Query psy11345
Match_columns 282
No_of_seqs 290 out of 1903
Neff 8.3
Searched_HMMs 46136
Date Fri Aug 16 16:01:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11345.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11345hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 100.0 2.3E-33 4.9E-38 250.6 5.0 169 107-281 270-456 (468)
2 KOG2272|consensus 99.9 4.9E-28 1.1E-32 202.7 -4.1 159 112-281 74-306 (332)
3 KOG1044|consensus 99.9 1.5E-25 3.3E-30 206.8 4.5 156 115-275 69-245 (670)
4 KOG1703|consensus 99.9 4.3E-25 9.2E-30 209.9 4.0 161 111-281 303-475 (479)
5 KOG2272|consensus 99.9 1.4E-26 3E-31 194.0 -6.5 160 110-281 11-246 (332)
6 KOG4577|consensus 99.8 7.4E-22 1.6E-26 168.4 -3.6 117 159-282 32-148 (383)
7 KOG1044|consensus 99.8 6E-20 1.3E-24 169.9 7.2 158 112-281 17-184 (670)
8 KOG1701|consensus 99.8 7.1E-21 1.5E-25 170.7 -2.7 110 162-281 276-386 (468)
9 KOG4577|consensus 99.7 9.2E-19 2E-23 149.6 -3.2 111 110-223 32-158 (383)
10 KOG1703|consensus 99.6 2.4E-16 5.2E-21 150.1 5.8 157 114-281 246-414 (479)
11 PF00412 LIM: LIM domain; Int 99.2 2.4E-12 5.2E-17 87.2 2.0 56 114-171 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.2 8E-12 1.7E-16 84.6 4.4 57 163-219 1-58 (58)
13 KOG1700|consensus 99.0 7.2E-11 1.6E-15 99.8 -0.4 112 161-281 8-160 (200)
14 smart00735 ZM ZASP-like motif. 98.9 7.3E-10 1.6E-14 62.1 1.1 26 8-33 1-26 (26)
15 KOG1700|consensus 98.8 1.2E-09 2.6E-14 92.4 1.1 106 112-219 8-167 (200)
16 smart00132 LIM Zinc-binding do 98.6 6E-08 1.3E-12 59.6 3.3 37 222-258 1-37 (39)
17 smart00132 LIM Zinc-binding do 98.4 1.9E-07 4.1E-12 57.3 2.7 36 113-150 1-38 (39)
18 KOG0490|consensus 97.6 5.7E-06 1.2E-10 71.5 -2.7 90 175-266 11-104 (235)
19 KOG1702|consensus 97.2 4.4E-05 9.5E-10 63.3 -1.8 60 161-220 5-64 (264)
20 KOG1702|consensus 96.2 0.00071 1.5E-08 56.3 -1.3 59 112-172 5-64 (264)
21 KOG0490|consensus 96.0 0.0013 2.9E-08 56.6 -0.6 100 116-218 1-119 (235)
22 PF14446 Prok-RING_1: Prokaryo 83.4 0.65 1.4E-05 30.5 1.2 38 220-257 5-50 (54)
23 PF10367 Vps39_2: Vacuolar sor 82.2 1.1 2.4E-05 33.4 2.3 30 221-250 79-108 (109)
24 PF09943 DUF2175: Uncharacteri 81.8 0.36 7.8E-06 36.0 -0.5 32 222-253 4-35 (101)
25 PF14835 zf-RING_6: zf-RING of 80.6 1.7 3.7E-05 29.6 2.5 47 188-234 8-54 (65)
26 PF08394 Arc_trans_TRASH: Arch 76.3 1.1 2.4E-05 27.0 0.6 28 114-141 1-30 (37)
27 PF14634 zf-RING_5: zinc-RING 73.7 4.2 9.1E-05 25.2 2.8 39 190-228 2-44 (44)
28 PF08394 Arc_trans_TRASH: Arch 73.5 1.6 3.6E-05 26.3 0.8 29 223-251 1-29 (37)
29 PF10235 Cript: Microtubule-as 67.8 3.5 7.7E-05 30.1 1.6 37 188-232 45-81 (90)
30 PF11781 RRN7: RNA polymerase 65.9 3.9 8.4E-05 24.5 1.3 25 188-216 9-33 (36)
31 COG1645 Uncharacterized Zn-fin 65.5 3.5 7.7E-05 32.3 1.3 23 189-216 30-52 (131)
32 PF14471 DUF4428: Domain of un 64.5 4.7 0.0001 26.2 1.6 29 189-218 1-30 (51)
33 PF13248 zf-ribbon_3: zinc-rib 62.7 5.9 0.00013 21.7 1.5 10 222-231 4-13 (26)
34 COG4847 Uncharacterized protei 62.2 2.2 4.8E-05 31.2 -0.3 37 221-257 7-43 (103)
35 PRK14890 putative Zn-ribbon RN 60.6 10 0.00023 25.3 2.7 17 211-227 39-55 (59)
36 PRK14559 putative protein seri 58.6 9.4 0.0002 38.2 3.2 38 189-233 3-40 (645)
37 PF00645 zf-PARP: Poly(ADP-rib 58.3 2.9 6.2E-05 29.8 -0.3 30 221-250 8-47 (82)
38 KOG0320|consensus 57.6 6.8 0.00015 32.3 1.7 51 181-231 125-178 (187)
39 smart00504 Ubox Modified RING 56.4 11 0.00023 25.0 2.3 44 188-232 2-47 (63)
40 PF13920 zf-C3HC4_3: Zinc fing 56.0 7.9 0.00017 24.6 1.6 43 188-231 3-48 (50)
41 TIGR00595 priA primosomal prot 54.6 8.8 0.00019 37.3 2.3 39 188-229 223-262 (505)
42 PRK14873 primosome assembly pr 54.3 8.5 0.00018 38.7 2.2 39 188-229 393-431 (665)
43 KOG4739|consensus 53.8 12 0.00027 32.3 2.8 40 192-231 8-48 (233)
44 COG4357 Zinc finger domain con 52.8 2.1 4.5E-05 31.5 -1.8 48 164-211 39-86 (105)
45 PF10083 DUF2321: Uncharacteri 52.2 8.4 0.00018 31.1 1.4 48 207-257 27-77 (158)
46 PF10367 Vps39_2: Vacuolar sor 51.6 11 0.00025 27.7 2.0 25 190-214 81-106 (109)
47 PF12773 DZR: Double zinc ribb 51.1 19 0.00041 22.7 2.8 25 208-232 12-41 (50)
48 cd00162 RING RING-finger (Real 50.1 12 0.00027 22.1 1.7 39 190-229 2-44 (45)
49 PF01258 zf-dskA_traR: Prokary 49.2 2.7 5.8E-05 25.0 -1.4 28 190-217 6-33 (36)
50 COG0068 HypF Hydrogenase matur 48.7 12 0.00025 37.6 2.1 77 110-197 100-183 (750)
51 PF11571 Med27: Mediator compl 48.4 6 0.00013 28.9 0.0 17 215-231 49-65 (90)
52 PF06827 zf-FPG_IleRS: Zinc fi 48.0 5.4 0.00012 22.5 -0.2 11 221-231 2-12 (30)
53 PF06677 Auto_anti-p27: Sjogre 46.0 12 0.00026 23.2 1.1 22 189-214 19-40 (41)
54 COG1645 Uncharacterized Zn-fin 45.0 13 0.00028 29.2 1.4 18 251-281 31-48 (131)
55 PF06906 DUF1272: Protein of u 43.9 33 0.00072 22.7 3.0 43 189-231 7-52 (57)
56 PF07191 zinc-ribbons_6: zinc- 40.8 27 0.00059 24.2 2.4 43 190-241 4-47 (70)
57 COG1198 PriA Primosomal protei 39.7 20 0.00043 36.4 2.2 39 188-229 445-484 (730)
58 PF10886 DUF2685: Protein of u 39.4 22 0.00047 23.3 1.6 25 221-246 2-26 (54)
59 COG2191 Formylmethanofuran deh 39.1 12 0.00026 31.6 0.5 32 188-219 173-204 (206)
60 PRK05580 primosome assembly pr 37.7 23 0.00049 35.8 2.2 39 188-229 391-430 (679)
61 KOG0978|consensus 37.5 9 0.0002 38.4 -0.6 46 188-234 644-692 (698)
62 KOG1813|consensus 37.4 19 0.00041 32.2 1.4 43 188-231 242-286 (313)
63 PRK00420 hypothetical protein; 37.1 18 0.00039 27.6 1.1 25 188-216 24-48 (112)
64 cd02249 ZZ Zinc finger, ZZ typ 36.0 31 0.00066 21.5 1.9 30 188-217 1-32 (46)
65 PF12674 Zn_ribbon_2: Putative 35.5 20 0.00043 25.7 1.1 29 189-217 2-35 (81)
66 PRK04023 DNA polymerase II lar 35.4 30 0.00065 36.2 2.7 39 188-234 639-677 (1121)
67 smart00291 ZnF_ZZ Zinc-binding 35.3 27 0.00059 21.6 1.6 30 188-217 5-36 (44)
68 PRK00807 50S ribosomal protein 35.3 23 0.00049 23.1 1.2 34 221-257 2-37 (52)
69 PF13240 zinc_ribbon_2: zinc-r 33.7 29 0.00062 18.4 1.3 7 144-150 4-10 (23)
70 COG5152 Uncharacterized conser 33.0 12 0.00027 31.4 -0.4 44 187-231 196-241 (259)
71 PF05502 Dynactin_p62: Dynacti 32.0 33 0.0007 33.2 2.2 12 241-252 82-93 (483)
72 COG2888 Predicted Zn-ribbon RN 32.0 22 0.00047 23.8 0.7 37 188-228 10-46 (61)
73 PF07503 zf-HYPF: HypF finger; 31.5 22 0.00048 21.1 0.6 31 163-198 2-32 (35)
74 COG0068 HypF Hydrogenase matur 30.7 24 0.00052 35.5 1.1 83 159-257 100-182 (750)
75 KOG4443|consensus 30.0 23 0.00049 35.2 0.8 22 239-261 106-127 (694)
76 PF02069 Metallothio_Pro: Prok 29.7 40 0.00087 22.0 1.7 29 189-217 9-38 (52)
77 PF13639 zf-RING_2: Ring finge 28.9 14 0.00031 22.6 -0.5 28 222-249 2-30 (44)
78 KOG2893|consensus 27.3 19 0.00041 31.2 -0.3 38 221-262 11-48 (341)
79 cd02336 ZZ_RSC8 Zinc finger, Z 26.7 59 0.0013 20.4 2.0 30 188-217 1-32 (45)
80 PF04570 DUF581: Protein of un 25.8 37 0.0008 22.7 1.0 24 189-212 18-43 (58)
81 KOG1280|consensus 25.7 43 0.00093 30.7 1.7 67 163-257 11-88 (381)
82 PF07754 DUF1610: Domain of un 25.2 47 0.001 18.0 1.1 9 223-231 1-9 (24)
83 TIGR00570 cdk7 CDK-activating 25.0 67 0.0014 29.1 2.8 44 189-232 5-55 (309)
84 TIGR00143 hypF [NiFe] hydrogen 24.6 47 0.001 33.8 1.9 77 110-197 67-150 (711)
85 PLN03208 E3 ubiquitin-protein 24.1 1E+02 0.0022 25.9 3.6 46 187-233 18-81 (193)
86 PF13923 zf-C3HC4_2: Zinc fing 24.1 35 0.00076 20.2 0.6 30 190-219 1-30 (39)
87 COG0266 Nei Formamidopyrimidin 23.9 47 0.001 29.6 1.6 27 220-248 245-271 (273)
88 cd02341 ZZ_ZZZ3 Zinc finger, Z 23.5 75 0.0016 20.2 2.1 31 188-218 1-36 (48)
89 PF04161 Arv1: Arv1-like famil 23.4 41 0.0009 28.5 1.2 41 188-240 1-41 (208)
90 PF04981 NMD3: NMD3 family ; 23.2 69 0.0015 27.7 2.5 24 190-219 1-24 (236)
91 smart00659 RPOLCX RNA polymera 23.2 42 0.0009 21.0 0.8 28 138-171 3-30 (44)
92 KOG2932|consensus 22.5 44 0.00094 30.2 1.1 43 189-231 92-134 (389)
93 KOG3002|consensus 22.3 68 0.0015 29.0 2.3 43 188-231 49-91 (299)
94 PRK11595 DNA utilization prote 21.8 80 0.0017 27.0 2.6 37 189-231 7-45 (227)
95 PRK14559 putative protein seri 21.5 94 0.002 31.3 3.3 47 113-171 3-52 (645)
96 cd00472 Ribosomal_L24e_L24 Rib 21.3 64 0.0014 21.2 1.4 25 221-245 4-30 (54)
97 KOG4443|consensus 20.3 65 0.0014 32.1 1.9 114 110-232 34-175 (694)
98 COG2191 Formylmethanofuran deh 20.3 54 0.0012 27.8 1.2 14 156-169 189-202 (206)
99 KOG2462|consensus 20.0 57 0.0012 28.9 1.3 10 249-258 216-225 (279)
No 1
>KOG1701|consensus
Probab=99.98 E-value=2.3e-33 Score=250.55 Aligned_cols=169 Identities=28% Similarity=0.657 Sum_probs=148.7
Q ss_pred CCCCCCcccccCccccC--ceeecCCcccCcCCcccccCCCCCCCCCCCceecCCccccccccccccCC----------c
Q psy11345 107 PGARVPLCGQCYQQIRG--PFITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYLAP----------D 174 (282)
Q Consensus 107 ~~~~~~~C~~C~~~I~~--~~v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~----------~ 174 (282)
....+.+|.+|++.|.| ..+.||++.||.+||+|. .|++.|..+.||.+++++||+.||.....+ +
T Consensus 270 ~~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~--~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~ 347 (468)
T KOG1701|consen 270 VEDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCR--TCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDR 347 (468)
T ss_pred hhhhhhhhhhcCCcccCcchHHHHhhhhhcccceehH--hhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHHHHH
Confidence 33455699999999975 469999999999999999 999999999999999999999999765543 3
Q ss_pred eeeecCccccccCccCCccCcccCCCCeeee-CCeecCHhhhhcccCCCCccCCCccccCC-----cEEEeCCcccccCC
Q psy11345 175 CLNAIGKHYHPECFTCAYCGKLFGNNPFFLE-EGLPYCENDWNDLFTTKCFACGFPIEAGD-----RWVEALNNNYHSLC 248 (282)
Q Consensus 175 ~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~-~~~~yC~~c~~~~~~~~C~~C~~~I~~~~-----~~~~~~~~~~H~~C 248 (282)
.++|.|+.||+.||+|.+|++.|++..|.+. ++++||..||+++|+++|..|+++|.+.+ ..|.++++.||.+|
T Consensus 348 iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~C 427 (468)
T KOG1701|consen 348 ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNC 427 (468)
