Query psy16551
Match_columns 281
No_of_seqs 235 out of 1469
Neff 8.1
Searched_HMMs 46136
Date Sat Aug 17 00:05:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16551.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16551hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 7.4E-27 1.6E-31 210.5 -0.3 141 92-279 271-412 (468)
2 KOG2272|consensus 99.8 5.7E-22 1.2E-26 167.7 0.1 129 83-256 183-311 (332)
3 KOG4577|consensus 99.8 2.7E-22 5.9E-27 172.5 -3.0 126 93-262 31-158 (383)
4 KOG1701|consensus 99.8 7.9E-21 1.7E-25 171.7 3.1 124 96-262 335-467 (468)
5 KOG2272|consensus 99.8 2.8E-21 6.1E-26 163.6 -1.8 187 84-275 62-270 (332)
6 KOG1703|consensus 99.7 8.8E-18 1.9E-22 160.8 5.2 130 93-267 301-430 (479)
7 KOG1044|consensus 99.7 1.6E-17 3.5E-22 155.0 4.9 169 95-269 16-202 (670)
8 KOG1703|consensus 99.6 4.1E-17 8.9E-22 156.2 2.0 126 84-254 352-478 (479)
9 KOG1044|consensus 99.6 6.9E-17 1.5E-21 150.9 1.9 117 94-255 132-248 (670)
10 KOG1700|consensus 99.6 2E-16 4.4E-21 134.3 3.7 166 95-263 7-173 (200)
11 PF00412 LIM: LIM domain; Int 99.4 3.2E-13 7E-18 92.0 2.5 57 98-155 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.3 4.5E-13 9.7E-18 91.3 2.4 57 201-258 1-58 (58)
13 KOG4577|consensus 99.2 1.1E-12 2.4E-17 113.5 -3.8 76 198-275 33-108 (383)
14 smart00132 LIM Zinc-binding do 98.5 1.1E-07 2.3E-12 58.8 2.7 37 200-236 1-38 (39)
15 smart00132 LIM Zinc-binding do 98.5 9.5E-08 2.1E-12 59.1 2.4 37 97-133 1-38 (39)
16 KOG1700|consensus 97.8 5.7E-06 1.2E-10 70.5 0.9 65 92-157 105-169 (200)
17 KOG0490|consensus 97.7 8.2E-06 1.8E-10 70.8 0.1 114 100-256 1-118 (235)
18 KOG1702|consensus 97.6 1.1E-05 2.4E-10 67.4 -0.7 61 95-156 4-64 (264)
19 KOG1702|consensus 97.3 3.1E-05 6.8E-10 64.7 -1.1 63 200-263 6-68 (264)
20 KOG0490|consensus 93.8 0.027 5.9E-07 48.6 1.3 64 204-269 2-69 (235)
21 PF14446 Prok-RING_1: Prokaryo 86.0 0.55 1.2E-05 31.2 1.8 37 199-235 6-51 (54)
22 PF09943 DUF2175: Uncharacteri 83.2 0.36 7.8E-06 36.3 -0.0 33 200-232 4-37 (101)
23 PF14446 Prok-RING_1: Prokaryo 76.2 1.6 3.4E-05 29.0 1.3 29 95-123 5-36 (54)
24 PF10367 Vps39_2: Vacuolar sor 75.8 2.3 4.9E-05 31.8 2.3 31 197-227 77-108 (109)
25 KOG0320|consensus 73.1 1.4 3.1E-05 36.5 0.6 37 119-155 128-164 (187)
26 PF08394 Arc_trans_TRASH: Arch 72.6 2.7 5.9E-05 25.6 1.6 28 201-228 1-29 (37)
27 PF14471 DUF4428: Domain of un 71.9 1.9 4.2E-05 28.2 0.9 30 227-257 1-30 (51)
28 PF13240 zinc_ribbon_2: zinc-r 69.2 3 6.4E-05 22.5 1.1 9 98-106 2-10 (23)
29 PF10235 Cript: Microtubule-as 69.0 3 6.6E-05 30.7 1.5 12 200-211 71-82 (90)
30 smart00504 Ubox Modified RING 68.2 3.6 7.9E-05 27.5 1.7 32 123-156 2-33 (63)
31 PF09943 DUF2175: Uncharacteri 67.9 1.4 3.1E-05 33.1 -0.4 31 97-127 4-35 (101)
32 COG4847 Uncharacterized protei 66.1 2.1 4.4E-05 31.7 0.1 35 200-234 8-43 (103)
33 PF14835 zf-RING_6: zf-RING of 64.3 7 0.00015 26.9 2.5 34 123-157 8-41 (65)
34 PLN03123 poly [ADP-ribose] pol 63.6 9.7 0.00021 40.2 4.5 32 196-227 114-154 (981)
35 COG2191 Formylmethanofuran deh 56.7 5.5 0.00012 33.8 1.1 31 123-154 173-203 (206)
36 PF10367 Vps39_2: Vacuolar sor 56.3 7.2 0.00016 29.0 1.6 33 92-124 75-108 (109)
37 PF00645 zf-PARP: Poly(ADP-rib 50.2 6.2 0.00013 28.2 0.4 17 93-109 5-21 (82)
38 KOG0978|consensus 48.5 4.4 9.5E-05 40.8 -0.9 34 122-157 643-676 (698)
39 PF07754 DUF1610: Domain of un 46.7 16 0.00034 20.1 1.5 9 98-106 1-9 (24)
40 PF11781 RRN7: RNA polymerase 46.0 11 0.00023 22.8 0.8 25 123-152 9-33 (36)
41 PF12773 DZR: Double zinc ribb 45.3 24 0.00051 22.4 2.5 9 200-208 14-22 (50)
42 COG1645 Uncharacterized Zn-fin 43.7 11 0.00023 29.9 0.8 21 228-254 31-51 (131)
43 KOG4443|consensus 43.3 15 0.00033 36.5 1.9 22 216-237 106-127 (694)
44 KOG2893|consensus 43.2 8.5 0.00018 33.5 0.2 38 94-134 9-46 (341)
45 PF14634 zf-RING_5: zinc-RING 42.7 23 0.0005 21.9 2.1 31 125-155 2-33 (44)
46 PRK14559 putative protein seri 42.7 25 0.00054 35.5 3.4 9 200-208 43-51 (645)
47 KOG2462|consensus 41.6 7.2 0.00016 34.7 -0.5 38 200-237 217-255 (279)
48 PF10083 DUF2321: Uncharacteri 41.5 12 0.00027 30.4 0.8 37 200-237 41-80 (158)
49 PF06827 zf-FPG_IleRS: Zinc fi 41.2 11 0.00024 21.4 0.4 11 199-209 2-12 (30)
50 PF06677 Auto_anti-p27: Sjogre 40.7 13 0.00029 23.1 0.7 22 124-150 19-40 (41)
51 PF10886 DUF2685: Protein of u 40.0 17 0.00036 24.1 1.1 25 200-224 3-27 (54)
52 PF13920 zf-C3HC4_3: Zinc fing 39.7 12 0.00027 23.8 0.5 30 124-155 4-34 (50)
53 PRK04023 DNA polymerase II lar 38.6 46 0.00099 35.2 4.5 35 94-152 625-659 (1121)
54 COG2191 Formylmethanofuran deh 38.0 16 0.00034 31.1 1.0 31 226-257 173-203 (206)
55 PRK14890 putative Zn-ribbon RN 37.3 29 0.00062 23.5 2.0 28 95-131 7-34 (59)
56 PF13834 DUF4193: Domain of un 34.9 15 0.00033 27.5 0.4 29 122-150 70-98 (99)
57 KOG2462|consensus 32.7 33 0.00071 30.6 2.1 37 200-237 189-227 (279)
58 PF05502 Dynactin_p62: Dynacti 32.5 30 0.00064 33.7 2.1 37 200-237 28-64 (483)
59 PF13248 zf-ribbon_3: zinc-rib 32.0 32 0.0007 18.9 1.3 9 200-208 4-12 (26)
60 PF02069 Metallothio_Pro: Prok 32.0 30 0.00065 22.8 1.4 27 125-152 10-37 (52)
61 KOG1813|consensus 31.8 27 0.00059 31.4 1.5 33 123-157 242-274 (313)
62 PF06906 DUF1272: Protein of u 31.5 38 0.00082 22.6 1.8 22 248-269 30-51 (57)
63 PF04502 DUF572: Family of unk 31.4 33 0.00072 31.4 2.1 45 89-133 34-88 (324)
64 COG2888 Predicted Zn-ribbon RN 31.3 28 0.00062 23.5 1.2 29 95-132 9-37 (61)
65 PF12674 Zn_ribbon_2: Putative 31.2 29 0.00063 25.0 1.4 29 228-256 3-35 (81)
66 cd00162 RING RING-finger (Real 30.0 26 0.00057 20.7 0.8 8 98-105 2-9 (45)
67 PF04570 DUF581: Protein of un 29.0 36 0.00079 22.9 1.4 29 125-153 19-49 (58)
68 PF09723 Zn-ribbon_8: Zinc rib 28.5 25 0.00054 21.8 0.5 29 123-152 6-34 (42)
69 COG5152 Uncharacterized conser 28.1 18 0.00039 30.6 -0.2 32 123-156 197-228 (259)
70 PF08746 zf-RING-like: RING-li 27.9 17 0.00036 22.8 -0.4 13 98-110 1-13 (43)
71 PRK00420 hypothetical protein; 25.8 40 0.00088 25.9 1.4 26 123-153 24-49 (112)
72 PLN03208 E3 ubiquitin-protein 25.3 61 0.0013 27.5 2.4 16 200-215 70-85 (193)
73 KOG3579|consensus 25.2 43 0.00094 30.1 1.6 48 95-148 268-315 (352)
74 TIGR00373 conserved hypothetic 24.7 23 0.0005 28.9 -0.1 32 95-134 109-140 (158)
75 PF14255 Cys_rich_CPXG: Cystei 24.2 40 0.00087 22.2 0.9 29 97-125 2-30 (52)
