
++||.||+||.+||..||.+|+.++|....+|++ |++.||||||||||.|.||.+...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 7899999999999999999999999999998888 999999999999999999976553
No 10
>KOG0487|consensus
Probab=99.64 E-value=6.7e-17 Score=144.54 Aligned_cols=60 Identities=17% Similarity=0.112 Sum_probs=54.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849 105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS 164 (267)
Q Consensus 105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~ 164 (267)
+..|++|..+|..|+.+||++|-.|.|.++..|-+ ||+|||||||||||+|.||+.+.+.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 55677899999999999999999999999988887 9999999999999999999886443
No 11
>KOG0492|consensus
Probab=99.63 E-value=1.7e-16 Score=132.66 Aligned_cols=62 Identities=18% Similarity=0.153 Sum_probs=56.7
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
.+++..|..||.||.+||..||+.|...+|.++.+|.+ |+|.||||||||||||.||.++..
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 45566788999999999999999999999999999998 999999999999999999987654
No 12
>KOG0485|consensus
Probab=99.61 E-value=5.4e-16 Score=130.42 Aligned_cols=58 Identities=22% Similarity=0.300 Sum_probs=53.5
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
++|+.||+|+..|+.+||.+|+..+|.+...|.. |+|.||||||||||.||||+....
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 4688999999999999999999999999988877 999999999999999999987554
No 13
>KOG0842|consensus
Probab=99.60 E-value=1.4e-15 Score=135.99 Aligned_cols=65 Identities=17% Similarity=0.224 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849 100 PRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS 164 (267)
Q Consensus 100 ~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~ 164 (267)
+..+.++.||.|-.|+..|+.|||+.|..++|.+..+||+ ||++||||||||||.|.||++++..
T Consensus 146 ~~t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 146 PQTGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred CccccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 3445667788899999999999999999999999999999 9999999999999999999887664
No 14
>KOG0848|consensus
Probab=99.55 E-value=1e-15 Score=132.33 Aligned_cols=55 Identities=20% Similarity=0.200 Sum_probs=49.9
Q ss_pred CCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 109 RPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 109 r~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
+.|.++|+.|+.+||++|..++|..+..+.+ |+||||||||||||||.||+.++.
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 4689999999999999999999998876666 999999999999999999977665
No 15
>KOG0844|consensus
Probab=99.53 E-value=4.2e-15 Score=130.65 Aligned_cols=65 Identities=17% Similarity=0.086 Sum_probs=57.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhccCCCC
Q psy10849 104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISSMPCR 168 (267)
Q Consensus 104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~~~~~ 168 (267)
....||.||.||.+||..||++|.+..|.++..|-+ |+|..|||||||||+|.||+...-.+|..
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhp 248 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHP 248 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCC
Confidence 344689999999999999999999999988887777 99999999999999999998766556655
No 16
>KOG0493|consensus
Probab=99.50 E-value=7.9e-15 Score=126.44 Aligned_cols=57 Identities=25% Similarity=0.280 Sum_probs=51.4
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
-||.||.||.+||..|+.+|+.++|..-..|.+ |+|.||||||||+|||.||.....
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCC
Confidence 478999999999999999999999998887776 999999999999999999965433
No 17
>KOG0486|consensus
Probab=99.50 E-value=6.1e-15 Score=130.26 Aligned_cols=59 Identities=17% Similarity=0.225 Sum_probs=56.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
+|+||.||.||.+||.+||..|+++.||+..+||+ |+|.+|+|||.||||||||.++.+
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 38999999999999999999999999999999999 999999999999999999987655
No 18
>KOG0490|consensus
Probab=99.48 E-value=2.1e-14 Score=125.06 Aligned_cols=160 Identities=24% Similarity=0.368 Sum_probs=125.0
Q ss_pred CcccCCcccCcccccc--ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCC-eecchhhHH
Q psy10849 1 STSHNSHVSCHPRGFR--LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSG-QLFCRQDFE 77 (267)
Q Consensus 1 ~~~~dg~~yC~~cy~~--~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~-~lyC~~cy~ 77 (267)
||.++|..||+.+|.+ .+..+|.+|...|...|.+.++..+. |..||.|..|...+..+..+.+... +.+|..++.
T Consensus 39 ~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~ 117 (235)
T KOG0490|consen 39 CFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRK 117 (235)
T ss_pred cccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhh
Confidence 5778999999999998 88889999999997777777787777 9999999999998888888988875 888988876
Q ss_pred HHH--hh--hcCCCCCCCc--ccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCce
Q psy10849 78 KEM--YL--MQQSSPSDDM--MLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAK 145 (267)
Q Consensus 78 k~f--~~--~~~~~~~~~~--~~~~~~~~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v 145 (267)
+.- .. +......... .............+.++.||.++..|+..|+..|..+++|+...+++ +++++|
T Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~ 197 (235)
T KOG0490|consen 118 EERPLPEGENLPDLSGTAPPSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVI 197 (235)
T ss_pred hhccccccccCCCCCCCCCccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhh
Confidence 542 11 1111111110 00111122334567789999999999999999999999998888877 899999
Q ss_pred eeecchhhhhhhhhhh
Q psy10849 146 NILTPNQRRQFKSSFE 161 (267)
Q Consensus 146 ~vWFQNrRak~k~~~~ 161 (267)
+|||||+|++.++...
T Consensus 198 q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 198 QVWFQNRRAKLRKHKR 213 (235)
T ss_pred hhhcccHHHHHHhhcc
Confidence 9999999999998654
No 19
>KOG1701|consensus
Probab=99.48 E-value=2.3e-15 Score=137.74 Aligned_cols=77 Identities=27% Similarity=0.647 Sum_probs=70.6
Q ss_pred cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEee-CCeecchhhHHHHH
Q psy10849 2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILR-SGQLFCRQDFEKEM 80 (267)
Q Consensus 2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~-~~~lyC~~cy~k~f 80 (267)
|.+|+++||+.||+.. ..+|..|++.|. |+|++|.++.||+.||+|.+|++.| +|..|++. ++++||..||.++|
T Consensus 318 Y~v~~k~~CE~cyq~t-lekC~~Cg~~I~--d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kf 393 (468)
T KOG1701|consen 318 YQVDGKPYCEGCYQDT-LEKCNKCGEPIM--DRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKF 393 (468)
T ss_pred cccCCcccchHHHHHH-HHHHhhhhhHHH--HHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhhc
Confidence 6789999999999764 469999999999 5799999999999999999999999 58999986 69999999999999
Q ss_pred hh
Q psy10849 81 YL 82 (267)
Q Consensus 81 ~~ 82 (267)
+-
T Consensus 394 AP 395 (468)
T KOG1701|consen 394 AP 395 (468)
T ss_pred Cc
Confidence 85
No 20
>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=99.46 E-value=1.1e-13 Score=94.95 Aligned_cols=58 Identities=33% Similarity=0.875 Sum_probs=53.1
Q ss_pred CCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHH
Q psy10849 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80 (267)
Q Consensus 22 C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f 80 (267)
|.+|+++|.+++.++.+.++.||++||+|..|+++|.. ..|+..++++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLND-GDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTT-SSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCC-CeeEeECCEEECHHHHhhhC
Confidence 88999999988877789999999999999999999974 45899999999999999876
No 21
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.41 E-value=4.6e-14 Score=96.65 Aligned_cols=51 Identities=27% Similarity=0.351 Sum_probs=48.1
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849 108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKS 158 (267)
Q Consensus 108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~ 158 (267)
||.|+.||.+|+.+|++.|+.++||+...+++ |+..+|++||||||+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 57899999999999999999999999888877 9999999999999999986
No 22
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.38 E-value=3.8e-13 Score=92.02 Aligned_cols=46 Identities=20% Similarity=0.202 Sum_probs=43.6
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCC----CChhhhhh------cCCCceeeecchhh
Q psy10849 108 KRPRTILTSAQRRQFKSSFEVSPK----PCRKVSTM------NSKRAKNILTPNQR 153 (267)
Q Consensus 108 kr~Rt~ft~~Ql~~L~~~f~~~~~----p~~~~r~~------l~~~~v~vWFQNrR 153 (267)
||.||.||.+|+..|++.|+.++| |+...+++ |++++|||||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 789999999999999999999999 99998888 99999999999954
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.38 E-value=3.1e-13 Score=110.85 Aligned_cols=64 Identities=23% Similarity=0.273 Sum_probs=57.0
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 100 PRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 100 ~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
..++....++.|++.|..|+.+|++.|+.+++|+...|.+ |+++.|||||||||++.|+.....