T ss_pred HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccccccc
Confidence 4889999999999999999999999889885 68999999999999999999999999732 34678999999999
Q ss_pred CcCCCCCCCCCCCCcccccCCceecCCCeeecC
Q psy11345 249 FNCSSPSSPALSGAKPYGTQNTIKSTSGTIVCL 281 (282)
Q Consensus 249 f~C~~C~~~l~~g~~~~~~~~~~~~~~g~~~C~ 281 (282)
++|..|+..|. .+ .+....|..||.++|+
T Consensus 428 Y~CEDCg~~LS-~e---~e~qgCyPld~HllCk 456 (468)
T KOG1701|consen 428 YKCEDCGLLLS-SE---EEGQGCYPLDGHLLCK 456 (468)
T ss_pred eehhhcCcccc-cc---CCCCcceeccCceeec
Confidence 99999999954 22 4566788999999997
No 2
>KOG2272|consensus
Probab=99.93 E-value=4.9e-28 Score=202.72 Aligned_cols=159 Identities=35% Similarity=0.694 Sum_probs=138.2
Q ss_pred CcccccCccccCceeecCCcccCcCCcccccCCCCCCCCCCCceecCCcccccccccc----------------------
Q psy11345 112 PLCGQCYQQIRGPFITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQ---------------------- 169 (282)
Q Consensus 112 ~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~---------------------- 169 (282)
|.|.+|+..|.|++|++++.+|||.||+|. .|.+.|.+.+|+-..|+.+|..|..+
T Consensus 74 PcC~kC~EFiiGrVikamnnSwHp~CF~Cd--~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~ 151 (332)
T KOG2272|consen 74 PCCGKCGEFIIGRVIKAMNNSWHPACFRCD--LCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQP 151 (332)
T ss_pred hhhcccccchhhHHHHhhccccCcccchhH--HHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccccc
Confidence 699999999999999999999999999999 99999988888777776666665543
Q ss_pred -----------------------------------------ccCC-----------ceeeecCccccccCccCCccCccc
Q psy11345 170 -----------------------------------------YLAP-----------DCLNAIGKHYHPECFTCAYCGKLF 197 (282)
Q Consensus 170 -----------------------------------------~~~~-----------~~~~~~~~~~H~~Cf~C~~C~~~l 197 (282)
..-+ ..+.++|++||.+.|+|+.|.+++
T Consensus 152 l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPF 231 (332)
T KOG2272|consen 152 LTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPF 231 (332)
T ss_pred ccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcc
Confidence 1111 115678999999999999999999
Q ss_pred CCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCCcEEEeCCcccccCCCcCCCCCCCCCCCCcccccCCceecCCCe
Q psy11345 198 GNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGDRWVEALNNNYHSLCFNCSSPSSPALSGAKPYGTQNTIKSTSGT 277 (282)
Q Consensus 198 ~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~g~~~~~~~~~~~~~~g~ 277 (282)
-+.+.|.+.|..||+.+|.++|+..|..|+..|. ..++.+.++.|.++||+|+.|++.|....+|| +.|.+
T Consensus 232 lGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~--G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~-------E~Dmk 302 (332)
T KOG2272|consen 232 LGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIG--GDVVSALNKAWCVECFSCSTCDKKLTQKNKFY-------EFDMK 302 (332)
T ss_pred cchhhhhhcCchhHHHHHHHHhhhhheecCCccC--ccHHHHhhhhhcccccccccccccccccccee-------eeccc
Confidence 9888999999999999999999999999999997 45888999999999999999999976666666 88888
Q ss_pred eecC
Q psy11345 278 IVCL 281 (282)
Q Consensus 278 ~~C~ 281 (282)
++|+
T Consensus 303 P~CK 306 (332)
T KOG2272|consen 303 PVCK 306 (332)
T ss_pred hHHH
Confidence 8886
No 3
>KOG1044|consensus
Probab=99.91 E-value=1.5e-25 Score=206.75 Aligned_cols=156 Identities=27% Similarity=0.575 Sum_probs=139.3
Q ss_pred cccCccccCceeecCCcccCcCCcccccCCCCCCCCCCCceecC---------------------CccccccccccccCC
Q psy11345 115 GQCYQQIRGPFITALGKIWCPDHFLCVRPQCKRPLQDIGFVEED---------------------SGLYCEFCFEQYLAP 173 (282)
Q Consensus 115 ~~C~~~I~~~~v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~---------------------~~~yC~~c~~~~~~~ 173 (282)
..|...|.+.+|.++|++||+.||.|+ .|..++....-.... +---|..|...+...
T Consensus 69 ~~c~~~~~gevvsa~gktyh~~cf~cs--~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~g 146 (670)
T KOG1044|consen 69 DDCRAFVEGEVVSTLGKTYHPKCFSCS--TCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNG 146 (670)
T ss_pred cchhhhccceeEecccceeccccceec--ccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhcc
Confidence 779999999999999999999999999 999999765433222 223466677777777
Q ss_pred ceeeecCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCCcEEEeCCcccccCCCcCCC
Q psy11345 174 DCLNAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGDRWVEALNNNYHSLCFNCSS 253 (282)
Q Consensus 174 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 253 (282)
..+.|+++.||+.||+|..|...|.+ +|+.+++.+||+.||.+.|+-+|..|.+.|. .+++.+.+++||+.|-+|..
T Consensus 147 q~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fis--gkvLqag~kh~HPtCARCsR 223 (670)
T KOG1044|consen 147 QALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFIS--GKVLQAGDKHFHPTCARCSR 223 (670)
T ss_pred ceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhh--hhhhhccCcccCcchhhhhh
Confidence 88999999999999999999999964 7899999999999999999999999999998 68999999999999999999
Q ss_pred CCCCCCCCCcccccCCceecCC
Q psy11345 254 PSSPALSGAKPYGTQNTIKSTS 275 (282)
Q Consensus 254 C~~~l~~g~~~~~~~~~~~~~~ 275 (282)
|+.+|.+|++.|+..+.+|+-+
T Consensus 224 CgqmF~eGEEMYlQGs~iWHP~ 245 (670)
T KOG1044|consen 224 CGQMFGEGEEMYLQGSEIWHPD 245 (670)
T ss_pred hccccccchheeeccccccCCc
Confidence 9999999999999999999876
No 4
>KOG1703|consensus
Probab=99.90 E-value=4.3e-25 Score=209.90 Aligned_cols=161 Identities=42% Similarity=0.859 Sum_probs=149.5
Q ss_pred CCcccccCccccC-ceeecCCcccCcCCcccccCCCCCCCCCCCceecCCccccccccccccCCce-----------eee
Q psy11345 111 VPLCGQCYQQIRG-PFITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYLAPDC-----------LNA 178 (282)
Q Consensus 111 ~~~C~~C~~~I~~-~~v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~-----------~~~ 178 (282)
.+.|..|++.|.+ +++.++++.||+.+|.|. .|...+....+...+|.+||..|+...+.+.| |.+
T Consensus 303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~--~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a 380 (479)
T KOG1703|consen 303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCE--VCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCA 380 (479)
T ss_pred cccccccccCcccceeEeeccccccccceeec--cccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhh
Confidence 3899999999999 999999999999999999 99999999999999999999999998888744 778
Q ss_pred cCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCCcEEEeCCcccccCCCcCCCCCCCC
Q psy11345 179 IGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGDRWVEALNNNYHSLCFNCSSPSSPA 258 (282)
Q Consensus 179 ~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 258 (282)
++..||++||.|..|++.|.+..|++.++.+||+.||++++.++|..|+++|..++..+.+++..||..||+|..|.+.
T Consensus 381 ~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~- 459 (479)
T KOG1703|consen 381 LGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKK- 459 (479)
T ss_pred ccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhcc-
Confidence 8999999999999999999999999999999999999999999999999999988999999999999999999999999
Q ss_pred CCCCcccccCCceecCCCeeecC
Q psy11345 259 LSGAKPYGTQNTIKSTSGTIVCL 281 (282)
Q Consensus 259 ~~g~~~~~~~~~~~~~~g~~~C~ 281 (282)
+.++.|+ ...++++|.
T Consensus 460 l~~~~~~-------~~~~~p~c~ 475 (479)
T KOG1703|consen 460 LTKKTFF-------ETLDKPLCQ 475 (479)
T ss_pred ccCCcee-------ecCCccccc
Confidence 6666566 777777775
No 5
>KOG2272|consensus
Probab=99.90 E-value=1.4e-26 Score=194.01 Aligned_cols=160 Identities=29% Similarity=0.628 Sum_probs=135.5
Q ss_pred CCCcccccCccc--cCceeecCCcccCcCCcccccCCCCCCCCCCCceecCCccccccccccccCCc-----------ee
Q psy11345 110 RVPLCGQCYQQI--RGPFITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYLAPD-----------CL 176 (282)
Q Consensus 110 ~~~~C~~C~~~I--~~~~v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~-----------~~ 176 (282)
...+|.+|.... ..++|...|..||..||.|+ +|-.|+.+..||..+|+.||+.+++-++++- ++
T Consensus 11 ~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCA--QCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVi 88 (332)
T KOG2272|consen 11 ANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCA--QCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVI 88 (332)
T ss_pred HHHHHHHHhccCCchhhhhccCchhhHHHHHHHH--HhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHH
Confidence 446899999887 46789999999999999999 9999999999999999999999999999983 37
Q ss_pred eecCccccccCccCCccCcccCCCCeeeeCCe------------------------------------------------
Q psy11345 177 NAIGKHYHPECFTCAYCGKLFGNNPFFLEEGL------------------------------------------------ 208 (282)
Q Consensus 177 ~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~------------------------------------------------ 208 (282)
.+.+..||+.||+|..|++.|.+..|+...|.
T Consensus 89 kamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~ 168 (332)
T KOG2272|consen 89 KAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTT 168 (332)
T ss_pred HhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceeccc
Confidence 78899999999999999888876555544444
Q ss_pred ---------------ecCHhhhhcccCCCCccCCCccccCCcEEEeCCcccccCCCcCCCCCCCCCCCCcccccCCceec
Q psy11345 209 ---------------PYCENDWNDLFTTKCFACGFPIEAGDRWVEALNNNYHSLCFNCSSPSSPALSGAKPYGTQNTIKS 273 (282)
Q Consensus 209 ---------------~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~g~~~~~~~~~~~~ 273 (282)
+||..|+.++-.+.|..|++||. +++|.++|++||.++|+|+.|.++|+.- +.++
T Consensus 169 C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe--ervi~amgKhWHveHFvCa~CekPFlGH--------rHYE 238 (332)
T KOG2272|consen 169 CGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE--ERVIFAMGKHWHVEHFVCAKCEKPFLGH--------RHYE 238 (332)
T ss_pred ccccccchhhhhccceeccccccccCCcccccccCchH--HHHHHHhccccchhheeehhcCCcccch--------hhhh
Confidence 55555555555688999999998 8899999999999999999999996543 4668
Q ss_pred CCCeeecC
Q psy11345 274 TSGTIVCL 281 (282)
Q Consensus 274 ~~g~~~C~ 281 (282)
.+|..||.