76 PF01286 XPA_N: XPA protein N- 24.0 46 0.00099 19.9 1.1 10 97-106 5-14 (34)
77 KOG3039|consensus 23.8 1.1E+02 0.0023 27.1 3.7 84 92-215 180-276 (303)
78 COG0266 Nei Formamidopyrimidin 23.6 50 0.0011 29.6 1.7 29 196-225 243-271 (273)
79 PRK06266 transcription initiat 23.1 31 0.00068 28.8 0.3 31 96-134 118-148 (178)
80 PRK00807 50S ribosomal protein 23.0 63 0.0014 21.1 1.7 31 200-233 3-36 (52)
81 cd02249 ZZ Zinc finger, ZZ typ 22.4 60 0.0013 20.3 1.5 9 249-257 25-33 (46)
82 PF07503 zf-HYPF: HypF finger; 22.3 22 0.00048 21.3 -0.5 30 98-132 2-31 (35)
83 smart00531 TFIIE Transcription 22.3 35 0.00075 27.4 0.4 37 95-134 99-135 (147)
84 PHA02929 N1R/p28-like protein; 22.1 51 0.0011 28.9 1.5 39 95-133 174-227 (238)
85 PF04810 zf-Sec23_Sec24: Sec23 21.9 65 0.0014 19.6 1.5 29 200-233 4-32 (40)
86 PF14569 zf-UDP: Zinc-binding 21.7 16 0.00034 26.1 -1.4 32 195-234 6-37 (80)
87 PF01927 Mut7-C: Mut7-C RNAse 21.4 59 0.0013 26.0 1.6 43 95-137 91-139 (147)
88 TIGR02098 MJ0042_CXXC MJ0042 f 21.3 42 0.00091 19.9 0.6 32 200-235 4-35 (38)
89 PF06524 NOA36: NOA36 protein; 21.1 84 0.0018 27.9 2.5 14 91-104 59-72 (314)
90 PF06750 DiS_P_DiS: Bacterial 21.0 47 0.001 24.5 0.9 40 95-136 33-72 (92)
91 PF02591 DUF164: Putative zinc 21.0 41 0.00089 22.1 0.5 35 95-132 22-56 (56)
92 PRK14873 primosome assembly pr 20.9 85 0.0018 31.9 3.0 39 123-207 393-431 (665)
93 PF12760 Zn_Tnp_IS1595: Transp 20.5 1.4E+02 0.0031 18.6 3.0 33 90-130 13-45 (46)
94 PF13639 zf-RING_2: Ring finge 20.4 36 0.00077 20.9 0.1 28 200-227 2-31 (44)
95 smart00834 CxxC_CXXC_SSSS Puta 20.3 46 0.001 19.9 0.6 11 123-133 6-16 (41)
96 PLN02638 cellulose synthase A 20.2 79 0.0017 33.7 2.6 53 194-254 13-66 (1079)
97 PF11331 DUF3133: Protein of u 20.1 39 0.00084 21.6 0.2 35 96-132 7-41 (46)
No 1
>KOG1701|consensus
Probab=99.92 E-value=7.4e-27 Score=210.47 Aligned_cols=141 Identities=29% Similarity=0.608 Sum_probs=122.7
Q ss_pred CCCCCCCcCCCccccccce-eeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCCcccCCcccc
Q psy16551 92 AAPGKGCPRCGGVVFAAEQ-VLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYGFAAGSGFLQ 170 (281)
Q Consensus 92 ~~~~~~C~~C~~~I~~~~~-~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~~~c~~~~~~ 170 (281)
..+..+|++|+|.|+..+- +.|+++.||..||+|..|++.|.+..|+. .|+++||+.||....
T Consensus 271 ~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~-v~~k~~CE~cyq~tl--------------- 334 (468)
T KOG1701|consen 271 EDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQ-VDGKPYCEGCYQDTL--------------- 334 (468)
T ss_pred hhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccc-cCCcccchHHHHHHH---------------
Confidence 3344699999999976443 68999999999999999999999988875 999999999998643
Q ss_pred cCCCccccccCCCCCcCCCCccccCCCCCCCCCCCCcccccceeeecCcccccccccccccCCCCCCCccccCCCCcccC
Q psy16551 171 TDGLTEDEISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYC 250 (281)
Q Consensus 171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~~~~~~~~~~g~~~C 250 (281)
.+|..|+++|++. ++.+.|+.||+.||+|..|++.|++..|....++++||
T Consensus 335 ----------------------------ekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~C 385 (468)
T KOG1701|consen 335 ----------------------------EKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYC 385 (468)
T ss_pred ----------------------------HHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceee
Confidence 3899999999543 56699999999999999999999999999999999999
Q ss_pred hhhhccccCCCCCcCCCCCcccccCCCCC
Q psy16551 251 KACYGKNFGPKGFGYGHSPTLVSTSGEST 279 (281)
Q Consensus 251 ~~c~~~~f~~~c~~c~~~~~~~s~~~~~~ 279 (281)
..||+++|+++|+.|+. +|++ .+|+.|
T Consensus 386 v~dfh~kfAPrCs~C~~-PI~P-~~G~~e 412 (468)
T KOG1701|consen 386 VPDFHKKFAPRCSVCGN-PILP-RDGKDE 412 (468)
T ss_pred ehhhhhhcCcchhhccC-CccC-CCCCcc
Confidence 99999999999999987 5555 566553
No 2
>KOG2272|consensus
Probab=99.83 E-value=5.7e-22 Score=167.74 Aligned_cols=129 Identities=23% Similarity=0.489 Sum_probs=118.1
Q ss_pred ccccccccCCCCCCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCCc
Q psy16551 83 TVIDTAKIKAAPGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYGF 162 (281)
Q Consensus 83 ~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~~ 162 (281)
..++.++...-..++|.+|.++| +.++|.++|+.||.++|+|+.|.+++.+...+ ++.|..||+.||.++|+-
T Consensus 183 eLyClrChD~mgipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHY-EkkGlaYCe~h~~qLfG~----- 255 (332)
T KOG2272|consen 183 ELYCLRCHDKMGIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHY-EKKGLAYCETHYHQLFGN----- 255 (332)
T ss_pred ceeccccccccCCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhh-hhcCchhHHHHHHHHhhh-----
Confidence 45778888888889999999999 46778999999999999999999999998877 599999999999999986
Q ss_pred ccCCcccccCCCccccccCCCCCcCCCCccccCCCCCCCCCCCCcccccceeeecCcccccccccccccCCCCCCCcccc
Q psy16551 163 AAGSGFLQTDGLTEDEISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACD 242 (281)
Q Consensus 163 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~~~~~~~ 242 (281)
.|..|+.+| .++.+.++++.|.++||+|+.|++.|.....++
T Consensus 256 -------------------------------------~CF~C~~~i-~G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~ 297 (332)
T KOG2272|consen 256 -------------------------------------LCFICNRVI-GGDVVSALNKAWCVECFSCSTCDKKLTQKNKFY 297 (332)
T ss_pred -------------------------------------hheecCCcc-CccHHHHhhhhhcccccccccccccccccccee
Confidence 899999999 788899999999999999999999998888888
Q ss_pred CCCCcccChhhhcc
Q psy16551 243 GPDKEIYCKACYGK 256 (281)
Q Consensus 243 ~~~g~~~C~~c~~~ 256 (281)
+.|.+|.|+.||.+
T Consensus 298 E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 298 EFDMKPVCKKCYDR 311 (332)
T ss_pred eeccchHHHHHHhh
Confidence 99999999999974
No 3
>KOG4577|consensus
Probab=99.82 E-value=2.7e-22 Score=172.45 Aligned_cols=126 Identities=24% Similarity=0.517 Sum_probs=112.4
Q ss_pred CCCCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCCcccCCcccccC
Q psy16551 93 APGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYGFAAGSGFLQTD 172 (281)
Q Consensus 93 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~~~c~~~~~~~~ 172 (281)
...++|++|.+.|.+..++.++++.||..|++|+.|+.+|....| .++|.+||+++|.|+|+.