T Consensus 44 ~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 44 KQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred cccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 3456677888889999999999999999999999999988 899999999999999999976554
No 24
>KOG4577|consensus
Probab=99.36 E-value=8e-15 Score=128.03 Aligned_cols=158 Identities=20% Similarity=0.347 Sum_probs=124.3
Q ss_pred ccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh----hcCCCC
Q psy10849 13 RGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL----MQQSSP 88 (267)
Q Consensus 13 cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~----~~~~~~ 88 (267)
++...--++|+.|.+.|.+. +|++++++.||..|++|+.|..+| ++.++.+++.+||+++|.++|+. ++..+|
T Consensus 27 df~~~eip~CagC~q~IlDr-FilKvl~R~wHs~CLkCs~C~~qL--~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIp 103 (383)
T KOG4577|consen 27 DFSNVEIPICAGCDQHILDR-FILKVLDRHWHSSCLKCSDCHDQL--ADRCFSREGSVYCKEDFFKRFGTKCSACQEGIP 103 (383)
T ss_pred cccccccccccchHHHHHHH-HHHHHHhhhhhhhhcchhhhhhHH--HHHHhhcCCceeehHHHHHHhCCcchhhcCCCC
Confidence 34333456899999999976 788999999999999999999999 57899999999999999999997 567777
Q ss_pred CCCcc---------cCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh--cCCCceeeecchhhhhhh
Q psy10849 89 SDDMM---------LDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM--NSKRAKNILTPNQRRQFK 157 (267)
Q Consensus 89 ~~~~~---------~~~~~~~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~--l~~~~v~vWFQNrRak~k 157 (267)
++.+| ++++++...+++........+.++-+.+.+..||....-.-...+. -.+|...+....+....|
T Consensus 104 PtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK 183 (383)
T KOG4577|consen 104 PTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLK 183 (383)
T ss_pred hHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHH
Confidence 77655 5667777888888888999999998888899887653222111111 566777777777778888
Q ss_pred hhhhhccCCCCCCCcC
Q psy10849 158 SSFEISSMPCRKVGVH 173 (267)
Q Consensus 158 ~~~~~~~~~~~~~~~~ 173 (267)
..+..+.+|++++++.
T Consensus 184 ~AYn~SpKPARHVREQ 199 (383)
T KOG4577|consen 184 QAYNTSPKPARHVREQ 199 (383)
T ss_pred HHhcCCCchhHHHHHH
Confidence 8888888888777664
No 25
>KOG0491|consensus
Probab=99.36 E-value=5.9e-14 Score=113.48 Aligned_cols=57 Identities=16% Similarity=0.155 Sum_probs=52.3
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849 108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS 164 (267)
Q Consensus 108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~ 164 (267)
++.||+|+..|+..|++.|+.++|.+...|.+ |+++|||+||||||+|.||..++..
T Consensus 101 ~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 101 RKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 45799999999999999999999999988888 8999999999999999999876653
No 26
>KOG1701|consensus
Probab=99.29 E-value=1.7e-12 Score=119.13 Aligned_cols=79 Identities=24% Similarity=0.599 Sum_probs=68.8
Q ss_pred ccCCcccCccccccccCCCCCCCCCcccCCC-----cEEEecCceeecCCcccccccccCC---CCCceEeeCCeecchh
Q psy10849 3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHE-----MVMRAQSHVYHLPCFVCVICCQPLQ---KGEQFILRSGQLFCRQ 74 (267)
Q Consensus 3 ~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e-----~~~~a~~~~wH~~CF~C~~C~~~L~---~g~~f~~~~~~lyC~~ 74 (267)
..++++||..||+++|+++|+.|+++|++.+ ..|.++++.||.+|++|..|+..|. +|..+|..|+.|+|+.
T Consensus 378 d~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~ 457 (468)
T KOG1701|consen 378 DSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKT 457 (468)
T ss_pred cCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeech
Confidence 4678999999999999999999999998643 2245799999999999999999996 4678999999999999
Q ss_pred hHHHHHh
Q psy10849 75 DFEKEMY 81 (267)
Q Consensus 75 cy~k~f~ 81 (267)
|+.++..
T Consensus 458 Ch~~Rl~ 464 (468)
T KOG1701|consen 458 CHLKRLQ 464 (468)
T ss_pred hhhhhhc
Confidence 9877654
No 27
>KOG0847|consensus
Probab=99.23 E-value=5.1e-12 Score=106.74 Aligned_cols=54 Identities=17% Similarity=0.223 Sum_probs=48.4
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849 108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE 161 (267)
Q Consensus 108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~ 161 (267)
+..|..|+-.||..||..|+..+|+-...|.+ +++.+|+|||||||.||||..-
T Consensus 168 k~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 168 KQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred cccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 45677899999999999999999998887777 8999999999999999999653
No 28
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.20 E-value=5.8e-12 Score=85.64 Aligned_cols=50 Identities=28% Similarity=0.452 Sum_probs=45.5
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhh
Q psy10849 108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFK 157 (267)
Q Consensus 108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k 157 (267)
++.|+.|+.+|+..|++.|+.++||+...+++ |+..+|+.||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35788899999999999999999999888777 899999999999999864
No 29
>KOG0483|consensus
Probab=99.13 E-value=1.2e-11 Score=105.05 Aligned_cols=54 Identities=22% Similarity=0.182 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 110 PRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 110 ~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
.+-+||.+|+..||+.|+...+.....+.. |.+|||.|||||||||||..+...
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence 344689999999999999998866554444 999999999999999999965443
No 30
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.13 E-value=1.8e-11 Score=83.85 Aligned_cols=52 Identities=31% Similarity=0.447 Sum_probs=47.3
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849 108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS 159 (267)
Q Consensus 108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~ 159 (267)
++.|+.|+..|+.+|++.|+.++||+..+++. |++++|++||+|||++.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 35678999999999999999999999888777 99999999999999998864
No 31
>KOG1703|consensus
Probab=99.09 E-value=2e-11 Score=117.48 Aligned_cols=77 Identities=25% Similarity=0.578 Sum_probs=70.9
Q ss_pred ccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849 3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL 82 (267)
Q Consensus 3 ~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~ 82 (267)
..+|++||..||.+.+.+.|.+|+++|.+. +|.+.+..||++||+|..|+++|. +..|++.++.+||..||.+++.+
T Consensus 347 ~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~--~v~a~~~~wH~~cf~C~~C~~~~~-~~~~~~~~~~pyce~~~~~~~~~ 423 (479)
T KOG1703|consen 347 ELDGKILCHECFHAPFRPNCKRCLLPILEE--GVCALGRLWHPECFVCADCGKPLK-NSSFFESDGEPYCEDHYKKLFTT 423 (479)
T ss_pred ccCCCccHHHHHHHhhCccccccCCchHHh--HhhhccCeechhceeeecccCCCC-CCcccccCCccchhhhHhhhccc
Confidence 568999999999999999999999999964 778889999999999999999995 68899999999999999999863
No 32
>KOG0849|consensus
Probab=99.09 E-value=1.2e-10 Score=107.77 Aligned_cols=61 Identities=18% Similarity=0.260 Sum_probs=55.6
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849 102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI 162 (267)
Q Consensus 102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~ 162 (267)
...++.+|.||+|+..|+..|++.|++++||++..|++ +++.+|+|||+|||+||+|....