T Consensus 239 kkGlaYCe 246 (332)
T KOG2272|consen 239 KKGLAYCE 246 (332)
T ss_pred hcCchhHH
Confidence 89999985
No 6
>KOG4577|consensus
Probab=99.81 E-value=7.4e-22 Score=168.44 Aligned_cols=117 Identities=27% Similarity=0.523 Sum_probs=106.5
Q ss_pred CccccccccccccCCceeeecCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCCcEEE
Q psy11345 159 SGLYCEFCFEQYLAPDCLNAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGDRWVE 238 (282)
Q Consensus 159 ~~~yC~~c~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~ 238 (282)
..+.|..|.+.|.++..+++++++||..|++|++|+.+|.. .+|.+++.+||+++|.++|+++|..|...|.+...+.+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk 110 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK 110 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence 56889999999999999999999999999999999999975 56788999999999999999999999999998655557
Q ss_pred eCCcccccCCCcCCCCCCCCCCCCcccccCCceecCCCeeecCC
Q psy11345 239 ALNNNYHSLCFNCSSPSSPALSGAKPYGTQNTIKSTSGTIVCLE 282 (282)
Q Consensus 239 ~~~~~~H~~Cf~C~~C~~~l~~g~~~~~~~~~~~~~~g~~~C~~ 282 (282)
+.+..||..||.|.+|++.|..|++||+ ..|++++||+
T Consensus 111 Aqd~VYHl~CF~C~iC~R~L~TGdEFYL------meD~rLvCK~ 148 (383)
T KOG4577|consen 111 AQDFVYHLHCFACFICKRQLATGDEFYL------MEDARLVCKD 148 (383)
T ss_pred hhcceeehhhhhhHhhhcccccCCeeEE------eccceeehhh
Confidence 9999999999999999999999999995 4568999974
No 7
>KOG1044|consensus
Probab=99.80 E-value=6e-20 Score=169.92 Aligned_cols=158 Identities=25% Similarity=0.562 Sum_probs=133.9
Q ss_pred CcccccCccccCceeecCCcccCcCCcccccCCCCCCCCCCCceecCC-ccccccccccccCCceeeecCccccccCccC
Q psy11345 112 PLCGQCYQQIRGPFITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDS-GLYCEFCFEQYLAPDCLNAIGKHYHPECFTC 190 (282)
Q Consensus 112 ~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~-~~yC~~c~~~~~~~~~~~~~~~~~H~~Cf~C 190 (282)
..|.+|++.-.|+++++.++.||..||.|. .|+..|...+||.+++ +.||..........+++.++|+.||+.||.|
T Consensus 17 i~c~~c~~kc~gevlrv~d~~fhi~cf~c~--~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~c 94 (670)
T KOG1044|consen 17 IKCDKCRKKCSGEVLRVNDNHFHINCFQCK--KCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSC 94 (670)
T ss_pred eehhhhCCccccceeEeeccccceeeeecc--ccCCCcccccceecccceeecccchhhhccceeEecccceecccccee
Confidence 489999999999999999999999999999 9999999999997765 5677755555566688999999999999999
Q ss_pred CccCcccCCCC-eeeeCCeecCHhhhhcc--------cCCCCccCCCccccCCcEEEeCCcccccCCCcCCCCCCCCCCC
Q psy11345 191 AYCGKLFGNNP-FFLEEGLPYCENDWNDL--------FTTKCFACGFPIEAGDRWVEALNNNYHSLCFNCSSPSSPALSG 261 (282)
Q Consensus 191 ~~C~~~l~~~~-f~~~~~~~yC~~c~~~~--------~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~g 261 (282)
+.|+.++..+. ..+......|+.|..-. ....|++|++.|..| ..+.+.++.||..||+|..|+.. |.|
T Consensus 95 s~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~g-q~llald~qwhv~cfkc~~c~~v-L~g 172 (670)
T KOG1044|consen 95 STCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNG-QALLALDKQWHVSCFKCKSCSAV-LNG 172 (670)
T ss_pred cccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhcc-ceeeeeccceeeeeeehhhhccc-ccc
Confidence 99999997666 55566678899995432 224799999999875 57789999999999999999999 777
Q ss_pred CcccccCCceecCCCeeecC
Q psy11345 262 AKPYGTQNTIKSTSGTIVCL 281 (282)
Q Consensus 262 ~~~~~~~~~~~~~~g~~~C~ 281 (282)
+ +..+||.+||.
T Consensus 173 e--------y~skdg~pyce 184 (670)
T KOG1044|consen 173 E--------YMSKDGVPYCE 184 (670)
T ss_pred e--------eeccCCCcchh
Confidence 6 34788888885
No 8
>KOG1701|consensus
Probab=99.78 E-value=7.1e-21 Score=170.71 Aligned_cols=110 Identities=32% Similarity=0.744 Sum_probs=100.1
Q ss_pred ccccccccccCC-ceeeecCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCCcEEEeC
Q psy11345 162 YCEFCFEQYLAP-DCLNAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGDRWVEAL 240 (282)
Q Consensus 162 yC~~c~~~~~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~ 240 (282)
.|..|.+.+++. ....|+++.||..||+|..|++.|.+..||..++++||+.||.... .||..|+++|. |++++++
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~--d~iLrA~ 352 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-EKCNKCGEPIM--DRILRAL 352 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-HHHhhhhhHHH--HHHHHhc
Confidence 788888888776 3478899999999999999999999999999999999999998876 89999999999 8999999
Q ss_pred CcccccCCCcCCCCCCCCCCCCcccccCCceecCCCeeecC
Q psy11345 241 NNNYHSLCFNCSSPSSPALSGAKPYGTQNTIKSTSGTIVCL 281 (282)
Q Consensus 241 ~~~~H~~Cf~C~~C~~~l~~g~~~~~~~~~~~~~~g~~~C~ 281 (282)
|+.||+.||+|.+|.+. |+|..|.+ +.++++||.
T Consensus 353 GkayHp~CF~Cv~C~r~-ldgipFtv------d~~n~v~Cv 386 (468)
T KOG1701|consen 353 GKAYHPGCFTCVVCARC-LDGIPFTV------DSQNNVYCV 386 (468)
T ss_pred ccccCCCceEEEEeccc-cCCccccc------cCCCceeee
Confidence 99999999999999999 88887774 667788886
No 9
>KOG4577|consensus
Probab=99.69 E-value=9.2e-19 Score=149.62 Aligned_cols=111 Identities=26% Similarity=0.688 Sum_probs=98.7
Q ss_pred CCCcccccCccccCce-eecCCcccCcCCcccccCCCCCCCCCCCceecCCccccccccccccCCce-------------
Q psy11345 110 RVPLCGQCYQQIRGPF-ITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYLAPDC------------- 175 (282)
Q Consensus 110 ~~~~C~~C~~~I~~~~-v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~------------- 175 (282)
..++|++|.+.|.++| ++++++.||..|++|+ +|..+|.+ .+|.+++..||+.++.+.|+.+|
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs--~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVV 108 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCS--DCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVV 108 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchh--hhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHH
Confidence 4579999999999998 5899999999999999 99999987 68899999999999999999977
Q ss_pred eeecCccccccCccCCccCcccCCCC-eee-eCCeecCHhhhhcccCCCC
Q psy11345 176 LNAIGKHYHPECFTCAYCGKLFGNNP-FFL-EEGLPYCENDWNDLFTTKC 223 (282)
Q Consensus 176 ~~~~~~~~H~~Cf~C~~C~~~l~~~~-f~~-~~~~~yC~~c~~~~~~~~C 223 (282)
.+|.+.+||.+||.|..|+++|.+++ ||+ .|.++.|+.+|++.-..-|
T Consensus 109 RkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 109 RKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred HHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 45789999999999999999997766 665 6789999999988665555
No 10
>KOG1703|consensus
Probab=99.63 E-value=2.4e-16 Score=150.13 Aligned_cols=157 Identities=21% Similarity=0.366 Sum_probs=131.7
Q ss_pred ccccCccccCceeecCCcccCcCCcccccCCCCCCCCCCCceecCCc------------cccccccccccCCceeeecCc
Q psy11345 114 CGQCYQQIRGPFITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDSG------------LYCEFCFEQYLAPDCLNAIGK 181 (282)
Q Consensus 114 C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~~------------~yC~~c~~~~~~~~~~~~~~~ 181 (282)
|..+..++.+..+.+....||+..|.|.. .+...+....++..... +.|..|...+.....+.+.++
T Consensus 246 ~~~~~~p~~~p~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~c~~c~~~i~~~~~i~~~~~ 324 (479)
T KOG1703|consen 246 SASMDSPECQPLVSAPRPASEGLHMKVEK-ELPLLLVESEALKKLREEEKPAEYHNVTRPLCLSCNQKIRSVKVIVALGK 324 (479)
T ss_pred CcccCCCccCcceeccccccccccccccc-ccchhhcccccccccccccccccccccccccccccccCcccceeEeeccc
Confidence 66677778788888999999999999973 67777766666554443 556666677666678899999
Q ss_pred cccccCccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCCcEEEeCCcccccCCCcCCCCCCCCCCC
Q psy11345 182 HYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGDRWVEALNNNYHSLCFNCSSPSSPALSG 261 (282)
Q Consensus 182 ~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~g 261 (282)
.||+.+|.|..|+..+....|...+|++||..|+.+.+.++|.+|.++|. ++.|.+.++.||++||.|..|.+. +.+
T Consensus 325 ~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~--~~~v~a~~~~wH~~cf~C~~C~~~-~~~ 401 (479)
T KOG1703|consen 325 EWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPIL--EEGVCALGRLWHPECFVCADCGKP-LKN 401 (479)
T ss_pred cccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchH--HhHhhhccCeechhceeeecccCC-CCC
Confidence 99999999999999999888988999999999999999999999999999 778889999999999999999777 555
Q ss_pred CcccccCCceecCCCeeecC
Q psy11345 262 AKPYGTQNTIKSTSGTIVCL 281 (282)
Q Consensus 262 ~~~~~~~~~~~~~~g~~~C~ 281 (282)
..|| ..+|.+||.
T Consensus 402 ~~~~-------~~~~~pyce 414 (479)
T KOG1703|consen 402 SSFF-------ESDGEPYCE 414 (479)
T ss_pred Cccc-------ccCCccchh
Confidence 5555 777777774
No 11
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.25 E-value=2.4e-12 Score=87.16 Aligned_cols=56 Identities=39% Similarity=0.982 Sum_probs=50.1
Q ss_pred ccccCccccCc-e-eecCCcccCcCCcccccCCCCCCCCCCCceecCCcccccccccccc
Q psy11345 114 CGQCYQQIRGP-F-ITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYL 171 (282)
Q Consensus 114 C~~C~~~I~~~-~-v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~ 171 (282)
|.+|+++|.+. . +.++|+.||++||+|. .|+++|....++..++++||+.|+.+.|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~--~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCS--KCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBET--TTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccC--CCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 78999999753 3 4699999999999999 9999999988999999999999997653
No 12
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.24 E-value=8e-12 Score=84.55 Aligned_cols=57 Identities=35% Similarity=0.952 Sum_probs=48.7
Q ss_pred cccccccccCCcee-eecCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhccc
Q psy11345 163 CEFCFEQYLAPDCL-NAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLF 219 (282)
Q Consensus 163 C~~c~~~~~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~ 219 (282)
|..|.+.+.....+ .+.++.||++||+|..|+++|....|+..++++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 45566666655544 6899999999999999999999888999999999999998875
No 13
>KOG1700|consensus
Probab=98.97 E-value=7.2e-11 Score=99.79 Aligned_cols=112 Identities=24% Similarity=0.513 Sum_probs=90.0
Q ss_pred cccccccccccCCceeeecCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhcccC--------------------
Q psy11345 161 LYCEFCFEQYLAPDCLNAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFT-------------------- 220 (282)
Q Consensus 161 ~yC~~c~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~-------------------- 220 (282)
.-|..|.+.++..+-+...|..||..||+|..|++.|....+...++.+||..||...++
T Consensus 8 ~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKDG 87 (200)
T ss_pred chhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCccc
Confidence 357777777777766667899999999999999999999889999999999996555443
Q ss_pred ---------------------CCCccCCCccccCCcEEEeCCcccccCCCcCCCCCCCCCCCCcccccCCceecCCCeee
Q psy11345 221 ---------------------TKCFACGFPIEAGDRWVEALNNNYHSLCFNCSSPSSPALSGAKPYGTQNTIKSTSGTIV 279 (282)
Q Consensus 221 ---------------------~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~g~~~~~~~~~~~~~~g~~~ 279 (282)
..|.+|++.+.+.+ .+...+..||..||+|..|+..| +...+...+|.++
T Consensus 88 ~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E-k~~~~~~~~hk~cfrc~~~~~~l--------s~~~~~~~~g~l~ 158 (200)
T KOG1700|consen 88 KSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE-KVTGNGLEFHKSCFRCTHCGKKL--------SPKNYAALEGVLY 158 (200)
T ss_pred ccccccccccchhHHhhhccccccccccceeeehH-HHhhhhhhhhhhheeeccccccc--------CCcchhhcCCccc
Confidence 36999999998644 45578999999999999999994 3334556666777
Q ss_pred cC
Q psy11345 280 CL 281 (282)
Q Consensus 280 C~ 281 (282)
|+
T Consensus 159 ~~ 160 (200)
T KOG1700|consen 159 CK 160 (200)
T ss_pred cc
Confidence 65
No 14
>smart00735 ZM ZASP-like motif. Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules.