T Consensus 31 ~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCF--sR~~s~yCkedFfKrfGT--------------- 93 (383)
T KOG4577|consen 31 VEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCF--SREGSVYCKEDFFKRFGT--------------- 93 (383)
T ss_pred cccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHh--hcCCceeehHHHHHHhCC---------------
Confidence 356899999999998777899999999999999999999998776 499999999999999998
Q ss_pred CCccccccCCCCCcCCCCccccCCCCCCCCCCCCcccccceee-ecCcccccccccccccCCCCC-CCccccCCCCcccC
Q psy16551 173 GLTEDEISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLD-SVLACDGPDKEIYC 250 (281)
Q Consensus 173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~-~~g~~~H~~Cf~C~~C~~~L~-~~~~~~~~~g~~~C 250 (281)
+|..|...|.+...|. +.+.+||..||.|..|++.|. +.+|+...|++++|
T Consensus 94 ---------------------------KCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvC 146 (383)
T KOG4577|consen 94 ---------------------------KCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVC 146 (383)
T ss_pred ---------------------------cchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeeh
Confidence 8999999998777665 889999999999999999995 56677789999999
Q ss_pred hhhhccccCCCC
Q psy16551 251 KACYGKNFGPKG 262 (281)
Q Consensus 251 ~~c~~~~f~~~c 262 (281)
+.+|+.--...|
T Consensus 147 K~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 147 KDDYETAKQKHC 158 (383)
T ss_pred hhhHHHHHhccc
Confidence 999988655555
No 4
>KOG1701|consensus
Probab=99.81 E-value=7.9e-21 Score=171.68 Aligned_cols=124 Identities=27% Similarity=0.665 Sum_probs=109.3
Q ss_pred CCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCCcccCCcccccCCCc
Q psy16551 96 KGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYGFAAGSGFLQTDGLT 175 (281)
Q Consensus 96 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~~~c~~~~~~~~~~~ 175 (281)
..|..|++.|.+ .++.|+|+.||..||+|..|.+.|++..|.+..++++||-.||+++|+|
T Consensus 335 ekC~~Cg~~I~d-~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAP------------------ 395 (468)
T KOG1701|consen 335 EKCNKCGEPIMD-RILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAP------------------ 395 (468)
T ss_pred HHHhhhhhHHHH-HHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCc------------------
Confidence 568999999964 6779999999999999999999999988888899999999999999999
Q ss_pred cccccCCCCCcCCCCccccCCCCCCCCCCCCcccccc------eeeecCcccccccccccccCCCCC---CCccccCCCC
Q psy16551 176 EDEISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAE------QQLAKGTMWHKQCFSCNVCKRPLD---SVLACDGPDK 246 (281)
Q Consensus 176 ~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~------~v~~~g~~~H~~Cf~C~~C~~~L~---~~~~~~~~~g 246 (281)
+|+.|+++|+..+ +|+++++.||.+|++|..|+..|+ .+...+-.||
T Consensus 396 ------------------------rCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~ 451 (468)
T KOG1701|consen 396 ------------------------RCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDG 451 (468)
T ss_pred ------------------------chhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccC
Confidence 9999999998754 566899999999999999999997 2344557899
Q ss_pred cccChhhhccccCCCC
Q psy16551 247 EIYCKACYGKNFGPKG 262 (281)
Q Consensus 247 ~~~C~~c~~~~f~~~c 262 (281)
.++|+.|..++....+
T Consensus 452 HllCk~Ch~~Rl~~~~ 467 (468)
T KOG1701|consen 452 HLLCKTCHLKRLQAGS 467 (468)
T ss_pred ceeechhhhhhhcccC
Confidence 9999999988866543
No 5
>KOG2272|consensus
Probab=99.80 E-value=2.8e-21 Score=163.56 Aligned_cols=187 Identities=20% Similarity=0.365 Sum_probs=137.9
Q ss_pred cccccccCCCCCCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCC-c
Q psy16551 84 VIDTAKIKAAPGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYG-F 162 (281)
Q Consensus 84 ~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~-~ 162 (281)
.++..++...+.|.|.+|++-|. +++|.+++.+||+.||+|..|++.|.+..++. ..|..+|..|..+.- +++-| +
T Consensus 62 kYCEhDF~~LfaPcC~kC~EFii-GrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~r-nqgr~LC~~Cn~k~K-a~~~g~Y 138 (332)
T KOG2272|consen 62 KYCEHDFHVLFAPCCGKCGEFII-GRVIKAMNNSWHPACFRCDLCNKHLADQGFYR-NQGRALCRECNQKEK-AKGRGRY 138 (332)
T ss_pred ccccccchhhhchhhcccccchh-hHHHHhhccccCcccchhHHHHHHHhhhhhHh-hcchHHhhhhhhhhc-cccccee
Confidence 37888888999999999999995 78999999999999999999999999877663 789999999987633 22322 3
Q ss_pred ccCCcccccCCC----ccccccCCCCCcCCCCccc-----------------cCCCCCCCCCCCCcccccceeeecCccc
Q psy16551 163 AAGSGFLQTDGL----TEDEISANRPFYNPNTTSI-----------------MARKGEGCPRCGGAVFAAEQQLAKGTMW 221 (281)
Q Consensus 163 ~c~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~C~~C~~~I~~~~~v~~~g~~~ 221 (281)
.|+++..-.|.. .+.+.++..--+......+ ..-+.++|..|.++| ++..+.++|+.|
T Consensus 139 vC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpI-eervi~amgKhW 217 (332)
T KOG2272|consen 139 VCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPI-EERVIFAMGKHW 217 (332)
T ss_pred ehhhhhhhcccccccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCch-HHHHHHHhcccc
Confidence 555544444431 1111111111111111111 113566999999999 454566999999
Q ss_pred ccccccccccCCCCCCCccccCCCCcccChhhhccccCCCCCcCCCCCcccccC
Q psy16551 222 HKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYGKNFGPKGFGYGHSPTLVSTS 275 (281)
Q Consensus 222 H~~Cf~C~~C~~~L~~~~~~~~~~g~~~C~~c~~~~f~~~c~~c~~~~~~~s~~ 275 (281)
|.++|+|+.|.+++-+-.. +++.|.+||+.||.++||-.|..|++.++..+++
T Consensus 218 HveHFvCa~CekPFlGHrH-YEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~ 270 (332)
T KOG2272|consen 218 HVEHFVCAKCEKPFLGHRH-YEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVS 270 (332)
T ss_pred chhheeehhcCCcccchhh-hhhcCchhHHHHHHHHhhhhheecCCccCccHHH
Confidence 9999999999999865544 4899999999999999999999999988665544
No 6
>KOG1703|consensus
Probab=99.70 E-value=8.8e-18 Score=160.83 Aligned_cols=130 Identities=28% Similarity=0.605 Sum_probs=115.8
Q ss_pred CCCCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCCcccCCcccccC
Q psy16551 93 APGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYGFAAGSGFLQTD 172 (281)
Q Consensus 93 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~~~c~~~~~~~~ 172 (281)
...+.|..|++.|...+.+.++++.||+.+|.|..|...+....+. ..+|++||..|+.+.+.+
T Consensus 301 ~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~-~~~g~~~c~~~~~~~~~p--------------- 364 (479)
T KOG1703|consen 301 VTRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPR-ELDGKILCHECFHAPFRP--------------- 364 (479)
T ss_pred cccccccccccCcccceeEeeccccccccceeeccccccccCCCcc-ccCCCccHHHHHHHhhCc---------------
Confidence 4458999999999654889999999999999999999999877664 599999999999999988
Q ss_pred CCccccccCCCCCcCCCCccccCCCCCCCCCCCCcccccceeeecCcccccccccccccCCCCCCCccccCCCCcccChh
Q psy16551 173 GLTEDEISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKA 252 (281)
Q Consensus 173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~~~~~~~~~~g~~~C~~ 252 (281)
.|.+|.++|. ++.|.+.+..||++||+|..|++.|....++ ..+|.+||+.