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 34566788899999999999999999999999999998 89999999999999999998744
No 33
>KOG2272|consensus
Probab=99.00 E-value=4e-11 Score=103.40 Aligned_cols=75 Identities=19% Similarity=0.471 Sum_probs=69.8
Q ss_pred cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHH
Q psy10849 2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78 (267)
Q Consensus 2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k 78 (267)
|.+.|.+||+.+|.++||..|..|+.+|.++ ++.|+++.|-++||.|+.|.+.|.-...|+..|-++.|+.||.+
T Consensus 237 YEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~--vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 237 YEKKGLAYCETHYHQLFGNLCFICNRVIGGD--VVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred hhhcCchhHHHHHHHHhhhhheecCCccCcc--HHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 6799999999999999999999999999876 77899999999999999999999766789999999999999975
No 34
>KOG3802|consensus
Probab=98.99 E-value=8e-10 Score=101.38 Aligned_cols=56 Identities=21% Similarity=0.236 Sum_probs=50.0
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849 106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE 161 (267)
Q Consensus 106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~ 161 (267)
|.|++||.|....+..||+.|.+|+.|+..+... |.+.+|+|||-|||.|.||...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 5577899999999999999999999999765544 8999999999999999999654
No 35
>KOG2272|consensus
Probab=98.98 E-value=7.2e-11 Score=101.82 Aligned_cols=77 Identities=19% Similarity=0.423 Sum_probs=70.6
Q ss_pred cCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhhh
Q psy10849 4 HNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLM 83 (267)
Q Consensus 4 ~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~~ 83 (267)
.+|.+||..|+.+.--++|..|.++|. |.++.++++.||.+.|+|+.|-+++. |-.-+.+.|..||+.+|.++||.+
T Consensus 180 vk~eLyClrChD~mgipiCgaC~rpIe--ervi~amgKhWHveHFvCa~CekPFl-GHrHYEkkGlaYCe~h~~qLfG~~ 256 (332)
T KOG2272|consen 180 VKGELYCLRCHDKMGIPICGACRRPIE--ERVIFAMGKHWHVEHFVCAKCEKPFL-GHRHYEKKGLAYCETHYHQLFGNL 256 (332)
T ss_pred hccceeccccccccCCcccccccCchH--HHHHHHhccccchhheeehhcCCccc-chhhhhhcCchhHHHHHHHHhhhh
Confidence 467899999999888889999999998 56888999999999999999999996 788888999999999999999973
No 36
>KOG1044|consensus
Probab=98.97 E-value=9.8e-11 Score=111.08 Aligned_cols=74 Identities=23% Similarity=0.470 Sum_probs=68.4
Q ss_pred cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHH
Q psy10849 2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFE 77 (267)
Q Consensus 2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~ 77 (267)
+.+||.+||+.||++.|+.+|..|.+.|.+. |+.|.++.||+.|-+|+.|+..|.+|++-++.+..++-..|-.
T Consensus 175 ~skdg~pyce~dy~~~fgvkc~~c~~fisgk--vLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 175 MSKDGVPYCEKDYQAKFGVKCEECEKFISGK--VLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred eccCCCcchhhhhhhhcCeehHHhhhhhhhh--hhhccCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence 4689999999999999999999999999975 8999999999999999999999999999999999988777743
No 37
>KOG1703|consensus
Probab=98.67 E-value=4.5e-09 Score=101.33 Aligned_cols=75 Identities=20% Similarity=0.448 Sum_probs=68.5
Q ss_pred CcccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhH
Q psy10849 1 STSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76 (267)
Q Consensus 1 ~~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy 76 (267)
.|.+||.+||+.||.++|.++|..|.++|...+..+++.+..||..||+|..|...|. +..|+...++++|..|+
T Consensus 404 ~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~-~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 404 FFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLT-KKTFFETLDKPLCQKHF 478 (479)
T ss_pred ccccCCccchhhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhcccc-CCceeecCCccccccCC
Confidence 3689999999999999999999999999886666788999999999999999999996 68899999999999885
No 38
>KOG1168|consensus
Probab=98.59 E-value=2e-08 Score=88.39 Aligned_cols=57 Identities=25% Similarity=0.347 Sum_probs=48.3
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhh----h--cCCCceeeecchhhhhhhhhhhhc
Q psy10849 107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVST----M--NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~----~--l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
.||+||.+-.-..+.||++|..+++|+..... . |.+.+|+|||-|+|.|.||.....
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred cccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 48899999999999999999999999853222 2 999999999999999999965433
No 39
>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=98.52 E-value=7e-08 Score=60.07 Aligned_cols=38 Identities=45% Similarity=0.947 Sum_probs=34.2
Q ss_pred CCCCCCCcccCCCcEEEecCceeecCCcccccccccCC
Q psy10849 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQ 58 (267)
Q Consensus 21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~ 58 (267)
+|.+|++.|.+.+.++.+.++.||..||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58999999998756788899999999999999999984
No 40
>KOG1044|consensus
Probab=98.41 E-value=9.5e-08 Score=91.12 Aligned_cols=59 Identities=25% Similarity=0.723 Sum_probs=53.5
Q ss_pred CCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL 82 (267)
Q Consensus 21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~ 82 (267)
.|++|++.|..+ .++.|+++.||..||+|..|...|. ..|+.+++.+||..||.++|++
T Consensus 135 ~cagc~~~lk~g-q~llald~qwhv~cfkc~~c~~vL~--gey~skdg~pyce~dy~~~fgv 193 (670)
T KOG1044|consen 135 TCAGCGEELKNG-QALLALDKQWHVSCFKCKSCSAVLN--GEYMSKDGVPYCEKDYQAKFGV 193 (670)
T ss_pred cccchhhhhhcc-ceeeeeccceeeeeeehhhhccccc--ceeeccCCCcchhhhhhhhcCe
Confidence 699999999887 4666999999999999999999994 4688899999999999999987
No 41
>KOG1700|consensus
Probab=98.00 E-value=1e-06 Score=75.51 Aligned_cols=58 Identities=31% Similarity=0.755 Sum_probs=49.3
Q ss_pred CCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHH
Q psy10849 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80 (267)
Q Consensus 21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f 80 (267)
.|..|.+.+.+.|+++ ..+..||..||+|..|+..|. ...+...++.+||..++..+|
T Consensus 110 ~c~~c~k~vy~~Ek~~-~~~~~~hk~cfrc~~~~~~ls-~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 110 KCARCQKTVYPLEKVT-GNGLEFHKSCFRCTHCGKKLS-PKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred ccccccceeeehHHHh-hhhhhhhhhheeecccccccC-CcchhhcCCccccchhhheee
Confidence 3999999999877665 778899999999999999996 467888889999988876654
No 42
>KOG0775|consensus
Probab=97.58 E-value=0.0002 Score=63.15 Aligned_cols=58 Identities=19% Similarity=0.214 Sum_probs=44.0
Q ss_pred CCCCCCCCCCCC---------HHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849 104 RRGPKRPRTILT---------SAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE 161 (267)
Q Consensus 104 ~~~~kr~Rt~ft---------~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~ 161 (267)
|||.--+||+.. +.-+..|++-|..++||....+.+ |+..||--||.|||.+.|....
T Consensus 164 RrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 164 RRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred eccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 344444576654 445678899999999998765544 9999999999999999995433
No 43
>KOG1146|consensus
Probab=97.54 E-value=5.4e-05 Score=78.72 Aligned_cols=57 Identities=19% Similarity=0.173 Sum_probs=50.2
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
.|+.||.++..||.+|+..|+...+|...+.|. ++.|+|+|||||-|+|.|+.....