Probab=98.86 E-value=7.3e-10 Score=62.07 Aligned_cols=26 Identities=65% Similarity=1.054 Sum_probs=23.5
Q ss_pred ccccccccCCcccCchhHHHHHHHHh
Q psy11345 8 QLVNKQYNSPVGIYSEESIAETLSAQ 33 (282)
Q Consensus 8 ~~~~~qyn~p~~lys~~ni~~~~~~~ 33 (282)
+|+|+|||+|+||||++||+++|.+|
T Consensus 1 ~vv~~qyn~P~glys~~n~~~~l~~~ 26 (26)
T smart00735 1 RVVHKQYNSPIGLYSSENIAETLQGQ 26 (26)
T ss_pred CccccccCCCCCCCCcccHHHhhccC
Confidence 58999999999999999999998754
No 15
>KOG1700|consensus
Probab=98.80 E-value=1.2e-09 Score=92.41 Aligned_cols=106 Identities=27% Similarity=0.680 Sum_probs=88.2
Q ss_pred CcccccCcccc-CceeecCCcccCcCCcccccCCCCCCCCCCCceecCCccccccccccccCC-----------------
Q psy11345 112 PLCGQCYQQIR-GPFITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYLAP----------------- 173 (282)
Q Consensus 112 ~~C~~C~~~I~-~~~v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~----------------- 173 (282)
..|..|++.+. -..+...|..||+.||+|. .|...|....+...++.+||..|+-.++++
T Consensus 8 ~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~--~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEKVQKDGVDFHKECFKCE--KCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK 85 (200)
T ss_pred chhhhccCcchHHHHHhccCcchhhhHHhcc--ccccccccccccccccccccccchHhhhCcccccccccccccCCCCc
Confidence 48999999995 3455688999999999999 999999999999999999999975433332
Q ss_pred ------------------------ce------------eeecCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhc
Q psy11345 174 ------------------------DC------------LNAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWND 217 (282)
Q Consensus 174 ------------------------~~------------~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~ 217 (282)
.| +...+..||..||+|+.|+..|....+...++.+||..++.+
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~ 165 (200)
T KOG1700|consen 86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQ 165 (200)
T ss_pred ccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhhe
Confidence 00 234578999999999999999999889998999999888776
Q ss_pred cc
Q psy11345 218 LF 219 (282)
Q Consensus 218 ~~ 219 (282)
++
T Consensus 166 ~~ 167 (200)
T KOG1700|consen 166 LF 167 (200)
T ss_pred ee
Confidence 55
No 16
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.56 E-value=6e-08 Score=59.59 Aligned_cols=37 Identities=41% Similarity=0.872 Sum_probs=33.3
Q ss_pred CCccCCCccccCCcEEEeCCcccccCCCcCCCCCCCC
Q psy11345 222 KCFACGFPIEAGDRWVEALNNNYHSLCFNCSSPSSPA 258 (282)
Q Consensus 222 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 258 (282)
+|.+|+++|..++..+.+.++.||+.||+|..|+++|
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcC
Confidence 5899999998655788899999999999999999984
No 17
>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=98.41 E-value=1.9e-07 Score=57.31 Aligned_cols=36 Identities=44% Similarity=1.066 Sum_probs=32.3
Q ss_pred cccccCccccC--ceeecCCcccCcCCcccccCCCCCCCC
Q psy11345 113 LCGQCYQQIRG--PFITALGKIWCPDHFLCVRPQCKRPLQ 150 (282)
Q Consensus 113 ~C~~C~~~I~~--~~v~~~~~~~H~~Cf~C~~~~C~~~l~ 150 (282)
.|.+|+++|.+ ..+.++++.||++||+|. .|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~--~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCS--KCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCc--ccCCcCc
Confidence 48999999976 678899999999999999 9999885
No 18
>KOG0490|consensus
Probab=97.58 E-value=5.7e-06 Score=71.53 Aligned_cols=90 Identities=28% Similarity=0.616 Sum_probs=76.1
Q ss_pred eeeecCccccccCccCCccCcccC--CCCeeeeCCeecCHhhhhc--ccCCCCccCCCccccCCcEEEeCCcccccCCCc
Q psy11345 175 CLNAIGKHYHPECFTCAYCGKLFG--NNPFFLEEGLPYCENDWND--LFTTKCFACGFPIEAGDRWVEALNNNYHSLCFN 250 (282)
Q Consensus 175 ~~~~~~~~~H~~Cf~C~~C~~~l~--~~~f~~~~~~~yC~~c~~~--~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~ 250 (282)
-+.+.+..||..|..|..|...|. ...|.. ++..||..++.. .+..+|.+|.+.+...+.+..+..+. |..||.
T Consensus 11 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~ 88 (235)
T KOG0490|consen 11 LLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFA 88 (235)
T ss_pred HhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccc
Confidence 344458999999999999999997 444656 999999999998 77889999999997666666777777 999999
Q ss_pred CCCCCCCCCCCCcccc
Q psy11345 251 CSSPSSPALSGAKPYG 266 (282)
Q Consensus 251 C~~C~~~l~~g~~~~~ 266 (282)
|..|...++.+.++.+
T Consensus 89 ~r~~la~~~~~~e~rV 104 (235)
T KOG0490|consen 89 CRECLALLLTGDEFRV 104 (235)
T ss_pred hHHHHhhcCCCCeeee
Confidence 9999999888887763
No 19
>KOG1702|consensus
Probab=97.18 E-value=4.4e-05 Score=63.32 Aligned_cols=60 Identities=20% Similarity=0.477 Sum_probs=51.5
Q ss_pred cccccccccccCCceeeecCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhcccC
Q psy11345 161 LYCEFCFEQYLAPDCLNAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFT 220 (282)
Q Consensus 161 ~yC~~c~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~ 220 (282)
.-|+.|.+..+..+-++.+++.||..||+|..|+..|....|...+.++||..+|.+..+
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 446777777777777888899999999999999999988888889999999999987553
No 20
>KOG1702|consensus
Probab=96.22 E-value=0.00071 Score=56.26 Aligned_cols=59 Identities=20% Similarity=0.390 Sum_probs=51.0
Q ss_pred CcccccCccccC-ceeecCCcccCcCCcccccCCCCCCCCCCCceecCCccccccccccccC
Q psy11345 112 PLCGQCYQQIRG-PFITALGKIWCPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYLA 172 (282)
Q Consensus 112 ~~C~~C~~~I~~-~~v~~~~~~~H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~ 172 (282)
..|..|++.+.- +-|+.+++.||..||.|. .|+-+|....+-..+.++||..+|-...+
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce--~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCE--VCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheee--eccCChhhhhccccccCCCcCccccccee
Confidence 467889998863 568999999999999999 99999999888889999999999965443
No 21
>KOG0490|consensus
Probab=96.04 E-value=0.0013 Score=56.62 Aligned_cols=100 Identities=23% Similarity=0.508 Sum_probs=74.3
Q ss_pred ccCccccCce-eecCCcccCcCCcccccCCCCCCCC-CCCceecCCcccccccccc--ccCCce-------------eee
Q psy11345 116 QCYQQIRGPF-ITALGKIWCPDHFLCVRPQCKRPLQ-DIGFVEEDSGLYCEFCFEQ--YLAPDC-------------LNA 178 (282)
Q Consensus 116 ~C~~~I~~~~-v~~~~~~~H~~Cf~C~~~~C~~~l~-~~~~~~~~~~~yC~~c~~~--~~~~~~-------------~~~ 178 (282)
+|+..|.+.+ +.+.+..||..|..|. .|...|. ....+..++..||...+.. .+...+ .++
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~ 78 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCA--ECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERA 78 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhh--hhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHh
Confidence 4778888765 5677999999999999 9999996 3344444999999999886 333222 345
Q ss_pred cCccccccCccCCccCcccCCCC-eeeeCC-eecCHhhhhcc
Q psy11345 179 IGKHYHPECFTCAYCGKLFGNNP-FFLEEG-LPYCENDWNDL 218 (282)
Q Consensus 179 ~~~~~H~~Cf~C~~C~~~l~~~~-f~~~~~-~~yC~~c~~~~ 218 (282)
..+. |..||.|..|...+.... +.+... +..|..++.+.
T Consensus 79 f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 79 FEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 5666 999999999988775544 666654 88898887553
No 22
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=83.39 E-value=0.65 Score=30.53 Aligned_cols=38 Identities=29% Similarity=0.586 Sum_probs=28.6
Q ss_pred CCCCccCCCccccCCcEEE--eCCcccccCCC----cCCC--CCCC
Q psy11345 220 TTKCFACGFPIEAGDRWVE--ALNNNYHSLCF----NCSS--PSSP 257 (282)
Q Consensus 220 ~~~C~~C~~~I~~~~~~~~--~~~~~~H~~Cf----~C~~--C~~~ 257 (282)
+.+|..|+++|.++|.+|. .-+..||.+|+ .|.. |+..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~ 50 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTG 50 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCC
Confidence 5789999999986665654 35899999999 3665 5554
No 23
>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=82.18 E-value=1.1 Score=33.39 Aligned_cols=30 Identities=30% Similarity=0.470 Sum_probs=20.5
Q ss_pred CCCccCCCccccCCcEEEeCCcccccCCCc
Q psy11345 221 TKCFACGFPIEAGDRWVEALNNNYHSLCFN 250 (282)
Q Consensus 221 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~ 250 (282)
..|..|+++|..+..++...|..+|..|++
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 578888888875433444456778888764
No 24
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=81.83 E-value=0.36 Score=35.97 Aligned_cols=32 Identities=31% Similarity=0.664 Sum_probs=26.8
Q ss_pred CCccCCCccccCCcEEEeCCcccccCCCcCCC
Q psy11345 222 KCFACGFPIEAGDRWVEALNNNYHSLCFNCSS 253 (282)
Q Consensus 222 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 253 (282)
+|..|+++|..|+.+-...+..-|-.||+=..
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 69999999998887777788889999997544
No 25
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=80.59 E-value=1.7 Score=29.64 Aligned_cols=47 Identities=17% Similarity=0.356 Sum_probs=23.9
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCC
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGD 234 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~ 234 (282)
.+|+.|..-|..--....=..+||..|....++..|..|..|....|
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHH
Confidence 57888877765421222335789999999999999999999987544
No 26
>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=76.28 E-value=1.1 Score=27.01 Aligned_cols=28 Identities=21% Similarity=0.433 Sum_probs=22.0
Q ss_pred ccccCccccCc--eeecCCcccCcCCcccc
Q psy11345 114 CGQCYQQIRGP--FITALGKIWCPDHFLCV 141 (282)
Q Consensus 114 C~~C~~~I~~~--~v~~~~~~~H~~Cf~C~ 141 (282)
|+-||.+|.|+ .++..++.||.-|-+|.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~ 30 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCL 30 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHH
Confidence 77899999864 36788899998777664
No 27
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=73.67 E-value=4.2 Score=25.22 Aligned_cols=39 Identities=26% Similarity=0.503 Sum_probs=26.9
Q ss_pred CCccCcccCC-CCeeeeC-CeecCHhhhhccc--CCCCccCCC
Q psy11345 190 CAYCGKLFGN-NPFFLEE-GLPYCENDWNDLF--TTKCFACGF 228 (282)
Q Consensus 190 C~~C~~~l~~-~~f~~~~-~~~yC~~c~~~~~--~~~C~~C~~ 228 (282)
|..|...+.. ..+++.. |.++|..|..++. ...|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 6677777732 2344444 8899999998877 567887764
No 28
>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=73.48 E-value=1.6 Score=26.31 Aligned_cols=29 Identities=31% Similarity=0.437 Sum_probs=20.6
Q ss_pred CccCCCccccCCcEEEeCCcccccCCCcC
Q psy11345 223 CFACGFPIEAGDRWVEALNNNYHSLCFNC 251 (282)
Q Consensus 223 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C 251 (282)
|..|+++|.....++...++.||.-|-.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC 29 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTC 29 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHH
Confidence 67899999854455678889888554444
No 29
>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=67.75 E-value=3.5 Score=30.13 Aligned_cols=37 Identities=24% Similarity=0.468 Sum_probs=27.2
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCcccc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEA 232 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~ 232 (282)
-+|..|+..+.. .+..||..|..+. -.|+-|++.|..