T Consensus 365 ---------------------------~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~-~~~~~pyce~ 415 (479)
T KOG1703|consen 365 ---------------------------NCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFF-ESDGEPYCED 415 (479)
T ss_pred ---------------------------cccccCCchH-HhHhhhccCeechhceeeecccCCCCCCccc-ccCCccchhh
Confidence 8999999994 6677788999999999999999999877665 6999999999
Q ss_pred hhccccCCCCCcCCC
Q psy16551 253 CYGKNFGPKGFGYGH 267 (281)
Q Consensus 253 c~~~~f~~~c~~c~~ 267 (281)
||+++|.++|..|.-
T Consensus 416 ~~~~~~~~~~~~~~~ 430 (479)
T KOG1703|consen 416 HYKKLFTTKCDYCKK 430 (479)
T ss_pred hHhhhccccchhccc
Confidence 999999999988744
No 7
>KOG1044|consensus
Probab=99.69 E-value=1.6e-17 Score=155.04 Aligned_cols=169 Identities=22% Similarity=0.453 Sum_probs=118.1
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhh------------ccCCCCC-C
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGK------------KWGPHGY-G 161 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~------------~~~~~~~-~ 161 (281)
...|..|++.- .++++.+.+++||..||+|..|+..|..+.||...+..+|+...... .+.++|+ +
T Consensus 16 ~i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~c 94 (670)
T KOG1044|consen 16 GIKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSC 94 (670)
T ss_pred ceehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceecccccee
Confidence 45699999998 47999999999999999999999999987777655667787633221 1112211 1
Q ss_pred cccCCcccccCCCccccccCCCCCcCCCCcc-----ccCCCCCCCCCCCCcccccceeeecCcccccccccccccCCCCC
Q psy16551 162 FAAGSGFLQTDGLTEDEISANRPFYNPNTTS-----IMARKGEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLD 236 (281)
Q Consensus 162 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~ 236 (281)
.-|...+...+..+. .+..-.++..-.. ...-+...|++|+..|..++.++++++.||..||+|..|...|.
T Consensus 95 s~ck~pf~~g~~vt~---~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ 171 (670)
T KOG1044|consen 95 STCKSPFKSGDKVTF---SGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN 171 (670)
T ss_pred cccCCCCCCCCeeee---cchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhccccc
Confidence 122222222221111 0000001111011 11124558999999999999999999999999999999999997
Q ss_pred CCccccCCCCcccChhhhccccCCCCCcCCCCC
Q psy16551 237 SVLACDGPDKEIYCKACYGKNFGPKGFGYGHSP 269 (281)
Q Consensus 237 ~~~~~~~~~g~~~C~~c~~~~f~~~c~~c~~~~ 269 (281)
+.+. .+||.+||+.||.+.||.+|..|-+-+
T Consensus 172 gey~--skdg~pyce~dy~~~fgvkc~~c~~fi 202 (670)
T KOG1044|consen 172 GEYM--SKDGVPYCEKDYQAKFGVKCEECEKFI 202 (670)
T ss_pred ceee--ccCCCcchhhhhhhhcCeehHHhhhhh
Confidence 6544 699999999999999999999987766
No 8
>KOG1703|consensus
Probab=99.64 E-value=4.1e-17 Score=156.23 Aligned_cols=126 Identities=28% Similarity=0.559 Sum_probs=110.1
Q ss_pred cccccccCCCCCCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCCcc
Q psy16551 84 VIDTAKIKAAPGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYGFA 163 (281)
Q Consensus 84 ~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~~~ 163 (281)
.++..++.....+.|.+|+++|. ++.|.+++..||++||.|..|++.|....++ .++|.+||+.||++++++
T Consensus 352 ~~c~~~~~~~~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~-~~~~~pyce~~~~~~~~~------ 423 (479)
T KOG1703|consen 352 ILCHECFHAPFRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFF-ESDGEPYCEDHYKKLFTT------ 423 (479)
T ss_pred ccHHHHHHHhhCccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCccc-ccCCccchhhhHhhhccc------
Confidence 34666777778899999999995 6888899999999999999999999887776 499999999999999976
Q ss_pred cCCcccccCCCccccccCCCCCcCCCCccccCCCCCCCCCCCCcccccc-eeeecCcccccccccccccCCCCCCCcccc
Q psy16551 164 AGSGFLQTDGLTEDEISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAE-QQLAKGTMWHKQCFSCNVCKRPLDSVLACD 242 (281)
Q Consensus 164 c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~-~v~~~g~~~H~~Cf~C~~C~~~L~~~~~~~ 242 (281)
+|..|.++|..++ .+.+++..||..||+|+.|.+.|.+..|+
T Consensus 424 ------------------------------------~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~- 466 (479)
T KOG1703|consen 424 ------------------------------------KCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFF- 466 (479)
T ss_pred ------------------------------------cchhccchhHhhhhHhhccCccccccceehhhhhccccCCcee-
Confidence 8999999886655 45599999999999999999999877665
Q ss_pred CCCCcccChhhh
Q psy16551 243 GPDKEIYCKACY 254 (281)
Q Consensus 243 ~~~g~~~C~~c~ 254 (281)
...++++|..|+
T Consensus 467 ~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 467 ETLDKPLCQKHF 478 (479)
T ss_pred ecCCccccccCC
Confidence 689999999886
No 9
>KOG1044|consensus
Probab=99.63 E-value=6.9e-17 Score=150.88 Aligned_cols=117 Identities=25% Similarity=0.556 Sum_probs=104.5
Q ss_pred CCCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCCcccCCcccccCC
Q psy16551 94 PGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYGFAAGSGFLQTDG 173 (281)
Q Consensus 94 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~~~c~~~~~~~~~ 173 (281)
....|++|++.|..++.+.|+++.||..||+|..|+..|.+.+. .++|.+||+.||.+.|+.