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 466899999999999999999999997665555 899999999999999999987654
No 44
>KOG1702|consensus
Probab=97.18 E-value=2.2e-05 Score=66.30 Aligned_cols=60 Identities=23% Similarity=0.580 Sum_probs=49.8
Q ss_pred CCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL 82 (267)
Q Consensus 21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~ 82 (267)
-|..|++.+.+.|.+ +.+++.||..||.|..|+..|. -..|--.+.++||..+|.+..+.
T Consensus 6 n~~~cgk~vYPvE~v-~cldk~whk~cfkce~c~mtln-mKnyKgy~kkpycn~hYpkq~at 65 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEV-KCLDKVWHKQCFKCEVCGMTLN-MKNYKGYDKKPYCNPHYPKQVAT 65 (264)
T ss_pred hhhhhccccccHHHH-hhHHHHHHHHhheeeeccCChh-hhhccccccCCCcCcccccceee
Confidence 577899999887644 5889999999999999999996 35565568899999999887655
No 45
>KOG0774|consensus
Probab=97.15 E-value=0.0013 Score=57.63 Aligned_cols=57 Identities=14% Similarity=0.207 Sum_probs=48.3
Q ss_pred CCCCCCCCCHHHHHHHHHhhh---cCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849 107 PKRPRTILTSAQRRQFKSSFE---VSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS 163 (267)
Q Consensus 107 ~kr~Rt~ft~~Ql~~L~~~f~---~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~ 163 (267)
++|+|--|+..-.++|.+.|. .++||+...+++ ++..||--||-|.|-+.||...+.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 466777899999999999996 568999888777 899999999999999999965443
No 46
>KOG2252|consensus
Probab=97.07 E-value=0.00024 Score=68.19 Aligned_cols=52 Identities=23% Similarity=0.356 Sum_probs=46.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhh
Q psy10849 105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQF 156 (267)
Q Consensus 105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~ 156 (267)
-..|+.|++||+.|++.|.+.|+.+++|+..+.+. |..+.|.-||-|-|.+.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 34788899999999999999999999999887776 88999999999988774
No 47
>KOG1700|consensus
Probab=97.05 E-value=0.00015 Score=62.18 Aligned_cols=62 Identities=23% Similarity=0.443 Sum_probs=51.9
Q ss_pred CCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849 19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL 82 (267)
Q Consensus 19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~ 82 (267)
..+|.+|++.+...+++. ..+..||..||.|..|...|. ...+...++.+||+.||..+++.
T Consensus 7 ~~kc~~c~k~vy~~e~~~-~~g~~~hk~c~~c~~~~k~l~-~~~~~~~e~~~yc~~~~~~~~~~ 68 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQ-KDGVDFHKECFKCEKCKKTLT-LSGYSEHEGVPYCKNCHVAQFGP 68 (200)
T ss_pred cchhhhccCcchHHHHHh-ccCcchhhhHHhccccccccc-cccccccccccccccchHhhhCc
Confidence 458999999998776554 778999999999999999996 46677789999999987777654
No 48
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=95.93 E-value=0.00077 Score=42.63 Aligned_cols=28 Identities=21% Similarity=0.258 Sum_probs=21.2
Q ss_pred cCCCCChhhhhh------cCCCceeeecchhhhh
Q psy10849 128 VSPKPCRKVSTM------NSKRAKNILTPNQRRQ 155 (267)
Q Consensus 128 ~~~~p~~~~r~~------l~~~~v~vWFQNrRak 155 (267)
.++||+..++++ |+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 368998887776 9999999999999964
No 49
>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=92.50 E-value=0.058 Score=33.38 Aligned_cols=33 Identities=27% Similarity=0.755 Sum_probs=25.9
Q ss_pred CCCCCCcccCCCcEEEecCceeecCCcccccccccC
Q psy10849 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL 57 (267)
Q Consensus 22 C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L 57 (267)
|.-|+..|.+.-.+++..++.|| |.|..|...|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence 77899999987677888899998 5666676655
No 50
>KOG3623|consensus
Probab=91.73 E-value=0.27 Score=49.30 Aligned_cols=46 Identities=9% Similarity=-0.005 Sum_probs=37.5
Q ss_pred HHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849 119 RRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS 164 (267)
Q Consensus 119 l~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~ 164 (267)
+..|+.+|..+..|....... |+.++|++||++++++..+..+.-+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 678899999999998654443 9999999999999999887654443
No 51
>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=82.10 E-value=1.2 Score=33.45 Aligned_cols=29 Identities=34% Similarity=0.655 Sum_probs=17.7
Q ss_pred CCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849 20 VKCARCGDRLLPHEMVMRAQSHVYHLPCF 48 (267)
Q Consensus 20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF 48 (267)
..|..|++.|.....++-..+..+|..|+
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 46777887776653333334566776665
No 52
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=79.90 E-value=0.26 Score=33.39 Aligned_cols=37 Identities=3% Similarity=-0.112 Sum_probs=21.0
Q ss_pred HHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhh
Q psy10849 119 RRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQ 155 (267)
Q Consensus 119 l~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak 155 (267)
++-|+++|.....+.-.+... |+..+|+.||-.|+..
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 456899998877664433333 9999999999877543
No 53
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=76.09 E-value=1.9 Score=29.01 Aligned_cols=31 Identities=26% Similarity=0.649 Sum_probs=22.4
Q ss_pred cCCCCCCCCCcccCCCcEEEe--cCceeecCCc
Q psy10849 18 YGVKCARCGDRLLPHEMVMRA--QSHVYHLPCF 48 (267)
Q Consensus 18 f~~~C~~C~~~I~~~e~~~~a--~~~~wH~~CF 48 (267)
.+.+|..|++.|.+++-++.- -+..||.+|.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 356899999999755556533 4667888876
No 54
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=75.55 E-value=0.91 Score=34.51 Aligned_cols=33 Identities=21% Similarity=0.475 Sum_probs=22.4
Q ss_pred ccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849 49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY 81 (267)
Q Consensus 49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~ 81 (267)
+|..|+..+..|+.|.+..+-+.--.||.+...