T Consensus 45 ~~C~~CK~~v~q------~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 45 SKCKICKTKVHQ------PGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred cccccccccccc------CCCccChhhhccc--CcccccCCeecc
Confidence 368888876532 2557999997765 589999999973
No 30
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=65.91 E-value=3.9 Score=24.50 Aligned_cols=25 Identities=28% Similarity=0.734 Sum_probs=18.7
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhh
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWN 216 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~ 216 (282)
+.|..|+.. .|...+|..||..|..
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 458888774 4677899999988754
No 31
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=65.49 E-value=3.5 Score=32.29 Aligned_cols=23 Identities=26% Similarity=0.628 Sum_probs=18.6
Q ss_pred cCCccCcccCCCCeeeeCCeecCHhhhh
Q psy11345 189 TCAYCGKLFGNNPFFLEEGLPYCENDWN 216 (282)
Q Consensus 189 ~C~~C~~~l~~~~f~~~~~~~yC~~c~~ 216 (282)
.|..|+.+| |.++|.+||..|-.
T Consensus 30 hCp~Cg~PL-----F~KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL-----FRKDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc-----eeeCCeEECCCCCc
Confidence 478899988 45999999988853
No 32
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=64.55 E-value=4.7 Score=26.18 Aligned_cols=29 Identities=34% Similarity=0.723 Sum_probs=23.3
Q ss_pred cCCccCcccCCCC-eeeeCCeecCHhhhhcc
Q psy11345 189 TCAYCGKLFGNNP-FFLEEGLPYCENDWNDL 218 (282)
Q Consensus 189 ~C~~C~~~l~~~~-f~~~~~~~yC~~c~~~~ 218 (282)
.|..|+..++-.. +-+.|| ..|.+|+.++
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 4899999987655 667788 6899999876
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=62.69 E-value=5.9 Score=21.71 Aligned_cols=10 Identities=40% Similarity=0.869 Sum_probs=5.2
Q ss_pred CCccCCCccc
Q psy11345 222 KCFACGFPIE 231 (282)
Q Consensus 222 ~C~~C~~~I~ 231 (282)
.|..|+..|.
T Consensus 4 ~Cp~Cg~~~~ 13 (26)
T PF13248_consen 4 FCPNCGAEID 13 (26)
T ss_pred CCcccCCcCC
Confidence 4555555444
No 34
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=62.24 E-value=2.2 Score=31.25 Aligned_cols=37 Identities=27% Similarity=0.548 Sum_probs=27.4
Q ss_pred CCCccCCCccccCCcEEEeCCcccccCCCcCCCCCCC
Q psy11345 221 TKCFACGFPIEAGDRWVEALNNNYHSLCFNCSSPSSP 257 (282)
Q Consensus 221 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~ 257 (282)
-+|+.|+++|..|+++.......-|-+||.=+.=+++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCc
Confidence 4799999999888877767777888888865543333
No 35
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.63 E-value=10 Score=25.34 Aligned_cols=17 Identities=29% Similarity=0.614 Sum_probs=6.6
Q ss_pred CHhhhhcccCCCCccCC
Q psy11345 211 CENDWNDLFTTKCFACG 227 (282)
Q Consensus 211 C~~c~~~~~~~~C~~C~ 227 (282)
|..|-.+....+|..|+
T Consensus 39 C~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 39 CEKCRKQSNPYTCPKCG 55 (59)
T ss_pred chhHHhcCCceECCCCC
Confidence 33333333333444444
No 36
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=58.55 E-value=9.4 Score=38.21 Aligned_cols=38 Identities=21% Similarity=0.432 Sum_probs=22.0
Q ss_pred cCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccC
Q psy11345 189 TCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAG 233 (282)
Q Consensus 189 ~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~ 233 (282)
+|..|+..... +..||..|-..+-...|..|+..+..+
T Consensus 3 ~Cp~Cg~~n~~-------~akFC~~CG~~l~~~~Cp~CG~~~~~~ 40 (645)
T PRK14559 3 ICPQCQFENPN-------NNRFCQKCGTSLTHKPCPQCGTEVPVD 40 (645)
T ss_pred cCCCCCCcCCC-------CCccccccCCCCCCCcCCCCCCCCCcc
Confidence 45666654432 334677775554445677777776644
No 37
>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=58.26 E-value=2.9 Score=29.76 Aligned_cols=30 Identities=30% Similarity=0.540 Sum_probs=19.5
Q ss_pred CCCccCCCccccCCcEE----Ee-CC-----cccccCCCc
Q psy11345 221 TKCFACGFPIEAGDRWV----EA-LN-----NNYHSLCFN 250 (282)
Q Consensus 221 ~~C~~C~~~I~~~~~~~----~~-~~-----~~~H~~Cf~ 250 (282)
.+|..|+..|..|+-.+ .. .+ .+||..||.
T Consensus 8 a~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~ 47 (82)
T PF00645_consen 8 AKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFF 47 (82)
T ss_dssp EBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHH
T ss_pred ccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccc
Confidence 47999999998765332 11 22 467889987
No 38
>KOG0320|consensus
Probab=57.61 E-value=6.8 Score=32.35 Aligned_cols=51 Identities=20% Similarity=0.378 Sum_probs=38.3
Q ss_pred ccccccCccCCccCcccCCCC-eeeeCCeecCHhhhhccc--CCCCccCCCccc
Q psy11345 181 KHYHPECFTCAYCGKLFGNNP-FFLEEGLPYCENDWNDLF--TTKCFACGFPIE 231 (282)
Q Consensus 181 ~~~H~~Cf~C~~C~~~l~~~~-f~~~~~~~yC~~c~~~~~--~~~C~~C~~~I~ 231 (282)
..--..+|+|-.|=....... +.-+=|.++|..|..... +.+|..|++.|.
T Consensus 125 ~~~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 125 PLRKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccccccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 334456789999977766554 555668999999987643 469999999887
No 39
>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=56.37 E-value=11 Score=24.96 Aligned_cols=44 Identities=18% Similarity=0.354 Sum_probs=32.5
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhccc--CCCCccCCCcccc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLF--TTKCFACGFPIEA 232 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~--~~~C~~C~~~I~~ 232 (282)
|.|..|+..+.. ......|..||..|..+.+ ...|..|++++..
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 678899888865 4555678999999976544 3478888888753
No 40
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=56.00 E-value=7.9 Score=24.57 Aligned_cols=43 Identities=30% Similarity=0.476 Sum_probs=28.5
Q ss_pred ccCCccCcccCCCCeeeeCCee-cCHhhhhcc--cCCCCccCCCccc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLP-YCENDWNDL--FTTKCFACGFPIE 231 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~-yC~~c~~~~--~~~~C~~C~~~I~ 231 (282)
+.|..|...... ..+..=|.. +|..|+.++ ...+|..|+++|.
T Consensus 3 ~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp SB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 356777776543 223334677 999998876 3579999999985
No 41
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=54.64 E-value=8.8 Score=37.29 Aligned_cols=39 Identities=21% Similarity=0.452 Sum_probs=28.0
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhc-ccCCCCccCCCc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWND-LFTTKCFACGFP 229 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~-~~~~~C~~C~~~ 229 (282)
.+|..|+.+|. |....+.+.|..|-.+ .+...|..|+..
T Consensus 223 ~~C~~C~~~l~---~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSLT---YHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCceE---EecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 56777777663 4556778889999544 456799999864
No 42
>PRK14873 primosome assembly protein PriA; Provisional
Probab=54.33 E-value=8.5 Score=38.72 Aligned_cols=39 Identities=23% Similarity=0.387 Sum_probs=28.5
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFP 229 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~ 229 (282)
++|..|+.+|. |....+.+.|..|-......+|..|+..
T Consensus 393 ~~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 56778887774 3445667889999665566799999875
No 43
>KOG4739|consensus
Probab=53.77 E-value=12 Score=32.27 Aligned_cols=40 Identities=25% Similarity=0.476 Sum_probs=30.3
Q ss_pred ccCcccCCCCeeeeC-CeecCHhhhhcccCCCCccCCCccc
Q psy11345 192 YCGKLFGNNPFFLEE-GLPYCENDWNDLFTTKCFACGFPIE 231 (282)
Q Consensus 192 ~C~~~l~~~~f~~~~-~~~yC~~c~~~~~~~~C~~C~~~I~ 231 (282)
.|...-....||+.. ..++|+.|...-.++.|.-|+++|.
T Consensus 8 ~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 8 KCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred cccccCCCCceeeeechhhhhhhhcccCCccccccccceee
Confidence 343433344577765 7899999998888789999999975
No 44
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=52.77 E-value=2.1 Score=31.50 Aligned_cols=48 Identities=19% Similarity=0.436 Sum_probs=29.5
Q ss_pred ccccccccCCceeeecCccccccCccCCccCcccCCCCeeeeCCeecC
Q psy11345 164 EFCFEQYLAPDCLNAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYC 211 (282)
Q Consensus 164 ~~c~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC 211 (282)
-.|..++.........-..+++.+..|.+|+..|+-.+|.+...-+||
T Consensus 39 y~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C 86 (105)
T COG4357 39 YHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC 86 (105)
T ss_pred HHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc
Confidence 334444444433444556788888889999888876666555543333
No 45
>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=52.21 E-value=8.4 Score=31.07 Aligned_cols=48 Identities=27% Similarity=0.523 Sum_probs=33.1
Q ss_pred CeecCHhhhhcccCCCCccCCCccccCCcEE---EeCCcccccCCCcCCCCCCC
Q psy11345 207 GLPYCENDWNDLFTTKCFACGFPIEAGDRWV---EALNNNYHSLCFNCSSPSSP 257 (282)
Q Consensus 207 ~~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~---~~~~~~~H~~Cf~C~~C~~~ 257 (282)
..-||..|-.+.. ..|..|+-+|. |+-++ ...+..|+.-- -|..|+++
T Consensus 27 ~~~fC~kCG~~tI-~~Cp~C~~~Ir-G~y~v~gv~~~g~~~~~Ps-YC~~CGkp 77 (158)
T PF10083_consen 27 REKFCSKCGAKTI-TSCPNCSTPIR-GDYHVEGVFGLGGHYEAPS-YCHNCGKP 77 (158)
T ss_pred HHHHHHHhhHHHH-HHCcCCCCCCC-CceecCCeeeeCCCCCCCh-hHHhCCCC
Confidence 4568999987765 89999999997 33222 23456666332 27788888
No 46
>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=51.58 E-value=11 Score=27.72 Aligned_cols=25 Identities=32% Similarity=0.527 Sum_probs=10.8
Q ss_pred CCccCcccCCCCeeee-CCeecCHhh
Q psy11345 190 CAYCGKLFGNNPFFLE-EGLPYCEND 214 (282)
Q Consensus 190 C~~C~~~l~~~~f~~~-~~~~yC~~c 214 (282)
|..|+++|....|.+. +|.++...|
T Consensus 81 C~vC~k~l~~~~f~~~p~~~v~H~~C 106 (109)
T PF10367_consen 81 CSVCGKPLGNSVFVVFPCGHVVHYSC 106 (109)
T ss_pred ccCcCCcCCCceEEEeCCCeEEeccc
Confidence 4555555544444333 234443333
No 47
>PF12773 DZR: Double zinc ribbon
Probab=51.06 E-value=19 Score=22.73 Aligned_cols=25 Identities=20% Similarity=0.349 Sum_probs=13.7
Q ss_pred eecCHhhhhccc-----CCCCccCCCcccc
Q psy11345 208 LPYCENDWNDLF-----TTKCFACGFPIEA 232 (282)
Q Consensus 208 ~~yC~~c~~~~~-----~~~C~~C~~~I~~ 232 (282)
..||..|-..+. ...|..|+..+.+
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPP 41 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcC
Confidence 345666644443 1357777776653
No 48
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=50.14 E-value=12 Score=22.13 Aligned_cols=39 Identities=26% Similarity=0.619 Sum_probs=21.0
Q ss_pred CCccCcccCCCCeeee-CCeecCHhhhhccc---CCCCccCCCc
Q psy11345 190 CAYCGKLFGNNPFFLE-EGLPYCENDWNDLF---TTKCFACGFP 229 (282)
Q Consensus 190 C~~C~~~l~~~~f~~~-~~~~yC~~c~~~~~---~~~C~~C~~~ 229 (282)
|..|...+.. .+... =+..+|..|....+ ..+|..|+..
T Consensus 2 C~iC~~~~~~-~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFRE-PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhC-ceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 5566665522 22222 45667777765443 2357666654
No 49
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=49.24 E-value=2.7 Score=24.99 Aligned_cols=28 Identities=18% Similarity=0.420 Sum_probs=20.3
Q ss_pred CCccCcccCCCCeeeeCCeecCHhhhhc
Q psy11345 190 CAYCGKLFGNNPFFLEEGLPYCENDWND 217 (282)
Q Consensus 190 C~~C~~~l~~~~f~~~~~~~yC~~c~~~ 217 (282)
|..|+.++....-....+..+|..|+..