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~gey~--skdg~pyce~dy~~~fgv---------------- 193 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGEYM--SKDGVPYCEKDYQAKFGV---------------- 193 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhcccccceee--ccCCCcchhhhhhhhcCe----------------
Confidence 34679999999999999999999999999999999999987665 599999999999999976
Q ss_pred CccccccCCCCCcCCCCccccCCCCCCCCCCCCcccccceeeecCcccccccccccccCCCCCCCccccCCCCcccChhh
Q psy16551 174 LTEDEISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKAC 253 (281)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~~~~~~~~~~g~~~C~~c 253 (281)
+|..|.+.| .+..+.+.|+.||+.|.+|+.|+..++.++-+++....+|-..|
T Consensus 194 --------------------------kc~~c~~fi-sgkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C 246 (670)
T KOG1044|consen 194 --------------------------KCEECEKFI-SGKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDC 246 (670)
T ss_pred --------------------------ehHHhhhhh-hhhhhhccCcccCcchhhhhhhccccccchheeeccccccCCcc
Confidence 899999999 46567799999999999999999999887777788888887777
Q ss_pred hc
Q psy16551 254 YG 255 (281)
Q Consensus 254 ~~ 255 (281)
-+
T Consensus 247 ~q 248 (670)
T KOG1044|consen 247 KQ 248 (670)
T ss_pred cc
Confidence 54
No 10
>KOG1700|consensus
Probab=99.62 E-value=2e-16 Score=134.35 Aligned_cols=166 Identities=28% Similarity=0.590 Sum_probs=123.9
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCCcccCCcccccCCC
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYGFAAGSGFLQTDGL 174 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~~~c~~~~~~~~~~ 174 (281)
...|.+|++.|+..+++...|..||+.||+|..|.+.|....+.. +++.+||+.+|...+++++.+++-+--....-..
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~-~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSE-HEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK 85 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccc-cccccccccchHhhhCcccccccccccccCCCCc
Confidence 457999999999999999999999999999999999999877664 9999999999999999987766553111000000
Q ss_pred ccccccCCCCCcCCCCccccCCCCCCCCCCCCcccccceeeecCcccccccccccccCCCCCCCccccCCCCcccChhhh
Q psy16551 175 TEDEISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACY 254 (281)
Q Consensus 175 ~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~~~~~~~~~~g~~~C~~c~ 254 (281)
... ......+.......+..+....|++|.+.+++.+.++..+..||..||+|+.|++.|+...+. ..+|.++|..++
T Consensus 86 ~~~-~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~-~~~g~l~~~~~~ 163 (200)
T KOG1700|consen 86 DGK-SLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYA-ALEGVLYCKHHF 163 (200)
T ss_pred ccc-cccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchh-hcCCccccchhh
Confidence 000 011111111123455667888999999999999999999999999999999999999877664 578888887776
Q ss_pred ccc-cCCCCC
Q psy16551 255 GKN-FGPKGF 263 (281)
Q Consensus 255 ~~~-f~~~c~ 263 (281)
-.+ +++...
T Consensus 164 ~~~~~~~~~~ 173 (200)
T KOG1700|consen 164 AQLFKGKGNY 173 (200)
T ss_pred heeecCCCcc
Confidence 554 444443
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=99.36 E-value=3.2e-13 Score=92.02 Aligned_cols=57 Identities=42% Similarity=0.987 Sum_probs=51.3
Q ss_pred CcCCCcccccccee-eccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhcc
Q psy16551 98 CPRCGGVVFAAEQV-LAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKW 155 (281)
Q Consensus 98 C~~C~~~I~~~~~~-~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~ 155 (281)
|++|+++|.+.+.+ .+.|+.||++||+|..|++.|.+..++ ..+|++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~-~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFY-EKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEE-EETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeE-eECCEEECHHHHhhhC
Confidence 88999999877776 699999999999999999999987755 4999999999999876
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=99.34 E-value=4.5e-13 Score=91.32 Aligned_cols=57 Identities=40% Similarity=0.981 Sum_probs=51.0
Q ss_pred CCCCCCccccccee-eecCcccccccccccccCCCCCCCccccCCCCcccChhhhcccc
Q psy16551 201 CPRCGGAVFAAEQQ-LAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYGKNF 258 (281)
Q Consensus 201 C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~L~~~~~~~~~~g~~~C~~c~~~~f 258 (281)
|++|+++|...+.+ .+.|+.||++||+|..|++.|....+ ...+|++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~-~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDF-YEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSE-EEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCee-EeECCEEECHHHHhhhC
Confidence 78999999888877 49999999999999999999987764 46899999999999876
No 13
>KOG4577|consensus
Probab=99.16 E-value=1.1e-12 Score=113.47 Aligned_cols=76 Identities=20% Similarity=0.393 Sum_probs=68.4
Q ss_pred CCCCCCCCCcccccceeeecCcccccccccccccCCCCCCCccccCCCCcccChhhhccccCCCCCcCCCCCcccccC
Q psy16551 198 GEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYGKNFGPKGFGYGHSPTLVSTS 275 (281)
Q Consensus 198 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~~~~~~~~~~g~~~C~~c~~~~f~~~c~~c~~~~~~~s~~ 275 (281)
..+|++|.+.|.+..++.++++.||..|++|+.|+.+|....| .++|.+||+.+|.++||+||..|..|+...-+.
T Consensus 33 ip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCF--sR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVV 108 (383)
T KOG4577|consen 33 IPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCF--SREGSVYCKEDFFKRFGTKCSACQEGIPPTQVV 108 (383)
T ss_pred cccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHh--hcCCceeehHHHHHHhCCcchhhcCCCChHHHH
Confidence 3499999999988887789999999999999999999987776 689999999999999999999999998765443
No 14
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.47 E-value=1.1e-07 Score=58.83 Aligned_cols=37 Identities=35% Similarity=0.934 Sum_probs=32.4
Q ss_pred CCCCCCCccccc-ceeeecCcccccccccccccCCCCC
Q psy16551 200 GCPRCGGAVFAA-EQQLAKGTMWHKQCFSCNVCKRPLD 236 (281)
Q Consensus 200 ~C~~C~~~I~~~-~~v~~~g~~~H~~Cf~C~~C~~~L~ 236 (281)
+|.+|+++|.+. ..+.+.++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999876 4566899999999999999999885
No 15
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.47 E-value=9.5e-08 Score=59.06 Aligned_cols=37 Identities=38% Similarity=0.896 Sum_probs=32.9
Q ss_pred CCcCCCcccccc-ceeeccCcccccCceeccccCCCCC
Q psy16551 97 GCPRCGGVVFAA-EQVLAKGSEWHRKCFKCRDCNKTLD 133 (281)
Q Consensus 97 ~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~L~ 133 (281)
.|.+|++.|.+. ..+.+.++.||..||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 489999999876 6678899999999999999999885
No 16
>KOG1700|consensus
Probab=97.82 E-value=5.7e-06 Score=70.51 Aligned_cols=65 Identities=31% Similarity=0.731 Sum_probs=56.2
Q ss_pred CCCCCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccCC
Q psy16551 92 AAPGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGP 157 (281)
Q Consensus 92 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~ 157 (281)
......|..|.+.+++.+.+...+..||..||+|..|+..|....+.. .+|.+||..++..++..
T Consensus 105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~-~~g~l~~~~~~~~~~~~ 169 (200)
T KOG1700|consen 105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAA-LEGVLYCKHHFAQLFKG 169 (200)
T ss_pred hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhh-cCCccccchhhheeecC
Confidence 344678999999999999999999999999999999999999877764 88999998877776543
No 17
>KOG0490|consensus
Probab=97.70 E-value=8.2e-06 Score=70.83 Aligned_cols=114 Identities=24% Similarity=0.444 Sum_probs=84.1
Q ss_pred CCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhh--ccCCCCCCcccCCcccccCCCccc
Q psy16551 100 RCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGK--KWGPHGYGFAAGSGFLQTDGLTED 177 (281)
Q Consensus 100 ~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~--~~~~~~~~~~c~~~~~~~~~~~~~ 177 (281)
.|+..|.+...+.+.+..||..|..|..|...|......+.++|..||..+|.. .+..
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~-------------------- 60 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSK-------------------- 60 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccc--------------------
Confidence 367778776667778999999999999999999732222246999999999987 3332
Q ss_pred cccCCCCCcCCCCccccCCCCCCCCCCCCcccccceee-ecCcccccccccccccCCCCCC-CccccCCCCcccChhhhc
Q psy16551 178 EISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLDS-VLACDGPDKEIYCKACYG 255 (281)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~-~~g~~~H~~Cf~C~~C~~~L~~-~~~~~~~~g~~~C~~c~~ 255 (281)
+|.+|...+...+.+. +..+. |..||.|..|...+.. ..+-.....+..|..++.