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~ 36 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKAS 36 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence 577777777777777776656666777766543
No 55
>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=75.26 E-value=1.6 Score=28.93 Aligned_cols=38 Identities=18% Similarity=0.375 Sum_probs=27.2
Q ss_pred cCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849 4 HNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCF 48 (267)
Q Consensus 4 ~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF 48 (267)
-.|+.|...|+ +|..|++.|.+++ .+...++.|-..||
T Consensus 17 ~~~~~~H~~Cf------~C~~C~~~l~~~~-~~~~~~~~~C~~c~ 54 (58)
T PF00412_consen 17 AMGKFWHPECF------KCSKCGKPLNDGD-FYEKDGKPYCKDCY 54 (58)
T ss_dssp ETTEEEETTTS------BETTTTCBTTTSS-EEEETTEEEEHHHH
T ss_pred eCCcEEEcccc------ccCCCCCccCCCe-eEeECCEEECHHHH
Confidence 35667777776 8999999998875 55567776655554
No 56
>KOG0773|consensus
Probab=72.79 E-value=4.1 Score=37.54 Aligned_cols=54 Identities=19% Similarity=0.183 Sum_probs=39.6
Q ss_pred CCCCCCCCCHHHHHHHHHhh-h--cCCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849 107 PKRPRTILTSAQRRQFKSSF-E--VSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF 160 (267)
Q Consensus 107 ~kr~Rt~ft~~Ql~~L~~~f-~--~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~ 160 (267)
.+|.+..+......+|++-. + ..+||....+.. |+..||..||.|.|-+..+..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 45566688888888887543 2 247887665533 999999999999998866543
No 57
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=72.76 E-value=2.9 Score=27.70 Aligned_cols=30 Identities=23% Similarity=0.617 Sum_probs=22.2
Q ss_pred ccccccccCCCCCceEeeCCeecchhhHHHH
Q psy10849 49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKE 79 (267)
Q Consensus 49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~ 79 (267)
.|..|+..++--..+-+.|| ..|..|+.++
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 37888888854333557778 6899999886
No 58
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=64.94 E-value=3.6 Score=32.79 Aligned_cols=24 Identities=33% Similarity=0.726 Sum_probs=19.2
Q ss_pred ccccccccCCCCCceEeeCCeecchhhHHH
Q psy10849 49 VCVICCQPLQKGEQFILRSGQLFCRQDFEK 78 (267)
Q Consensus 49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k 78 (267)
.|..|+.+| |- ++|.+||..|-.+
T Consensus 30 hCp~Cg~PL-----F~-KdG~v~CPvC~~~ 53 (131)
T COG1645 30 HCPKCGTPL-----FR-KDGEVFCPVCGYR 53 (131)
T ss_pred hCcccCCcc-----ee-eCCeEECCCCCce
Confidence 378899998 44 8999999999643
No 59
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=64.41 E-value=3.3 Score=27.52 Aligned_cols=46 Identities=17% Similarity=0.182 Sum_probs=30.6
Q ss_pred CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh-cCCCceeeecchhh
Q psy10849 108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM-NSKRAKNILTPNQR 153 (267)
Q Consensus 108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~-l~~~~v~vWFQNrR 153 (267)
||.|..+|-++-..+-+.++....-....++- ++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHhHH
Confidence 57899999999999999999887322222222 99999999988753
No 60
>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=62.07 E-value=1.9 Score=32.08 Aligned_cols=16 Identities=31% Similarity=0.754 Sum_probs=14.3
Q ss_pred cccccCCCCCCCCCcc
Q psy10849 14 GFRLYGVKCARCGDRL 29 (267)
Q Consensus 14 y~~~f~~~C~~C~~~I 29 (267)
|..+|..+|.+|++.+
T Consensus 49 Y~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLL 64 (90)
T ss_pred HhhhccchhhHHHhHh
Confidence 6778899999999988
No 61
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=61.05 E-value=6 Score=30.10 Aligned_cols=32 Identities=22% Similarity=0.458 Sum_probs=24.1
Q ss_pred CCCCCCCcccCCCcEEEecCceeecCCccccc
Q psy10849 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVI 52 (267)
Q Consensus 21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~ 52 (267)
+|..|++.|..++...-.....-|..||.=..
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 69999999998865443455677999986554
No 62
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=59.93 E-value=6.2 Score=21.59 Aligned_cols=10 Identities=30% Similarity=0.986 Sum_probs=5.7
Q ss_pred CCCCCCcccC
Q psy10849 22 CARCGDRLLP 31 (267)
Q Consensus 22 C~~C~~~I~~ 31 (267)
|..|+..|.+
T Consensus 2 Cp~CG~~~~~ 11 (23)
T PF13240_consen 2 CPNCGAEIED 11 (23)
T ss_pred CcccCCCCCC
Confidence 5566666543
No 63
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=59.66 E-value=5.4 Score=29.89 Aligned_cols=29 Identities=14% Similarity=0.432 Sum_probs=16.0
Q ss_pred cccccccccCCCCCceEeeCCeecchhhH
Q psy10849 48 FVCVICCQPLQKGEQFILRSGQLFCRQDF 76 (267)
Q Consensus 48 F~C~~C~~~L~~g~~f~~~~~~lyC~~cy 76 (267)
|+|..|+..+..|+.|.+...-..--.||
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl 35 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECL 35 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHH
Confidence 45666666666666666654333333444
No 64
>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=57.73 E-value=5.3 Score=28.76 Aligned_cols=15 Identities=27% Similarity=0.687 Sum_probs=10.8
Q ss_pred CCCCCCCcccCCCcE
Q psy10849 21 KCARCGDRLLPHEMV 35 (267)
Q Consensus 21 ~C~~C~~~I~~~e~~ 35 (267)
+|..|++.|..++..
T Consensus 9 ~Ck~C~~~I~kg~lR 23 (82)
T PF00645_consen 9 KCKGCKKKIAKGELR 23 (82)
T ss_dssp BETTTSCBE-TTSEE
T ss_pred cCcccCCcCCCCCEE
Confidence 788999999877633
No 65
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=57.42 E-value=3.6 Score=30.85 Aligned_cols=36 Identities=19% Similarity=0.414 Sum_probs=25.4
Q ss_pred CCCCCCCcccCCCcEEEecCceeecCCccccccccc
Q psy10849 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQP 56 (267)
Q Consensus 21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~ 56 (267)
+|+.|+..|..++...-......|-+||.=+.=+++
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCc
Confidence 799999999988755434455678888865544443
No 66
>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=56.34 E-value=6.3 Score=24.91 Aligned_cols=21 Identities=29% Similarity=0.760 Sum_probs=12.8
Q ss_pred cccccccCCCCCceEeeCCeecchhh
Q psy10849 50 CVICCQPLQKGEQFILRSGQLFCRQD 75 (267)
Q Consensus 50 C~~C~~~L~~g~~f~~~~~~lyC~~c 75 (267)
|..|+.+| |..+++++||..|
T Consensus 20 Cp~C~~PL-----~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 20 CPDCGTPL-----MRDKDGKIYCVSC 40 (41)
T ss_pred cCCCCCee-----EEecCCCEECCCC
Confidence 55666666 2345677777665
No 67
>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=55.11 E-value=7.7 Score=23.72 Aligned_cols=23 Identities=22% Similarity=0.506 Sum_probs=15.0
Q ss_pred ccccccccCCCCCceEeeCCeecchhhH
Q psy10849 49 VCVICCQPLQKGEQFILRSGQLFCRQDF 76 (267)
Q Consensus 49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy 76 (267)
.|..|+.. .|...+|..||..|-
T Consensus 10 ~C~~C~~~-----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 10 PCPVCGSR-----WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCCCCe-----EeEccCCEEEhhhCc
Confidence 36666553 356668888887763
No 68
>KOG3755|consensus
Probab=52.18 E-value=2.2 Score=42.13 Aligned_cols=23 Identities=9% Similarity=-0.111 Sum_probs=18.9
Q ss_pred cCCCceeeecchhhhhhhhhhhh
Q psy10849 140 NSKRAKNILTPNQRRQFKSSFEI 162 (267)
Q Consensus 140 l~~~~v~vWFQNrRak~k~~~~~ 162 (267)
...+-|+.||.|||++.|+.+..
T Consensus 738 ~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 738 FESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhhcchHHHHHHHHHHHhhhhcc
Confidence 45667999999999999997543
No 69
>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=50.55 E-value=6.3 Score=32.31 Aligned_cols=51 Identities=20% Similarity=0.374 Sum_probs=31.7
Q ss_pred cccCccccccccCCCCCCCCCcccCCCcE--EEecCceeecCCcccccccccCCC
Q psy10849 7 HVSCHPRGFRLYGVKCARCGDRLLPHEMV--MRAQSHVYHLPCFVCVICCQPLQK 59 (267)
Q Consensus 7 ~~yC~~cy~~~f~~~C~~C~~~I~~~e~~--~~a~~~~wH~~CF~C~~C~~~L~~ 59 (267)
.-||..|-.+. -..|..|+.+|.+...+ +-..+..|+.-- -|..|++++..