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 8889988876665566788999998764
No 50
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=48.66 E-value=12 Score=37.57 Aligned_cols=77 Identities=21% Similarity=0.549 Sum_probs=57.7
Q ss_pred CCCcccccCccccCceeecCCcccCcCCcccccCCCCCCCC-------CCCceecCCccccccccccccCCceeeecCcc
Q psy11345 110 RVPLCGQCYQQIRGPFITALGKIWCPDHFLCVRPQCKRPLQ-------DIGFVEEDSGLYCEFCFEQYLAPDCLNAIGKH 182 (282)
Q Consensus 110 ~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~~~C~~~l~-------~~~~~~~~~~~yC~~c~~~~~~~~~~~~~~~~ 182 (282)
...+|..|-.+|.++ .++.||=--..|. .|+-.++ ++.......-+.|+.|-++..++ .++.
T Consensus 100 D~a~C~~Cl~Ei~dp----~~rrY~YPF~~CT--~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP-----~nRR 168 (750)
T COG0068 100 DAATCEDCLEEIFDP----NSRRYLYPFINCT--NCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDP-----LNRR 168 (750)
T ss_pred chhhhHHHHHHhcCC----CCcceeccccccC--CCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCc-----cccc
Confidence 456999999999764 2455665566788 8987664 23344566788999998876554 6999
Q ss_pred ccccCccCCccCccc
Q psy11345 183 YHPECFTCAYCGKLF 197 (282)
Q Consensus 183 ~H~~Cf~C~~C~~~l 197 (282)
||..=..|-.|+-.+
T Consensus 169 fHAQp~aCp~CGP~~ 183 (750)
T COG0068 169 FHAQPIACPKCGPHL 183 (750)
T ss_pred cccccccCcccCCCe
Confidence 999999999998865
No 51
>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=48.36 E-value=6 Score=28.88 Aligned_cols=17 Identities=35% Similarity=0.868 Sum_probs=14.7
Q ss_pred hhcccCCCCccCCCccc
Q psy11345 215 WNDLFTTKCFACGFPIE 231 (282)
Q Consensus 215 ~~~~~~~~C~~C~~~I~ 231 (282)
|..+|..+|..|++.+.
T Consensus 49 Y~~lfs~pC~~C~klL~ 65 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLLS 65 (90)
T ss_pred HhhhccchhhHHHhHhh
Confidence 67788899999999883
No 52
>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=47.98 E-value=5.4 Score=22.55 Aligned_cols=11 Identities=45% Similarity=0.579 Sum_probs=6.1
Q ss_pred CCCccCCCccc
Q psy11345 221 TKCFACGFPIE 231 (282)
Q Consensus 221 ~~C~~C~~~I~ 231 (282)
.+|.+|+..|.
T Consensus 2 ~~C~rC~~~~~ 12 (30)
T PF06827_consen 2 EKCPRCWNYIE 12 (30)
T ss_dssp SB-TTT--BBE
T ss_pred CcCccCCCcce
Confidence 57888888876
No 53
>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=45.98 E-value=12 Score=23.15 Aligned_cols=22 Identities=27% Similarity=0.558 Sum_probs=14.3
Q ss_pred cCCccCcccCCCCeeeeCCeecCHhh
Q psy11345 189 TCAYCGKLFGNNPFFLEEGLPYCEND 214 (282)
Q Consensus 189 ~C~~C~~~l~~~~f~~~~~~~yC~~c 214 (282)
.|..|+.+|- -.++++.||..|
T Consensus 19 ~Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeE----EecCCCEECCCC
Confidence 3667777763 246777888665
No 54
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=45.03 E-value=13 Score=29.20 Aligned_cols=18 Identities=22% Similarity=0.615 Sum_probs=14.9
Q ss_pred CCCCCCCCCCCCcccccCCceecCCCeeecC
Q psy11345 251 CSSPSSPALSGAKPYGTQNTIKSTSGTIVCL 281 (282)
Q Consensus 251 C~~C~~~l~~g~~~~~~~~~~~~~~g~~~C~ 281 (282)
|..|+.+| |.+||++||.
T Consensus 31 Cp~Cg~PL-------------F~KdG~v~CP 48 (131)
T COG1645 31 CPKCGTPL-------------FRKDGEVFCP 48 (131)
T ss_pred CcccCCcc-------------eeeCCeEECC
Confidence 88999993 5689999995
No 55
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=43.92 E-value=33 Score=22.68 Aligned_cols=43 Identities=16% Similarity=0.460 Sum_probs=29.6
Q ss_pred cCCccCcccCCCC---eeeeCCeecCHhhhhcccCCCCccCCCccc
Q psy11345 189 TCAYCGKLFGNNP---FFLEEGLPYCENDWNDLFTTKCFACGFPIE 231 (282)
Q Consensus 189 ~C~~C~~~l~~~~---f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~ 231 (282)
.|..|++.|.... ++=.-.=-||..|...++...|..|+..+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccc
Confidence 4566777764322 333334468999999998899999987664
No 56
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=40.85 E-value=27 Score=24.24 Aligned_cols=43 Identities=28% Similarity=0.501 Sum_probs=19.4
Q ss_pred CCccCcccCCCCeeeeCCeecCHhhhhc-ccCCCCccCCCccccCCcEEEeCC
Q psy11345 190 CAYCGKLFGNNPFFLEEGLPYCENDWND-LFTTKCFACGFPIEAGDRWVEALN 241 (282)
Q Consensus 190 C~~C~~~l~~~~f~~~~~~~yC~~c~~~-~~~~~C~~C~~~I~~~~~~~~~~~ 241 (282)
|-.|+.+|. ..++..+|..|... .....|..|++++. ++.+-|
T Consensus 4 CP~C~~~L~-----~~~~~~~C~~C~~~~~~~a~CPdC~~~Le----~LkACG 47 (70)
T PF07191_consen 4 CPKCQQELE-----WQGGHYHCEACQKDYKKEAFCPDCGQPLE----VLKACG 47 (70)
T ss_dssp -SSS-SBEE-----EETTEEEETTT--EEEEEEE-TTT-SB-E----EEEETT
T ss_pred CCCCCCccE-----EeCCEEECccccccceecccCCCcccHHH----HHHHhc
Confidence 555555552 23355666666432 11246777787775 555655
No 57
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=39.67 E-value=20 Score=36.44 Aligned_cols=39 Identities=18% Similarity=0.370 Sum_probs=29.6
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhc-ccCCCCccCCCc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWND-LFTTKCFACGFP 229 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~-~~~~~C~~C~~~ 229 (282)
+.|..|...|. |....+.+.|..|-.+ .....|..|+..
T Consensus 445 ~~Cp~Cd~~lt---~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLT---LHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceE---EecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 67888888764 4555688999999555 556689999976
No 58
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=39.36 E-value=22 Score=23.35 Aligned_cols=25 Identities=28% Similarity=0.501 Sum_probs=18.2
Q ss_pred CCCccCCCccccCCcEEEeCCccccc
Q psy11345 221 TKCFACGFPIEAGDRWVEALNNNYHS 246 (282)
Q Consensus 221 ~~C~~C~~~I~~~~~~~~~~~~~~H~ 246 (282)
.+|..|++||.+. ..+...+..-|+
T Consensus 2 ~~CvVCKqpi~~a-~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDA-LVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcc-eEEEcCCCccCc
Confidence 5799999999865 455555567775
No 59
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=39.14 E-value=12 Score=31.57 Aligned_cols=32 Identities=25% Similarity=0.567 Sum_probs=26.0
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhccc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLF 219 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~ 219 (282)
-+|..|+..+-...-...+|++.|..||...+
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~~ 204 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKKY 204 (206)
T ss_pred eeccccCcccccchhhhcCCceeccccccccc
Confidence 68999999887666667789999999987643
No 60
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.66 E-value=23 Score=35.84 Aligned_cols=39 Identities=15% Similarity=0.295 Sum_probs=26.1
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhc-ccCCCCccCCCc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWND-LFTTKCFACGFP 229 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~-~~~~~C~~C~~~ 229 (282)
++|..|+.+|. |....+.+.|..|-.. ....+|..|+..
T Consensus 391 ~~C~~C~~~l~---~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLT---LHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCcee---EECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 35666666552 4445677889999544 445689999765
No 61
>KOG0978|consensus
Probab=37.52 E-value=9 Score=38.39 Aligned_cols=46 Identities=22% Similarity=0.551 Sum_probs=30.6
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhcccC---CCCccCCCccccCC
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFT---TKCFACGFPIEAGD 234 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~---~~C~~C~~~I~~~~ 234 (282)
.+|..|+....+ .....=+..+|..|-..+|. .+|+.|+.+..+.|
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 467777655432 12223356789999777765 48999999887665
No 62
>KOG1813|consensus
Probab=37.39 E-value=19 Score=32.21 Aligned_cols=43 Identities=28% Similarity=0.613 Sum_probs=30.9
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhcccC--CCCccCCCccc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFT--TKCFACGFPIE 231 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~--~~C~~C~~~I~ 231 (282)
|.|..|++.+.. ...-.-+..+|+.|+.+.|. ++|..|++.+.
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccccCCcceecccccc
Confidence 778888887643 22233466789999877664 58999999887
No 63
>PRK00420 hypothetical protein; Validated
Probab=37.09 E-value=18 Score=27.64 Aligned_cols=25 Identities=28% Similarity=0.543 Sum_probs=16.7
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhh
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWN 216 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~ 216 (282)
-.|..|+.+| |..++|+.||..|-.
T Consensus 24 ~~CP~Cg~pL----f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL----FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc----eecCCCceECCCCCC
Confidence 4577788776 234778887776643
No 64
>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=35.99 E-value=31 Score=21.55 Aligned_cols=30 Identities=17% Similarity=0.403 Sum_probs=15.3
Q ss_pred ccCCccCcccCCCCeeee--CCeecCHhhhhc
Q psy11345 188 FTCAYCGKLFGNNPFFLE--EGLPYCENDWND 217 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~--~~~~yC~~c~~~ 217 (282)
|.|..|+++|.+..|.=. .+--+|..||..
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~ 32 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAK 32 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCc
Confidence 456777776654222111 234567777654
No 65
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=35.46 E-value=20 Score=25.66 Aligned_cols=29 Identities=21% Similarity=0.529 Sum_probs=20.4
Q ss_pred cCCccCcccCCCCeeee--C---CeecCHhhhhc
Q psy11345 189 TCAYCGKLFGNNPFFLE--E---GLPYCENDWND 217 (282)
Q Consensus 189 ~C~~C~~~l~~~~f~~~--~---~~~yC~~c~~~ 217 (282)
.|..|+.||.....+.. + +.-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 48899999987662222 2 35699999865
No 66
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.45 E-value=30 Score=36.24 Aligned_cols=39 Identities=21% Similarity=0.387 Sum_probs=27.3
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCC
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGD 234 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~ 234 (282)
|+|..|+..- .....|..|-.......|..|+..+.+..
T Consensus 639 frCP~CG~~T--------e~i~fCP~CG~~~~~y~CPKCG~El~~~s 677 (1121)
T PRK04023 639 RRCPFCGTHT--------EPVYRCPRCGIEVEEDECEKCGREPTPYS 677 (1121)
T ss_pred ccCCCCCCCC--------CcceeCccccCcCCCCcCCCCCCCCCccc
Confidence 7788887751 22246888866665678999999888654
No 67
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=35.27 E-value=27 Score=21.59 Aligned_cols=30 Identities=17% Similarity=0.490 Sum_probs=16.3
Q ss_pred ccCCccCcccCCCCeee--eCCeecCHhhhhc
Q psy11345 188 FTCAYCGKLFGNNPFFL--EEGLPYCENDWND 217 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~--~~~~~yC~~c~~~ 217 (282)
+.|..|+.++.+..|.= -.+--+|..||.+
T Consensus 5 ~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~ 36 (44)
T smart00291 5 YSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAK 36 (44)
T ss_pred cCCCCCCCCCcCCEEECCCCCCccchHHHHhC
Confidence 34666666555443321 1244578888765
No 68
>PRK00807 50S ribosomal protein L24e; Validated
Probab=35.26 E-value=23 Score=23.07 Aligned_cols=34 Identities=24% Similarity=0.273 Sum_probs=22.1
Q ss_pred CCCccCCCccccCC--cEEEeCCcccccCCCcCCCCCCC
Q psy11345 221 TKCFACGFPIEAGD--RWVEALNNNYHSLCFNCSSPSSP 257 (282)
Q Consensus 221 ~~C~~C~~~I~~~~--~~~~~~~~~~H~~Cf~C~~C~~~ 257 (282)
..|..|+..|.+|. .++...|+.|.- -+..|.+.