T Consensus 61 ----------------------rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~ 117 (235)
T KOG0490|consen 61 ----------------------RCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRK 117 (235)
T ss_pred ----------------------cccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhh
Confidence 8999999887666666 55555 9999999999987643 333323344888887774
Q ss_pred c
Q psy16551 256 K 256 (281)
Q Consensus 256 ~ 256 (281)
+
T Consensus 118 ~ 118 (235)
T KOG0490|consen 118 E 118 (235)
T ss_pred h
Confidence 4
No 18
>KOG1702|consensus
Probab=97.59 E-value=1.1e-05 Score=67.39 Aligned_cols=61 Identities=36% Similarity=0.707 Sum_probs=53.3
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchhhccC
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWG 156 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~ 156 (281)
...|..|++.++..|.+.-+++.||..||+|..|+-+|..+.+- ..+.++||..||.+..+
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyK-gy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYK-GYDKKPYCNPHYPKQVA 64 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhcc-ccccCCCcCccccccee
Confidence 34588999999999999999999999999999999999876654 47899999999987654
No 19
>KOG1702|consensus
Probab=97.33 E-value=3.1e-05 Score=64.69 Aligned_cols=63 Identities=33% Similarity=0.666 Sum_probs=53.5
Q ss_pred CCCCCCCcccccceeeecCcccccccccccccCCCCCCCccccCCCCcccChhhhccccCCCCC
Q psy16551 200 GCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDSVLACDGPDKEIYCKACYGKNFGPKGF 263 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~~~~~~~~~~g~~~C~~c~~~~f~~~c~ 263 (281)
.|..|++.+++.+.+..+++.||..||.|..|+.+|....+ ...|.++||-.||.+..++--+
T Consensus 6 n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKny-Kgy~kkpycn~hYpkq~at~~a 68 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNY-KGYDKKPYCNPHYPKQVATVMA 68 (264)
T ss_pred hhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhc-cccccCCCcCcccccceeeeec
Confidence 68899999999999999999999999999999999975443 3578999999999887655433
No 20
>KOG0490|consensus
Probab=93.85 E-value=0.027 Score=48.62 Aligned_cols=64 Identities=25% Similarity=0.585 Sum_probs=51.9
Q ss_pred CCCcccccceeeecCcccccccccccccCCCCC--CCccccCCCCcccChhhhcc--ccCCCCCcCCCCC
Q psy16551 204 CGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLD--SVLACDGPDKEIYCKACYGK--NFGPKGFGYGHSP 269 (281)
Q Consensus 204 C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~--~~~~~~~~~g~~~C~~c~~~--~f~~~c~~c~~~~ 269 (281)
|+..|.+...+.+.+..||..|..|..|...|. ...+ ..+|..||...|.. .+..+|.+|.-.+
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~g~~~~~~d~~~~~~~~~rr~rt~~~~ 69 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCF--SKDGSIYCKRDYQREFKFSKRCARCKFTI 69 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcc--cCCCcccccccchhhhhccccccCCCCCc
Confidence 566676655556779999999999999999996 3333 34999999999998 8899999998765
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.03 E-value=0.55 Score=31.16 Aligned_cols=37 Identities=24% Similarity=0.685 Sum_probs=26.4
Q ss_pred CCCCCCCCcccccc-eee--ecCcccccccc----cccc--cCCCC
Q psy16551 199 EGCPRCGGAVFAAE-QQL--AKGTMWHKQCF----SCNV--CKRPL 235 (281)
Q Consensus 199 ~~C~~C~~~I~~~~-~v~--~~g~~~H~~Cf----~C~~--C~~~L 235 (281)
.+|..|+++|.+++ .|+ .=+..||++|. .|.. |+..+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 38999999997554 444 46778999997 3655 55443
No 22
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=83.21 E-value=0.36 Score=36.25 Aligned_cols=33 Identities=24% Similarity=0.465 Sum_probs=26.8
Q ss_pred CCCCCCCcccccceeee-cCcccccccccccccC
Q psy16551 200 GCPRCGGAVFAAEQQLA-KGTMWHKQCFSCNVCK 232 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~~-~g~~~H~~Cf~C~~C~ 232 (281)
+|..|+++|..++.+++ .+..-|..||.=..-.
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~~ 37 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKASK 37 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHHhh
Confidence 79999999999999984 5567899999865443
No 23
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=76.17 E-value=1.6 Score=29.00 Aligned_cols=29 Identities=31% Similarity=0.819 Sum_probs=21.4
Q ss_pred CCCCcCCCcccccccee---eccCcccccCce
Q psy16551 95 GKGCPRCGGVVFAAEQV---LAKGSEWHRKCF 123 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~---~~~~~~~H~~CF 123 (281)
+.+|..|+++|.+++-+ ..-+..||++|-
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 46799999999644433 356888999885
No 24
>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=75.77 E-value=2.3 Score=31.81 Aligned_cols=31 Identities=19% Similarity=0.434 Sum_probs=21.1
Q ss_pred CCCCCCCCCCcccccceee-ecCccccccccc
Q psy16551 197 KGEGCPRCGGAVFAAEQQL-AKGTMWHKQCFS 227 (281)
Q Consensus 197 ~~~~C~~C~~~I~~~~~v~-~~g~~~H~~Cf~ 227 (281)
....|+.|+++|.....+. ..|..+|..|+.
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4458999999996543333 456778887753
No 25
>KOG0320|consensus
Probab=73.08 E-value=1.4 Score=36.48 Aligned_cols=37 Identities=14% Similarity=0.427 Sum_probs=25.8
Q ss_pred ccCceeccccCCCCCCCCeeeCCCCcccCccchhhcc
Q psy16551 119 HRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKW 155 (281)
Q Consensus 119 H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~ 155 (281)
-..+++|-.|-.......-+--+=|.+||..|-....
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~al 164 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDAL 164 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHH
Confidence 3467899888776665432323678999999987654
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=72.59 E-value=2.7 Score=25.61 Aligned_cols=28 Identities=21% Similarity=0.597 Sum_probs=19.1
Q ss_pred CCCCCCcccccceee-ecCcccccccccc
Q psy16551 201 CPRCGGAVFAAEQQL-AKGTMWHKQCFSC 228 (281)
Q Consensus 201 C~~C~~~I~~~~~v~-~~g~~~H~~Cf~C 228 (281)
|.-|++.|.....+. ..++.||.-|-.|
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 677999996554443 7888898555444
No 27
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=71.90 E-value=1.9 Score=28.23 Aligned_cols=30 Identities=23% Similarity=0.522 Sum_probs=22.2
Q ss_pred cccccCCCCCCCccccCCCCcccChhhhccc
Q psy16551 227 SCNVCKRPLDSVLACDGPDKEIYCKACYGKN 257 (281)
Q Consensus 227 ~C~~C~~~L~~~~~~~~~~g~~~C~~c~~~~ 257 (281)
.|..|+..++....+...|| .+|..|+.+.
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 37888888865444456788 6899999876
No 28
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=69.18 E-value=3 Score=22.53 Aligned_cols=9 Identities=44% Similarity=1.305 Sum_probs=5.0
Q ss_pred CcCCCcccc
Q psy16551 98 CPRCGGVVF 106 (281)
Q Consensus 98 C~~C~~~I~ 106 (281)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 555665553
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=69.05 E-value=3 Score=30.71 Aligned_cols=12 Identities=25% Similarity=0.767 Sum_probs=9.1
Q ss_pred CCCCCCCccccc
Q psy16551 200 GCPRCGGAVFAA 211 (281)
Q Consensus 200 ~C~~C~~~I~~~ 211 (281)
+|+.|++.|.+.
T Consensus 71 iCamCGKki~dt 82 (90)
T PF10235_consen 71 ICAMCGKKILDT 82 (90)
T ss_pred cccccCCeeccc
Confidence 788888888543
No 30
>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=68.25 E-value=3.6 Score=27.46 Aligned_cols=32 Identities=16% Similarity=0.119 Sum_probs=23.6
Q ss_pred eeccccCCCCCCCCeeeCCCCcccCccchhhccC
Q psy16551 123 FKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWG 156 (281)
Q Consensus 123 F~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~ 156 (281)
|.|..|+..+... .....|..||+.|..+.+.