T Consensus 28 ~~fC~kCG~~t-I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~Ps-YC~~CGkpyPW 80 (158)
T PF10083_consen 28 EKFCSKCGAKT-ITSCPNCSTPIRGDYHVEGVFGLGGHYEAPS-YCHNCGKPYPW 80 (158)
T ss_pred HHHHHHhhHHH-HHHCcCCCCCCCCceecCCeeeeCCCCCCCh-hHHhCCCCCch
Confidence 35888887654 34899999999875222 112344455332 37778887753
No 70
>PRK00420 hypothetical protein; Validated
Probab=49.54 E-value=8.6 Score=29.88 Aligned_cols=23 Identities=35% Similarity=0.816 Sum_probs=16.4
Q ss_pred ccccccccCCCCCceEeeCCeecchhhH
Q psy10849 49 VCVICCQPLQKGEQFILRSGQLFCRQDF 76 (267)
Q Consensus 49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy 76 (267)
.|..|+.+| |.+++|+.||..|-
T Consensus 25 ~CP~Cg~pL-----f~lk~g~~~Cp~Cg 47 (112)
T PRK00420 25 HCPVCGLPL-----FELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCcc-----eecCCCceECCCCC
Confidence 467777777 44568888888773
No 71
>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=48.85 E-value=11 Score=28.10 Aligned_cols=29 Identities=21% Similarity=0.522 Sum_probs=21.1
Q ss_pred cccccccccCCCCCceEee-CCeecchhhHH
Q psy10849 48 FVCVICCQPLQKGEQFILR-SGQLFCRQDFE 77 (267)
Q Consensus 48 F~C~~C~~~L~~g~~f~~~-~~~lyC~~cy~ 77 (267)
-.|..|++.|.. ..|... +|.++...|+.
T Consensus 79 ~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 359999999974 555554 67888777754
No 72
>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=45.06 E-value=24 Score=23.47 Aligned_cols=33 Identities=33% Similarity=0.580 Sum_probs=25.8
Q ss_pred cccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849 48 FVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL 82 (267)
Q Consensus 48 F~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~ 82 (267)
|.|..|+..+. .......|..||+.|..+.+..
T Consensus 2 ~~Cpi~~~~~~--~Pv~~~~G~v~~~~~i~~~~~~ 34 (63)
T smart00504 2 FLCPISLEVMK--DPVILPSGQTYERRAIEKWLLS 34 (63)
T ss_pred cCCcCCCCcCC--CCEECCCCCEEeHHHHHHHHHH
Confidence 57888998885 4566667999999999887654
No 73
>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=44.28 E-value=17 Score=20.19 Aligned_cols=12 Identities=42% Similarity=1.171 Sum_probs=8.4
Q ss_pred CCCCCCcccCCC
Q psy10849 22 CARCGDRLLPHE 33 (267)
Q Consensus 22 C~~C~~~I~~~e 33 (267)
|.+|+..|.+.+
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 667787777654
No 74
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=43.11 E-value=21 Score=24.34 Aligned_cols=26 Identities=27% Similarity=0.848 Sum_probs=18.2
Q ss_pred ccccccccCCCCC-ceEeeCCeecchh
Q psy10849 49 VCVICCQPLQKGE-QFILRSGQLFCRQ 74 (267)
Q Consensus 49 ~C~~C~~~L~~g~-~f~~~~~~lyC~~ 74 (267)
.|..|++.|..|. .|..++.+.||..
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ 44 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSE 44 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccH
Confidence 4778888997444 5556678889843
No 75
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=40.36 E-value=22 Score=19.81 Aligned_cols=10 Identities=30% Similarity=0.860 Sum_probs=6.1
Q ss_pred CCCCCCCccc
Q psy10849 21 KCARCGDRLL 30 (267)
Q Consensus 21 ~C~~C~~~I~ 30 (267)
.|..|+..|.
T Consensus 4 ~Cp~Cg~~~~ 13 (26)
T PF13248_consen 4 FCPNCGAEID 13 (26)
T ss_pred CCcccCCcCC
Confidence 5666666554
No 76
>KOG3623|consensus
Probab=39.33 E-value=69 Score=32.88 Aligned_cols=55 Identities=13% Similarity=0.209 Sum_probs=40.0
Q ss_pred CCCCCCCCCHHHHHHHHHhhhcCCCCC------hhhhhhcCCCceeeecchhhhhhhhhhh
Q psy10849 107 PKRPRTILTSAQRRQFKSSFEVSPKPC------RKVSTMNSKRAKNILTPNQRRQFKSSFE 161 (267)
Q Consensus 107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~------~~~r~~l~~~~v~vWFQNrRak~k~~~~ 161 (267)
+.+.|+.+..++-.+|.+.++.+..+. +.++-.+.+.+|.|||++|+...+....
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcc
Confidence 455678778888888888887765443 3333337788999999999998877543
No 77
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=39.18 E-value=9.9 Score=32.58 Aligned_cols=31 Identities=19% Similarity=0.434 Sum_probs=24.5
Q ss_pred cccccccccCCCCCceEeeCCeecchhhHHHH
Q psy10849 48 FVCVICCQPLQKGEQFILRSGQLFCRQDFEKE 79 (267)
Q Consensus 48 F~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~ 79 (267)
-+|..|+..+. ...-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~-e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFM-EPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccc-cchhhhcCCceecccccccc
Confidence 57999998885 34555668999999999764
No 78
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=35.36 E-value=1.1e+02 Score=24.91 Aligned_cols=30 Identities=23% Similarity=0.546 Sum_probs=21.4
Q ss_pred cccccccCCCCCceEee-CCe--ecchhhHHHHHhh
Q psy10849 50 CVICCQPLQKGEQFILR-SGQ--LFCRQDFEKEMYL 82 (267)
Q Consensus 50 C~~C~~~L~~g~~f~~~-~~~--lyC~~cy~k~f~~ 82 (267)
|..|+..+. |..+.+. +|. ..|..|+ +||.
T Consensus 3 CEiCG~~i~-~~~~~v~iega~l~vC~~C~--k~G~ 35 (154)
T TIGR00270 3 CEICGRKIK-GKGFKIVIEGSEMTVCGECR--KFGK 35 (154)
T ss_pred cccCCCccC-CCCeEEEEcCeEEehhhhHH--hcCC
Confidence 889999995 6645443 553 3599998 6776
No 79
>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=34.33 E-value=7.5 Score=23.49 Aligned_cols=28 Identities=25% Similarity=0.650 Sum_probs=12.5
Q ss_pred cccccccCCCCCceEeeCCeecchhhHHH
Q psy10849 50 CVICCQPLQKGEQFILRSGQLFCRQDFEK 78 (267)
Q Consensus 50 C~~C~~~L~~g~~f~~~~~~lyC~~cy~k 78 (267)
|..|+..+.. .......+..+|..|..+
T Consensus 6 C~~CGe~I~~-~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPE-ERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEH-HHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHH-HHHHhCCCcEECHHHhCc
Confidence 4555555532 223333556666666543
No 80
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=33.83 E-value=25 Score=34.24 Aligned_cols=51 Identities=24% Similarity=0.413 Sum_probs=29.2
Q ss_pred CcccCcccccccc---------CCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCC
Q psy10849 6 SHVSCHPRGFRLY---------GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQ 58 (267)
Q Consensus 6 g~~yC~~cy~~~f---------~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~ 58 (267)
...||+.|..-+- ...|..|-..+-..+ ++..+..--.+||.|-.|...|.
T Consensus 4 ~L~fC~~C~~irc~~c~~~Ei~~~yCp~CL~~~p~~e--~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 4 ELYFCEHCHKIRCPRCVSEEIDSYYCPNCLFEVPSSE--ARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred cceecccccccCChhhcccccceeECccccccCChhh--heeccceeccccccCCCCCCcce
Confidence 4578999974321 113555555444332 11223333458999999999985
No 81
>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=33.82 E-value=46 Score=19.00 Aligned_cols=12 Identities=42% Similarity=0.897 Sum_probs=6.7
Q ss_pred CCCCCCCCCccc
Q psy10849 19 GVKCARCGDRLL 30 (267)
Q Consensus 19 ~~~C~~C~~~I~ 30 (267)
|.+|.+|+..|.