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~F---cs~KC~~~ 37 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYF---CSSKCEKN 37 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEE---eCHHHHHH
Confidence 46888999998765 345667887763 33344444
No 69
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=33.68 E-value=29 Score=18.43 Aligned_cols=7 Identities=14% Similarity=0.691 Sum_probs=3.1
Q ss_pred CCCCCCC
Q psy11345 144 QCKRPLQ 150 (282)
Q Consensus 144 ~C~~~l~ 150 (282)
.|+..+.
T Consensus 4 ~CG~~~~ 10 (23)
T PF13240_consen 4 NCGAEIE 10 (23)
T ss_pred ccCCCCC
Confidence 4444443
No 70
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=32.95 E-value=12 Score=31.36 Aligned_cols=44 Identities=25% Similarity=0.501 Sum_probs=31.7
Q ss_pred CccCCccCcccCCCCeeeeCCeecCHhhhhccc--CCCCccCCCccc
Q psy11345 187 CFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLF--TTKCFACGFPIE 231 (282)
Q Consensus 187 Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~--~~~C~~C~~~I~ 231 (282)
=|.|..|++-... ...-.=|..+|..|+.+.| ++.|..|++...
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~ 241 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATY 241 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence 3789999886543 2223346789999988766 468999998776
No 71
>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=31.99 E-value=33 Score=33.22 Aligned_cols=12 Identities=25% Similarity=0.564 Sum_probs=6.5
Q ss_pred CcccccCCCcCC
Q psy11345 241 NNNYHSLCFNCS 252 (282)
Q Consensus 241 ~~~~H~~Cf~C~ 252 (282)
++.|...|..|.
T Consensus 82 ~~~~~l~C~~C~ 93 (483)
T PF05502_consen 82 GKPYYLSCSYCR 93 (483)
T ss_pred CCCEEEECCCce
Confidence 345555555554
No 72
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=31.98 E-value=22 Score=23.84 Aligned_cols=37 Identities=19% Similarity=0.260 Sum_probs=16.9
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCC
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGF 228 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~ 228 (282)
-.|+.|+..|...+-+ -...|.+|-+... .+|..|++
T Consensus 10 ~~CtSCg~~i~p~e~~---v~F~CPnCGe~~I-~Rc~~CRk 46 (61)
T COG2888 10 PVCTSCGREIAPGETA---VKFPCPNCGEVEI-YRCAKCRK 46 (61)
T ss_pred ceeccCCCEeccCCce---eEeeCCCCCceee-ehhhhHHH
Confidence 3566666666322211 1344555543332 45555553
No 73
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=31.48 E-value=22 Score=21.10 Aligned_cols=31 Identities=26% Similarity=0.945 Sum_probs=18.7
Q ss_pred cccccccccCCceeeecCccccccCccCCccCcccC
Q psy11345 163 CEFCFEQYLAPDCLNAIGKHYHPECFTCAYCGKLFG 198 (282)
Q Consensus 163 C~~c~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 198 (282)
|+.|.++...+ .++.||-.=..|..|+-++.
T Consensus 2 C~~C~~Ey~~p-----~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDP-----SNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCST-----TSTTTT-TT--BTTCC-SCC
T ss_pred CHHHHHHHcCC-----CCCcccCcCccCCCCCCCEE
Confidence 56666655443 47899999889999987664
No 74
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.68 E-value=24 Score=35.47 Aligned_cols=83 Identities=24% Similarity=0.498 Sum_probs=52.3
Q ss_pred CccccccccccccCCceeeecCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCCcEEE
Q psy11345 159 SGLYCEFCFEQYLAPDCLNAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGDRWVE 238 (282)
Q Consensus 159 ~~~yC~~c~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~ 238 (282)
+-..|+.|-++++++ .++.||=-=-.|+.|+-+++ +...-+|=.....-.-=+-|..|.+. +-.
T Consensus 100 D~a~C~~Cl~Ei~dp-----~~rrY~YPF~~CT~CGPRfT-----Ii~alPYDR~nTsM~~F~lC~~C~~E------Y~d 163 (750)
T COG0068 100 DAATCEDCLEEIFDP-----NSRRYLYPFINCTNCGPRFT-----IIEALPYDRENTSMADFPLCPFCDKE------YKD 163 (750)
T ss_pred chhhhHHHHHHhcCC-----CCcceeccccccCCCCccee-----eeccCCCCcccCccccCcCCHHHHHH------hcC
Confidence 456678888887776 35666655567999987654 33333332222111111456666642 334
Q ss_pred eCCcccccCCCcCCCCCCC
Q psy11345 239 ALNNNYHSLCFNCSSPSSP 257 (282)
Q Consensus 239 ~~~~~~H~~Cf~C~~C~~~ 257 (282)
..++.||..=..|..|+-.
T Consensus 164 P~nRRfHAQp~aCp~CGP~ 182 (750)
T COG0068 164 PLNRRFHAQPIACPKCGPH 182 (750)
T ss_pred ccccccccccccCcccCCC
Confidence 7789999999999999987
No 75
>KOG4443|consensus
Probab=30.00 E-value=23 Score=35.16 Aligned_cols=22 Identities=23% Similarity=0.344 Sum_probs=16.9
Q ss_pred eCCcccccCCCcCCCCCCCCCCC
Q psy11345 239 ALNNNYHSLCFNCSSPSSPALSG 261 (282)
Q Consensus 239 ~~~~~~H~~Cf~C~~C~~~l~~g 261 (282)
..+.++.++|++|..|+.. +.|
T Consensus 106 ~sg~~~ckk~~~c~qc~~~-lpg 127 (694)
T KOG4443|consen 106 PSGPWLCKKCTRCRQCDST-LPG 127 (694)
T ss_pred cCcccccHHHHhhhhcccc-ccc
Confidence 4567778889999999887 555
No 76
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=29.75 E-value=40 Score=21.97 Aligned_cols=29 Identities=24% Similarity=0.521 Sum_probs=16.7
Q ss_pred cCCccCcccCCCCeeeeCCeecC-Hhhhhc
Q psy11345 189 TCAYCGKLFGNNPFFLEEGLPYC-ENDWND 217 (282)
Q Consensus 189 ~C~~C~~~l~~~~f~~~~~~~yC-~~c~~~ 217 (282)
.|..|...++...=+.++|+.|| +.|...
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~g 38 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACANG 38 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHHT
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhcc
Confidence 47788888876666788999998 666543
No 77
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=28.90 E-value=14 Score=22.60 Aligned_cols=28 Identities=25% Similarity=0.561 Sum_probs=16.4
Q ss_pred CCccCCCccccCCcEEEe-CCcccccCCC
Q psy11345 222 KCFACGFPIEAGDRWVEA-LNNNYHSLCF 249 (282)
Q Consensus 222 ~C~~C~~~I~~~~~~~~~-~~~~~H~~Cf 249 (282)
.|..|...+..++.++.. =+..||.+|+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci 30 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCI 30 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHH
Confidence 466677777654444433 3666776664
No 78
>KOG2893|consensus
Probab=27.28 E-value=19 Score=31.22 Aligned_cols=38 Identities=18% Similarity=0.371 Sum_probs=22.8
Q ss_pred CCCccCCCccccCCcEEEeCCcccccCCCcCCCCCCCCCCCC
Q psy11345 221 TKCFACGFPIEAGDRWVEALNNNYHSLCFNCSSPSSPALSGA 262 (282)
Q Consensus 221 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~g~ 262 (282)
+-|+.|++... |..|... +--..+|+|.+|++.|-+|-
T Consensus 11 pwcwycnrefd--dekiliq--hqkakhfkchichkkl~sgp 48 (341)
T KOG2893|consen 11 PWCWYCNREFD--DEKILIQ--HQKAKHFKCHICHKKLFSGP 48 (341)
T ss_pred ceeeecccccc--hhhhhhh--hhhhccceeeeehhhhccCC
Confidence 45777777666 3333222 22235788888888876665
No 79
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=26.70 E-value=59 Score=20.42 Aligned_cols=30 Identities=13% Similarity=0.413 Sum_probs=19.2
Q ss_pred ccCCccCcccCCCCeeee--CCeecCHhhhhc
Q psy11345 188 FTCAYCGKLFGNNPFFLE--EGLPYCENDWND 217 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~--~~~~yC~~c~~~ 217 (282)
+.|..|+.-++...|.-. .+..+|..||.+
T Consensus 1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred CcccCCCCccCceEEEecCCCccccChHHHhC
Confidence 357778887765444321 245689999876
No 80
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=25.81 E-value=37 Score=22.68 Aligned_cols=24 Identities=17% Similarity=0.592 Sum_probs=16.8
Q ss_pred cCCccCcccC-CCC-eeeeCCeecCH
Q psy11345 189 TCAYCGKLFG-NNP-FFLEEGLPYCE 212 (282)
Q Consensus 189 ~C~~C~~~l~-~~~-f~~~~~~~yC~ 212 (282)
.|..|++.|. +.. |.-+..+.+|.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS 43 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCS 43 (58)
T ss_pred HHHccCCCCCCCCCeeeecccccccc
Confidence 4788999997 444 54456778883
No 81
>KOG1280|consensus
Probab=25.66 E-value=43 Score=30.69 Aligned_cols=67 Identities=18% Similarity=0.359 Sum_probs=0.0
Q ss_pred cccccccccCCceeeecCccccccCccCCccCcccCCCCeeeeCCeecCHhhhhcccCC-----------CCccCCCccc
Q psy11345 163 CEFCFEQYLAPDCLNAIGKHYHPECFTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTT-----------KCFACGFPIE 231 (282)
Q Consensus 163 C~~c~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~-----------~C~~C~~~I~ 231 (282)
|++| ....|--.|++|-.|.. --+|..||...+.. .|..=..-+.
T Consensus 11 CdgC------------~k~~~t~rrYkCL~C~D------------yDlC~sCyen~~tt~~H~~dHPmqcil~~~dfeL~ 66 (381)
T KOG1280|consen 11 CDGC------------GKTAFTFRRYKCLRCSD------------YDLCFSCYENGATTPIHDEDHPMQCILSRVDFELY 66 (381)
T ss_pred eccc------------cccceeeeeeEeeeecc------------hhHHHHHhhcCCCCcccCCCCceeEEeeccceeeE
Q ss_pred cCCcEEEeCCcccccCCCcCCCCCCC
Q psy11345 232 AGDRWVEALNNNYHSLCFNCSSPSSP 257 (282)
Q Consensus 232 ~~~~~~~~~~~~~H~~Cf~C~~C~~~ 257 (282)
.+...+ .+|-+.+|+|..|++.
T Consensus 67 f~Ge~i----~~y~~qSftCPyC~~~ 88 (381)
T KOG1280|consen 67 FGGEPI----SHYDPQSFTCPYCGIM 88 (381)
T ss_pred ecCccc----cccccccccCCccccc
No 82
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=25.22 E-value=47 Score=17.99 Aligned_cols=9 Identities=56% Similarity=1.364 Sum_probs=4.4
Q ss_pred CccCCCccc
Q psy11345 223 CFACGFPIE 231 (282)
Q Consensus 223 C~~C~~~I~ 231 (282)
|..|+..|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 444555554
No 83
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.03 E-value=67 Score=29.12 Aligned_cols=44 Identities=23% Similarity=0.508 Sum_probs=27.5
Q ss_pred cCCccCcc--cCCCC-eeee-CCeecCHhhhhcccC---CCCccCCCcccc
Q psy11345 189 TCAYCGKL--FGNNP-FFLE-EGLPYCENDWNDLFT---TKCFACGFPIEA 232 (282)
Q Consensus 189 ~C~~C~~~--l~~~~-f~~~-~~~~yC~~c~~~~~~---~~C~~C~~~I~~ 232 (282)
.|..|+.. +.... +.+. =|..+|..|....|. ..|..|+.++..
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 46667663 32222 2222 377889999877663 378888888763
No 84
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=24.60 E-value=47 Score=33.84 Aligned_cols=77 Identities=18% Similarity=0.496 Sum_probs=56.3
Q ss_pred CCCcccccCccccCceeecCCcccCcCCcccccCCCCCCCC-------CCCceecCCccccccccccccCCceeeecCcc
Q psy11345 110 RVPLCGQCYQQIRGPFITALGKIWCPDHFLCVRPQCKRPLQ-------DIGFVEEDSGLYCEFCFEQYLAPDCLNAIGKH 182 (282)
Q Consensus 110 ~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~~~C~~~l~-------~~~~~~~~~~~yC~~c~~~~~~~~~~~~~~~~ 182 (282)
.+.+|..|-+++.++ .++.|+=--..|. .|+-..+ +.......+...|+.|.++...+ .++.