T Consensus 2 ~~Cpi~~~~~~~P--v~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKDP--VILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCCC--EECCCCCEEeHHHHHHHHH
Confidence 5688888887753 2247789999999877653
No 31
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=67.93 E-value=1.4 Score=33.10 Aligned_cols=31 Identities=23% Similarity=0.547 Sum_probs=23.1
Q ss_pred CCcCCCccccccceeec-cCcccccCceeccc
Q psy16551 97 GCPRCGGVVFAAEQVLA-KGSEWHRKCFKCRD 127 (281)
Q Consensus 97 ~C~~C~~~I~~~~~~~~-~~~~~H~~CF~C~~ 127 (281)
.|..|+++|+.++.+.. .+..-|-.||+=..
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 58889999988888754 45668888886543
No 32
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=66.11 E-value=2.1 Score=31.69 Aligned_cols=35 Identities=26% Similarity=0.543 Sum_probs=28.5
Q ss_pred CCCCCCCcccccceeee-cCcccccccccccccCCC
Q psy16551 200 GCPRCGGAVFAAEQQLA-KGTMWHKQCFSCNVCKRP 234 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~~-~g~~~H~~Cf~C~~C~~~ 234 (281)
+|..|++.|..++.+++ ....-|-+||.=+.-+++
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCc
Confidence 89999999999998884 455679999987766554
No 33
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=64.33 E-value=7 Score=26.90 Aligned_cols=34 Identities=24% Similarity=0.566 Sum_probs=15.2
Q ss_pred eeccccCCCCCCCCeeeCCCCcccCccchhhccCC
Q psy16551 123 FKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGP 157 (281)
Q Consensus 123 F~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~ 157 (281)
++|+.|...|...-.. ..=+.+||..|-...++.
T Consensus 8 LrCs~C~~~l~~pv~l-~~CeH~fCs~Ci~~~~~~ 41 (65)
T PF14835_consen 8 LRCSICFDILKEPVCL-GGCEHIFCSSCIRDCIGS 41 (65)
T ss_dssp TS-SSS-S--SS-B----SSS--B-TTTGGGGTTT
T ss_pred cCCcHHHHHhcCCcee-ccCccHHHHHHhHHhcCC
Confidence 5788888777643221 244567888888765554
No 34
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=63.57 E-value=9.7 Score=40.17 Aligned_cols=32 Identities=31% Similarity=0.854 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCcccccceeee--------cCccc-cccccc
Q psy16551 196 RKGEGCPRCGGAVFAAEQQLA--------KGTMW-HKQCFS 227 (281)
Q Consensus 196 ~~~~~C~~C~~~I~~~~~v~~--------~g~~~-H~~Cf~ 227 (281)
.+...|..|++.|..++.... ....| |..||.
T Consensus 114 S~Ra~Ck~C~~kI~KgelRig~~v~~~~g~~~~W~H~~Cf~ 154 (981)
T PLN03123 114 TSRATCRRCSEKILKGEVRISSKPEGQGYKGLAWHHAKCFL 154 (981)
T ss_pred CCCCccccCCceecCCceEEEeeecCCCCCccccccccccc
Confidence 345689999999987764321 11234 888884
No 35
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=56.72 E-value=5.5 Score=33.83 Aligned_cols=31 Identities=26% Similarity=0.514 Sum_probs=24.3
Q ss_pred eeccccCCCCCCCCeeeCCCCcccCccchhhc
Q psy16551 123 FKCRDCNKTLDSINACDGPDKDIYCKTCYGKK 154 (281)
Q Consensus 123 F~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~ 154 (281)
-+|..|+..+....-. ..+|+++|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~-~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAV-VLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhh-hcCCceecccccccc
Confidence 6889999877765544 489999999999753
No 36
>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=56.32 E-value=7.2 Score=28.98 Aligned_cols=33 Identities=24% Similarity=0.392 Sum_probs=22.6
Q ss_pred CCCCCCCcCCCccccccceeec-cCcccccCcee
Q psy16551 92 AAPGKGCPRCGGVVFAAEQVLA-KGSEWHRKCFK 124 (281)
Q Consensus 92 ~~~~~~C~~C~~~I~~~~~~~~-~~~~~H~~CF~ 124 (281)
-.....|..|+++|....++.. .|..+|..|++
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 3445679999999976444443 46668888764
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=50.22 E-value=6.2 Score=28.19 Aligned_cols=17 Identities=18% Similarity=0.374 Sum_probs=11.8
Q ss_pred CCCCCCcCCCccccccc
Q psy16551 93 APGKGCPRCGGVVFAAE 109 (281)
Q Consensus 93 ~~~~~C~~C~~~I~~~~ 109 (281)
.....|..|++.|..++
T Consensus 5 s~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 5 SGRAKCKGCKKKIAKGE 21 (82)
T ss_dssp SSTEBETTTSCBE-TTS
T ss_pred CCCccCcccCCcCCCCC
Confidence 34457999999996544
No 38
>KOG0978|consensus
Probab=48.54 E-value=4.4 Score=40.77 Aligned_cols=34 Identities=18% Similarity=0.528 Sum_probs=22.3
Q ss_pred ceeccccCCCCCCCCeeeCCCCcccCccchhhccCC
Q psy16551 122 CFKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGP 157 (281)
Q Consensus 122 CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~ 157 (281)
=++|..|+..+-+. +...=+..||..|...++..
T Consensus 643 ~LkCs~Cn~R~Kd~--vI~kC~H~FC~~Cvq~r~et 676 (698)
T KOG0978|consen 643 LLKCSVCNTRWKDA--VITKCGHVFCEECVQTRYET 676 (698)
T ss_pred ceeCCCccCchhhH--HHHhcchHHHHHHHHHHHHH
Confidence 47888888655431 11244578999998887764
No 39
>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=46.75 E-value=16 Score=20.05 Aligned_cols=9 Identities=33% Similarity=1.017 Sum_probs=4.5
Q ss_pred CcCCCcccc
Q psy16551 98 CPRCGGVVF 106 (281)
Q Consensus 98 C~~C~~~I~ 106 (281)
|..|+..|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 445555554
No 40
>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=45.96 E-value=11 Score=22.82 Aligned_cols=25 Identities=24% Similarity=0.422 Sum_probs=16.3
Q ss_pred eeccccCCCCCCCCeeeCCCCcccCccchh
Q psy16551 123 FKCRDCNKTLDSINACDGPDKDIYCKTCYG 152 (281)
Q Consensus 123 F~C~~C~~~L~~~~~~~~~~g~~~C~~cy~ 152 (281)
+.|..|+.. ++...+|..||..|-.