T Consensus 1 G~~C~rC~~~~~ 12 (30)
T PF06827_consen 1 GEKCPRCWNYIE 12 (30)
T ss_dssp TSB-TTT--BBE
T ss_pred CCcCccCCCcce
Confidence 357899998876
No 82
>KOG0320|consensus
Probab=32.27 E-value=26 Score=29.47 Aligned_cols=38 Identities=18% Similarity=0.449 Sum_probs=29.2
Q ss_pred cCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849 45 LPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL 82 (267)
Q Consensus 45 ~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~ 82 (267)
..||.|-.|-.....-..+.-+-|.+||+.|-......
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~ 166 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN 166 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHh
Confidence 56899999998886444465678999999998776543
No 83
>PRK00807 50S ribosomal protein L24e; Validated
Probab=32.08 E-value=41 Score=22.27 Aligned_cols=24 Identities=17% Similarity=0.490 Sum_probs=13.3
Q ss_pred CCCCCCCcccCCCcE--EEecCceee
Q psy10849 21 KCARCGDRLLPHEMV--MRAQSHVYH 44 (267)
Q Consensus 21 ~C~~C~~~I~~~e~~--~~a~~~~wH 44 (267)
.|..|+..|.++.-. ++..++.|.
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~~ 28 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTILY 28 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEEE
Confidence 577777777754322 333455554
No 84
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=31.98 E-value=35 Score=34.56 Aligned_cols=26 Identities=27% Similarity=0.576 Sum_probs=13.4
Q ss_pred CCcccCccccccccCCCCCCCCCccc
Q psy10849 5 NSHVSCHPRGFRLYGVKCARCGDRLL 30 (267)
Q Consensus 5 dg~~yC~~cy~~~f~~~C~~C~~~I~ 30 (267)
++.-||..|...+-...|..|+..+.
T Consensus 13 ~~akFC~~CG~~l~~~~Cp~CG~~~~ 38 (645)
T PRK14559 13 NNNRFCQKCGTSLTHKPCPQCGTEVP 38 (645)
T ss_pred CCCccccccCCCCCCCcCCCCCCCCC
Confidence 33445666654443345666665544
No 85
>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=31.32 E-value=35 Score=21.66 Aligned_cols=10 Identities=20% Similarity=0.401 Sum_probs=6.4
Q ss_pred eecchhhHHH
Q psy10849 69 QLFCRQDFEK 78 (267)
Q Consensus 69 ~lyC~~cy~k 78 (267)
.-+|..||.+
T Consensus 23 ~dLC~~Cf~~ 32 (46)
T cd02249 23 FDLCSSCYAK 32 (46)
T ss_pred CcCHHHHHCc
Confidence 3457788764
No 86
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=28.79 E-value=91 Score=19.40 Aligned_cols=33 Identities=21% Similarity=0.474 Sum_probs=17.7
Q ss_pred ccccccccCCCCCceEeeC-CeecchhhHHHHHh
Q psy10849 49 VCVICCQPLQKGEQFILRS-GQLFCRQDFEKEMY 81 (267)
Q Consensus 49 ~C~~C~~~L~~g~~f~~~~-~~lyC~~cy~k~f~ 81 (267)
.|+.|+++-.......... +..+|..|-...+.
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~~~ 36 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQAYE 36 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHHHH
Confidence 4777777765433333333 66778888765443
No 87
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=28.59 E-value=22 Score=22.32 Aligned_cols=21 Identities=33% Similarity=0.629 Sum_probs=10.9
Q ss_pred CcccCcccccccc--CCCCCCCC
Q psy10849 6 SHVSCHPRGFRLY--GVKCARCG 26 (267)
Q Consensus 6 g~~yC~~cy~~~f--~~~C~~C~ 26 (267)
|.++|..|..+.. ...|..|+
T Consensus 21 gH~~C~~C~~~~~~~~~~CP~C~ 43 (44)
T PF14634_consen 21 GHIFCEKCLKKLKGKSVKCPICR 43 (44)
T ss_pred CCHHHHHHHHhhcCCCCCCcCCC
Confidence 3455666665544 33555554
No 88
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=27.97 E-value=52 Score=20.21 Aligned_cols=13 Identities=23% Similarity=0.370 Sum_probs=11.2
Q ss_pred CCCHHHHHHHHHh
Q psy10849 113 ILTSAQRRQFKSS 125 (267)
Q Consensus 113 ~ft~~Ql~~L~~~ 125 (267)
.||..|+.+|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 6999999999764
No 89
>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=27.48 E-value=34 Score=25.49 Aligned_cols=23 Identities=26% Similarity=0.691 Sum_probs=10.5
Q ss_pred CcccCccccccccCCCCCCCCCccc
Q psy10849 6 SHVSCHPRGFRLYGVKCARCGDRLL 30 (267)
Q Consensus 6 g~~yC~~cy~~~f~~~C~~C~~~I~ 30 (267)
|.-||..|-.++ -+|+-|++.|.
T Consensus 58 g~~YCq~CAYkk--GiCamCGKki~ 80 (90)
T PF10235_consen 58 GAKYCQTCAYKK--GICAMCGKKIL 80 (90)
T ss_pred CCccChhhhccc--CcccccCCeec
Confidence 334555553332 14555555553
No 90
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=26.85 E-value=51 Score=20.73 Aligned_cols=9 Identities=33% Similarity=0.674 Sum_probs=6.1
Q ss_pred ecchhhHHH
Q psy10849 70 LFCRQDFEK 78 (267)
Q Consensus 70 lyC~~cy~k 78 (267)
-+|..||.+
T Consensus 28 dlC~~Cf~~ 36 (44)
T smart00291 28 DLCQSCFAK 36 (44)
T ss_pred cchHHHHhC
Confidence 458888754
No 91
>KOG1146|consensus
Probab=24.88 E-value=25 Score=38.13 Aligned_cols=58 Identities=12% Similarity=-0.012 Sum_probs=45.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849 104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE 161 (267)
Q Consensus 104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~ 161 (267)
+...+-.|+.++..|+..|...|+...+|.-.+++. +..|.+-+||++++.+|.+...
T Consensus 441 ~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~ 504 (1406)
T KOG1146|consen 441 KAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHP 504 (1406)
T ss_pred chhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccc
Confidence 334555788999999999999998888887655554 7889988888888888777543
No 92
>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=24.47 E-value=64 Score=19.92 Aligned_cols=30 Identities=27% Similarity=0.713 Sum_probs=13.0
Q ss_pred CCCCCCCCcccCCCcEEEecCceeecCCcccccccc
Q psy10849 20 VKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQ 55 (267)
Q Consensus 20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~ 55 (267)
.+|.+|+-.|.+- ..+...++.| +|..|+.
T Consensus 3 ~rC~~C~aylNp~-~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPF-CQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TT-SEEETTTTEE-----EETTT--
T ss_pred cccCCCCCEECCc-ceEcCCCCEE-----ECcCCCC
Confidence 4788888877653 2233344555 5666664
No 93
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=23.87 E-value=57 Score=22.35 Aligned_cols=28 Identities=32% Similarity=0.743 Sum_probs=18.5
Q ss_pred CCCCCCCCCcccCCCcEEEecCceeecCCccccccccc
Q psy10849 19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQP 56 (267)
Q Consensus 19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~ 56 (267)
.++|..|+..|.+.+..+ -|.|-.|+..