T Consensus 67 D~a~C~~Cl~E~~dp----~~Rry~YpF~nCt--~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p-----~~rr 135 (711)
T TIGR00143 67 DVATCSDCLEEMLDK----NDRRYLYPFISCT--HCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDP-----LDRR 135 (711)
T ss_pred chhhHHHHHHHhcCC----CcccccCCccccc--CCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCC-----cccc
Confidence 456999999998653 3555665666777 8886552 11223346778899999887655 5899
Q ss_pred ccccCccCCccCccc
Q psy11345 183 YHPECFTCAYCGKLF 197 (282)
Q Consensus 183 ~H~~Cf~C~~C~~~l 197 (282)
||-.=..|..|+=+|
T Consensus 136 ~h~~~~~C~~Cgp~l 150 (711)
T TIGR00143 136 FHAQPIACPRCGPQL 150 (711)
T ss_pred CCCCCccCCCCCcEE
Confidence 999999999999887
No 85
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=24.15 E-value=1e+02 Score=25.92 Aligned_cols=46 Identities=20% Similarity=0.364 Sum_probs=28.8
Q ss_pred CccCCccCcccCCCCeeeeCCeecCHhhhhcc------------------cCCCCccCCCccccC
Q psy11345 187 CFTCAYCGKLFGNNPFFLEEGLPYCENDWNDL------------------FTTKCFACGFPIEAG 233 (282)
Q Consensus 187 Cf~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~------------------~~~~C~~C~~~I~~~ 233 (282)
-|.|..|...+.. .....=+..||..|..+. -..+|..|+..|...
T Consensus 18 ~~~CpICld~~~d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~ 81 (193)
T PLN03208 18 DFDCNICLDQVRD-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA 81 (193)
T ss_pred ccCCccCCCcCCC-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence 4667777665532 233334677888886432 125899999999753
No 86
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=24.06 E-value=35 Score=20.24 Aligned_cols=30 Identities=13% Similarity=0.379 Sum_probs=17.4
Q ss_pred CCccCcccCCCCeeeeCCeecCHhhhhccc
Q psy11345 190 CAYCGKLFGNNPFFLEEGLPYCENDWNDLF 219 (282)
Q Consensus 190 C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~ 219 (282)
|..|...+.+-.....=|..||..|..+.+
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~ 30 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYL 30 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHH
Confidence 455666555421334458889999976543
No 87
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=23.92 E-value=47 Score=29.57 Aligned_cols=27 Identities=30% Similarity=0.610 Sum_probs=18.7
Q ss_pred CCCCccCCCccccCCcEEEeCCcccccCC
Q psy11345 220 TTKCFACGFPIEAGDRWVEALNNNYHSLC 248 (282)
Q Consensus 220 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~C 248 (282)
+..|.+|+.+|. ...+.-++.+|.+.|
T Consensus 245 GepC~~CGt~I~--k~~~~gR~t~~CP~C 271 (273)
T COG0266 245 GEPCRRCGTPIE--KIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCccCCEeE--EEEEcCCcCEeCCCC
Confidence 468999999997 334445566666655
No 88
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=23.46 E-value=75 Score=20.24 Aligned_cols=31 Identities=16% Similarity=0.440 Sum_probs=15.1
Q ss_pred ccCCccCc-ccCCCCeeee--C--CeecCHhhhhcc
Q psy11345 188 FTCAYCGK-LFGNNPFFLE--E--GLPYCENDWNDL 218 (282)
Q Consensus 188 f~C~~C~~-~l~~~~f~~~--~--~~~yC~~c~~~~ 218 (282)
|+|..|+. ++.+.+|.=. . +--+|..||...
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 34556655 5544332211 1 335677777653
No 89
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=23.43 E-value=41 Score=28.50 Aligned_cols=41 Identities=24% Similarity=0.399 Sum_probs=24.3
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccccCCcEEEeC
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIEAGDRWVEAL 240 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~~~~~~~~~~ 240 (282)
++|..|+.+.+. -|..... . ..+ -++|..|++.. |++++..
T Consensus 1 miCIeCg~~v~~-Ly~~Ys~-----~-~ir--Lt~C~~C~~va---DkYiE~d 41 (208)
T PF04161_consen 1 MICIECGHPVKS-LYRQYSP-----G-NIR--LTKCPNCGKVA---DKYIEYD 41 (208)
T ss_pred CEeccCCCcchh-hhhccCC-----C-cEE--EeeccccCCcc---cceeccc
Confidence 578899988543 2222211 1 112 27899999777 5787654
No 90
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=23.25 E-value=69 Score=27.69 Aligned_cols=24 Identities=25% Similarity=0.640 Sum_probs=15.8
Q ss_pred CCccCcccCCCCeeeeCCeecCHhhhhccc
Q psy11345 190 CAYCGKLFGNNPFFLEEGLPYCENDWNDLF 219 (282)
Q Consensus 190 C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~ 219 (282)
|..||++... ..+ -+|..||.+.+
T Consensus 1 C~~CG~~~~~----~~~--~lC~~C~~~~~ 24 (236)
T PF04981_consen 1 CPRCGREIEP----LID--GLCPDCYLKRF 24 (236)
T ss_pred CCCCCCCCCC----ccc--ccChHHhcccC
Confidence 6778885532 112 38999998765
No 91
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=23.16 E-value=42 Score=20.99 Aligned_cols=28 Identities=21% Similarity=0.471 Sum_probs=14.8
Q ss_pred cccccCCCCCCCCCCCceecCCcccccccccccc
Q psy11345 138 FLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYL 171 (282)
Q Consensus 138 f~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~ 171 (282)
|.|. .|+..+... ..+.+.|..|..++.
T Consensus 3 Y~C~--~Cg~~~~~~----~~~~irC~~CG~rIl 30 (44)
T smart00659 3 YICG--ECGRENEIK----SKDVVRCRECGYRIL 30 (44)
T ss_pred EECC--CCCCEeecC----CCCceECCCCCceEE
Confidence 3455 666654432 335566666665543
No 92
>KOG2932|consensus
Probab=22.51 E-value=44 Score=30.21 Aligned_cols=43 Identities=12% Similarity=0.151 Sum_probs=29.1
Q ss_pred cCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccc
Q psy11345 189 TCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIE 231 (282)
Q Consensus 189 ~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~ 231 (282)
.|..|+.+|..-...+-=+..+|.+|...---+.|..|..+|.
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQ 134 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHH
Confidence 4788888875422222235678888876655568999998775
No 93
>KOG3002|consensus
Probab=22.30 E-value=68 Score=28.96 Aligned_cols=43 Identities=23% Similarity=0.507 Sum_probs=27.8
Q ss_pred ccCCccCcccCCCCeeeeCCeecCHhhhhcccCCCCccCCCccc
Q psy11345 188 FTCAYCGKLFGNNPFFLEEGLPYCENDWNDLFTTKCFACGFPIE 231 (282)
Q Consensus 188 f~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~~~~C~~C~~~I~ 231 (282)
+-|-+|-..|..-.|.=.+|.+.|..|-.++. .+|..|..+|.
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~-~~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS-NKCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhhc-ccCCccccccc
Confidence 34555555665444555677777888765443 67888888776
No 94
>PRK11595 DNA utilization protein GntX; Provisional
Probab=21.77 E-value=80 Score=27.03 Aligned_cols=37 Identities=24% Similarity=0.427 Sum_probs=23.8
Q ss_pred cCCccCcccCCCCeeeeCCeecCHhhhhccc--CCCCccCCCccc
Q psy11345 189 TCAYCGKLFGNNPFFLEEGLPYCENDWNDLF--TTKCFACGFPIE 231 (282)
Q Consensus 189 ~C~~C~~~l~~~~f~~~~~~~yC~~c~~~~~--~~~C~~C~~~I~ 231 (282)
+|..|+..+... ...+|..|...+. ...|..|+.++.
T Consensus 7 ~C~~C~~~~~~~------~~~lC~~C~~~l~~~~~~C~~Cg~~~~ 45 (227)
T PRK11595 7 LCWLCRMPLALS------HWGICSVCSRALRTLKTCCPQCGLPAT 45 (227)
T ss_pred cCccCCCccCCC------CCcccHHHHhhCCcccCcCccCCCcCC
Confidence 477777766322 1247998876542 357999998754
No 95
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.48 E-value=94 Score=31.29 Aligned_cols=47 Identities=21% Similarity=0.362 Sum_probs=23.9
Q ss_pred cccccCcccc--CceeecCCccc-CcCCcccccCCCCCCCCCCCceecCCcccccccccccc
Q psy11345 113 LCGQCYQQIR--GPFITALGKIW-CPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYL 171 (282)
Q Consensus 113 ~C~~C~~~I~--~~~v~~~~~~~-H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~ 171 (282)
+|..||..+. .+|..--|... +. .|. .|+..+.. +..+|..|+..+.
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~~---~Cp--~CG~~~~~-------~~~fC~~CG~~~~ 52 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTHK---PCP--QCGTEVPV-------DEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCCC---cCC--CCCCCCCc-------ccccccccCCccc
Confidence 5666666652 23433222221 12 355 66665443 5667888876543
No 96
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=21.27 E-value=64 Score=21.19 Aligned_cols=25 Identities=28% Similarity=0.631 Sum_probs=19.1
Q ss_pred CCCccCCCccccCC--cEEEeCCcccc
Q psy11345 221 TKCFACGFPIEAGD--RWVEALNNNYH 245 (282)
Q Consensus 221 ~~C~~C~~~I~~~~--~~~~~~~~~~H 245 (282)
..|.-|+..|.||. .+|...|+.|+
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 46899999999864 56666777776
No 97
>KOG4443|consensus
Probab=20.29 E-value=65 Score=32.10 Aligned_cols=114 Identities=24% Similarity=0.410 Sum_probs=63.1
Q ss_pred CCCcccccCccccCceee-----c-CCccc-CcCCcccccCCCCCCCCCCCceecCCccccccccccccCCcee------
Q psy11345 110 RVPLCGQCYQQIRGPFIT-----A-LGKIW-CPDHFLCVRPQCKRPLQDIGFVEEDSGLYCEFCFEQYLAPDCL------ 176 (282)
Q Consensus 110 ~~~~C~~C~~~I~~~~v~-----~-~~~~~-H~~Cf~C~~~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~~------ 176 (282)
.+..|..|++.-.+-.|+ + +.+.| -+.|-.|. .|+.-=.. ...++|+.|-... ..+|+
T Consensus 34 ~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe--~c~~~gD~------~kf~~Ck~cDvsy-h~yc~~P~~~~ 104 (694)
T KOG4443|consen 34 RLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCE--ACGTTGDP------KKFLLCKRCDVSY-HCYCQKPPNDK 104 (694)
T ss_pred cchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeee--eccccCCc------ccccccccccccc-cccccCCcccc
Confidence 456888888765433332 1 22223 57888888 78732222 2235666664332 22222
Q ss_pred eecCccccccCccCCccCcccCCCC--eee-------eCCeecCHhhhhc------ccCCCCccCCCcccc
Q psy11345 177 NAIGKHYHPECFTCAYCGKLFGNNP--FFL-------EEGLPYCENDWND------LFTTKCFACGFPIEA 232 (282)
Q Consensus 177 ~~~~~~~H~~Cf~C~~C~~~l~~~~--f~~-------~~~~~yC~~c~~~------~~~~~C~~C~~~I~~ 232 (282)
...+..+-++|++|..|+..+.+.. +.. --.-.||..|+.- +-...|..|......
T Consensus 105 v~sg~~~ckk~~~c~qc~~~lpg~s~~~~~~~~~~~~c~s~~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~ 175 (694)
T KOG4443|consen 105 VPSGPWLCKKCTRCRQCDSTLPGLSLDLQEGYLQCAPCASLSYCPVCLIVYQDSESLPMVCCSICQRWSHG 175 (694)
T ss_pred ccCcccccHHHHhhhhccccccccchhhhccCcccccccccccCchHHHhhhhccchhhHHHHHhcccccC
Confidence 1246778889999999999887622 221 0112566666422 112367778777664
No 98
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=20.27 E-value=54 Score=27.76 Aligned_cols=14 Identities=21% Similarity=0.396 Sum_probs=8.4
Q ss_pred ecCCcccccccccc
Q psy11345 156 EEDSGLYCEFCFEQ 169 (282)
Q Consensus 156 ~~~~~~yC~~c~~~ 169 (282)
..+|++.|..|+..
T Consensus 189 ~~ng~~vC~~C~~~ 202 (206)
T COG2191 189 VLNGKPVCKPCAEK 202 (206)
T ss_pred hcCCceeccccccc
Confidence 34566677776653
No 99
>KOG2462|consensus
Probab=20.01 E-value=57 Score=28.93 Aligned_cols=10 Identities=20% Similarity=0.501 Sum_probs=6.0
Q ss_pred CcCCCCCCCC
Q psy11345 249 FNCSSPSSPA 258 (282)
Q Consensus 249 f~C~~C~~~l 258 (282)
|.|..|++.|
T Consensus 216 F~C~hC~kAF 225 (279)
T KOG2462|consen 216 FSCPHCGKAF 225 (279)
T ss_pred ccCCcccchh
Confidence 5566666663
Done!