T Consensus 7 ~~~CtSCg~~i~~~~~~~----------~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAV----------KFLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCccC----------EeeCCCCCCe
Confidence 347999999998765332 1556666665
No 94
>KOG2893|consensus
Probab=23.59 E-value=42 Score=29.62 Aligned_cols=63 Identities=19% Similarity=0.378 Sum_probs=35.2
Q ss_pred CCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhhhcCCCCCCC
Q psy10849 20 VKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQQSSPSDD 91 (267)
Q Consensus 20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~~~~~~~~~~ 91 (267)
+-|.-|+..+.+ |+|+.... ...+|+|.+|.+.|-.|-.. .+.|..-+.+.....--+..+.+
T Consensus 11 pwcwycnrefdd-ekiliqhq---kakhfkchichkkl~sgpgl-----sihcmqvhketid~ip~av~gr~ 73 (341)
T KOG2893|consen 11 PWCWYCNREFDD-EKILIQHQ---KAKHFKCHICHKKLFSGPGL-----SIHCMQVHKETIDKIPAAVHGRD 73 (341)
T ss_pred ceeeecccccch-hhhhhhhh---hhccceeeeehhhhccCCCc-----eeehhhhhhhhhhcccccccCCc
Confidence 457788877765 35542222 23468999999888555433 34575555554443333334443
No 95
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=22.71 E-value=40 Score=24.50 Aligned_cols=30 Identities=27% Similarity=0.608 Sum_probs=17.4
Q ss_pred ccccccccCCCCCceEe-eC---CeecchhhHHH
Q psy10849 49 VCVICCQPLQKGEQFIL-RS---GQLFCRQDFEK 78 (267)
Q Consensus 49 ~C~~C~~~L~~g~~f~~-~~---~~lyC~~cy~k 78 (267)
.|..|+.||.....+.- .+ +.-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 37778888753221211 12 45689999854
No 96
>KOG0956|consensus
Probab=22.63 E-value=8.7e+02 Score=25.14 Aligned_cols=15 Identities=13% Similarity=0.372 Sum_probs=9.2
Q ss_pred cccCCCCCCCCCccc
Q psy10849 16 RLYGVKCARCGDRLL 30 (267)
Q Consensus 16 ~~f~~~C~~C~~~I~ 30 (267)
.+|...|+-|.+.-.
T Consensus 114 dRfnKtCYIC~E~Gr 128 (900)
T KOG0956|consen 114 DRFNKTCYICNEEGR 128 (900)
T ss_pred hhhcceeeeecccCC
Confidence 345556777776543
No 97
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=22.59 E-value=48 Score=21.68 Aligned_cols=22 Identities=27% Similarity=0.522 Sum_probs=15.0
Q ss_pred CcccCcccccccc--CCCCCCCCC
Q psy10849 6 SHVSCHPRGFRLY--GVKCARCGD 27 (267)
Q Consensus 6 g~~yC~~cy~~~f--~~~C~~C~~ 27 (267)
.+..|..||.++- +..|.+|+-
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 4567888887653 347888874
No 98
>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=22.40 E-value=65 Score=23.65 Aligned_cols=10 Identities=40% Similarity=0.860 Sum_probs=5.6
Q ss_pred CCCCCCCccc
Q psy10849 21 KCARCGDRLL 30 (267)
Q Consensus 21 ~C~~C~~~I~ 30 (267)
.|..|+.+|.
T Consensus 2 ~C~HCg~~~p 11 (88)
T PF12156_consen 2 KCYHCGLPVP 11 (88)
T ss_pred CCCCCCCCCC
Confidence 3556666554
No 99
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=22.12 E-value=48 Score=22.74 Aligned_cols=18 Identities=28% Similarity=0.695 Sum_probs=13.5
Q ss_pred CCCCCCCCCcccCCCcEE
Q psy10849 19 GVKCARCGDRLLPHEMVM 36 (267)
Q Consensus 19 ~~~C~~C~~~I~~~e~~~ 36 (267)
.+.|..|+..|..+|..+
T Consensus 9 ~~~CtSCg~~i~p~e~~v 26 (61)
T COG2888 9 PPVCTSCGREIAPGETAV 26 (61)
T ss_pred CceeccCCCEeccCCcee
Confidence 468999999997665443
No 100
>PF12773 DZR: Double zinc ribbon
Probab=22.08 E-value=71 Score=20.32 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=5.7
Q ss_pred ccccccccCC
Q psy10849 49 VCVICCQPLQ 58 (267)
Q Consensus 49 ~C~~C~~~L~ 58 (267)
.|..|+..+.
T Consensus 31 ~C~~Cg~~~~ 40 (50)
T PF12773_consen 31 ICPNCGAENP 40 (50)
T ss_pred CCcCCcCCCc
Confidence 4666666553
No 101
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=21.88 E-value=84 Score=20.27 Aligned_cols=29 Identities=21% Similarity=0.539 Sum_probs=18.3
Q ss_pred ccccccccCCCCCceEeeCCeecchhhHHHHH
Q psy10849 49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80 (267)
Q Consensus 49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f 80 (267)
+|..|++....| .. ..++.+|..|-.++.
T Consensus 1 ~CiiC~~~~~~G--I~-I~~~fIC~~CE~~iv 29 (46)
T PF10764_consen 1 KCIICGKEKEEG--IH-IYGKFICSDCEKEIV 29 (46)
T ss_pred CeEeCCCcCCCC--EE-EECeEehHHHHHHhc
Confidence 366777776432 22 257788888876654
No 102
>PRK12495 hypothetical protein; Provisional
Probab=21.81 E-value=39 Score=29.41 Aligned_cols=26 Identities=27% Similarity=0.473 Sum_probs=18.2
Q ss_pred CCcccccccccCCCCCceEeeCCeecchhhHH
Q psy10849 46 PCFVCVICCQPLQKGEQFILRSGQLFCRQDFE 77 (267)
Q Consensus 46 ~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~ 77 (267)
.-+.|..|+.+|. . ..|..+|..|-.
T Consensus 41 sa~hC~~CG~PIp-----a-~pG~~~Cp~CQ~ 66 (226)
T PRK12495 41 TNAHCDECGDPIF-----R-HDGQEFCPTCQQ 66 (226)
T ss_pred chhhcccccCccc-----C-CCCeeECCCCCC
Confidence 3466888888883 2 378888888853
No 103
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=21.47 E-value=57 Score=30.01 Aligned_cols=15 Identities=20% Similarity=0.798 Sum_probs=11.9
Q ss_pred cCCCCCCCCCcccCC
Q psy10849 18 YGVKCARCGDRLLPH 32 (267)
Q Consensus 18 f~~~C~~C~~~I~~~ 32 (267)
|...|..|+..|.-+
T Consensus 39 f~i~C~~C~~~I~kG 53 (324)
T PF04502_consen 39 FNIWCNTCGEYIYKG 53 (324)
T ss_pred ccCcCCCCccccccc
Confidence 556899999999755
No 104
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=21.20 E-value=31 Score=26.14 Aligned_cols=29 Identities=24% Similarity=0.462 Sum_probs=15.9
Q ss_pred CcccccccccCCCCCceEeeCCeecchhh
Q psy10849 47 CFVCVICCQPLQKGEQFILRSGQLFCRQD 75 (267)
Q Consensus 47 CF~C~~C~~~L~~g~~f~~~~~~lyC~~c 75 (267)
=|+|+.|--.---.+--...+|.+||..|
T Consensus 70 EFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEechhhhccccCCCEecccc
Confidence 37777775332111112234688888877
No 105
>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=20.79 E-value=74 Score=20.21 Aligned_cols=10 Identities=30% Similarity=0.544 Sum_probs=7.2
Q ss_pred eecchhhHHH
Q psy10849 69 QLFCRQDFEK 78 (267)
Q Consensus 69 ~lyC~~cy~k 78 (267)
.-+|..||.+
T Consensus 28 ~dLC~~C~~~ 37 (46)
T PF00569_consen 28 YDLCEDCFSK 37 (46)
T ss_dssp -EEEHHHHHH
T ss_pred CchhhHHHhC
Confidence 3459999977
Done!