T Consensus 9 ~~C~~C~~~-----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR-----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe-----EeEccCCEEEhhhCce
Confidence 447777654 2335888888877654
No 41
>PF12773 DZR: Double zinc ribbon
Probab=45.31 E-value=24 Score=22.43 Aligned_cols=9 Identities=44% Similarity=1.243 Sum_probs=4.4
Q ss_pred CCCCCCCcc
Q psy16551 200 GCPRCGGAV 208 (281)
Q Consensus 200 ~C~~C~~~I 208 (281)
.|..|+..+
T Consensus 14 fC~~CG~~l 22 (50)
T PF12773_consen 14 FCPHCGTPL 22 (50)
T ss_pred CChhhcCCh
Confidence 455555444
No 42
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=43.70 E-value=11 Score=29.85 Aligned_cols=21 Identities=38% Similarity=0.963 Sum_probs=14.2
Q ss_pred ccccCCCCCCCccccCCCCcccChhhh
Q psy16551 228 CNVCKRPLDSVLACDGPDKEIYCKACY 254 (281)
Q Consensus 228 C~~C~~~L~~~~~~~~~~g~~~C~~c~ 254 (281)
|..|+.+| | .++|.+||..|-
T Consensus 31 Cp~Cg~PL----F--~KdG~v~CPvC~ 51 (131)
T COG1645 31 CPKCGTPL----F--RKDGEVFCPVCG 51 (131)
T ss_pred CcccCCcc----e--eeCCeEECCCCC
Confidence 56777776 2 367777777775
No 43
>KOG4443|consensus
Probab=43.27 E-value=15 Score=36.52 Aligned_cols=22 Identities=27% Similarity=0.664 Sum_probs=15.8
Q ss_pred ecCcccccccccccccCCCCCC
Q psy16551 216 AKGTMWHKQCFSCNVCKRPLDS 237 (281)
Q Consensus 216 ~~g~~~H~~Cf~C~~C~~~L~~ 237 (281)
..|..+.++|++|..|+..|.+
T Consensus 106 ~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 106 PSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred cCcccccHHHHhhhhccccccc
Confidence 3455667888888888887755
No 44
>KOG2893|consensus
Probab=43.24 E-value=8.5 Score=33.51 Aligned_cols=38 Identities=32% Similarity=0.472 Sum_probs=26.9
Q ss_pred CCCCCcCCCccccccceeeccCcccccCceeccccCCCCCC
Q psy16551 94 PGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDS 134 (281)
Q Consensus 94 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~ 134 (281)
..+-|..|+... +.|+|++.. -...+|+|..|++.|-.
T Consensus 9 ~kpwcwycnref-ddekiliqh--qkakhfkchichkkl~s 46 (341)
T KOG2893|consen 9 DKPWCWYCNREF-DDEKILIQH--QKAKHFKCHICHKKLFS 46 (341)
T ss_pred CCceeeeccccc-chhhhhhhh--hhhccceeeeehhhhcc
Confidence 456799999997 456664432 23457999999998854
No 45
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=42.75 E-value=23 Score=21.95 Aligned_cols=31 Identities=19% Similarity=0.385 Sum_probs=18.8
Q ss_pred ccccCCCCC-CCCeeeCCCCcccCccchhhcc
Q psy16551 125 CRDCNKTLD-SINACDGPDKDIYCKTCYGKKW 155 (281)
Q Consensus 125 C~~C~~~L~-~~~~~~~~~g~~~C~~cy~~~~ 155 (281)
|..|...+. ...++...=|..+|..|..+..
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc
Confidence 556666662 2233334567788888887655
No 46
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=42.69 E-value=25 Score=35.46 Aligned_cols=9 Identities=44% Similarity=1.353 Sum_probs=4.7
Q ss_pred CCCCCCCcc
Q psy16551 200 GCPRCGGAV 208 (281)
Q Consensus 200 ~C~~C~~~I 208 (281)
.|..|+..+
T Consensus 43 fC~~CG~~~ 51 (645)
T PRK14559 43 HCPNCGAET 51 (645)
T ss_pred cccccCCcc
Confidence 455555544
No 47
>KOG2462|consensus
Probab=41.56 E-value=7.2 Score=34.67 Aligned_cols=38 Identities=21% Similarity=0.417 Sum_probs=22.5
Q ss_pred CCCCCCCcccccceee-ecCcccccccccccccCCCCCC
Q psy16551 200 GCPRCGGAVFAAEQQL-AKGTMWHKQCFSCNVCKRPLDS 237 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~-~~g~~~H~~Cf~C~~C~~~L~~ 237 (281)
.|+.|++.+.+.--+. .+...=+..=|.|..|++.+..
T Consensus 217 ~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 217 SCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred cCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 7888888775543332 2333333445778888877643
No 48
>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=41.52 E-value=12 Score=30.36 Aligned_cols=37 Identities=19% Similarity=0.532 Sum_probs=25.1
Q ss_pred CCCCCCCccccccee---eecCcccccccccccccCCCCCC
Q psy16551 200 GCPRCGGAVFAAEQQ---LAKGTMWHKQCFSCNVCKRPLDS 237 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v---~~~g~~~H~~Cf~C~~C~~~L~~ 237 (281)
.|+.|+-+|.....+ ...|..|+.- -.|..|+++...
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~P-sYC~~CGkpyPW 80 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLGGHYEAP-SYCHNCGKPYPW 80 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeCCCCCCC-hhHHhCCCCCch
Confidence 799999999654333 2455666633 358889988764
No 49
>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=41.21 E-value=11 Score=21.37 Aligned_cols=11 Identities=45% Similarity=0.945 Sum_probs=5.8
Q ss_pred CCCCCCCCccc
Q psy16551 199 EGCPRCGGAVF 209 (281)
Q Consensus 199 ~~C~~C~~~I~ 209 (281)
..|.+|...|.
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 37999998873
No 50
>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=40.67 E-value=13 Score=23.14 Aligned_cols=22 Identities=41% Similarity=1.014 Sum_probs=13.7
Q ss_pred eccccCCCCCCCCeeeCCCCcccCccc
Q psy16551 124 KCRDCNKTLDSINACDGPDKDIYCKTC 150 (281)
Q Consensus 124 ~C~~C~~~L~~~~~~~~~~g~~~C~~c 150 (281)
.|..|+.+|.. .++|+.||..|
T Consensus 19 ~Cp~C~~PL~~-----~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMR-----DKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEE-----ecCCCEECCCC
Confidence 35566766633 36777777665
No 51
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=40.01 E-value=17 Score=24.11 Aligned_cols=25 Identities=16% Similarity=0.076 Sum_probs=18.6
Q ss_pred CCCCCCCcccccceeeecCcccccc
Q psy16551 200 GCPRCGGAVFAAEQQLAKGTMWHKQ 224 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~~~g~~~H~~ 224 (281)
+|..|+++|.....+...+..-|+.
T Consensus 3 ~CvVCKqpi~~a~~v~T~~G~VH~g 27 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVETESGPVHPG 27 (54)
T ss_pred eeeeeCCccCcceEEEcCCCccCcH
Confidence 8999999997776666556666764
No 52
>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=39.73 E-value=12 Score=23.82 Aligned_cols=30 Identities=17% Similarity=0.482 Sum_probs=18.5
Q ss_pred eccccCCCCCCCCeeeCCCCcc-cCccchhhcc
Q psy16551 124 KCRDCNKTLDSINACDGPDKDI-YCKTCYGKKW 155 (281)
Q Consensus 124 ~C~~C~~~L~~~~~~~~~~g~~-~C~~cy~~~~ 155 (281)
.|..|....... .+..=|.. +|..|..+.+
T Consensus 4 ~C~iC~~~~~~~--~~~pCgH~~~C~~C~~~~~ 34 (50)
T PF13920_consen 4 ECPICFENPRDV--VLLPCGHLCFCEECAERLL 34 (50)
T ss_dssp B-TTTSSSBSSE--EEETTCEEEEEHHHHHHHH
T ss_pred CCccCCccCCce--EEeCCCChHHHHHHhHHhc
Confidence 466676654432 22366777 9999988765
No 53
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.63 E-value=46 Score=35.16 Aligned_cols=35 Identities=23% Similarity=0.543 Sum_probs=23.1
Q ss_pred CCCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCccchh
Q psy16551 94 PGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCKTCYG 152 (281)
Q Consensus 94 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~~cy~ 152 (281)
....|..|+... .=|+|..|+.. .....+|..|-.
T Consensus 625 g~RfCpsCG~~t---------------~~frCP~CG~~---------Te~i~fCP~CG~ 659 (1121)
T PRK04023 625 GRRKCPSCGKET---------------FYRRCPFCGTH---------TEPVYRCPRCGI 659 (1121)
T ss_pred cCccCCCCCCcC---------------CcccCCCCCCC---------CCcceeCccccC
Confidence 357899998863 12888999875 122346888843
No 54
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=37.97 E-value=16 Score=31.10 Aligned_cols=31 Identities=23% Similarity=0.370 Sum_probs=22.9
Q ss_pred ccccccCCCCCCCccccCCCCcccChhhhccc
Q psy16551 226 FSCNVCKRPLDSVLACDGPDKEIYCKACYGKN 257 (281)
Q Consensus 226 f~C~~C~~~L~~~~~~~~~~g~~~C~~c~~~~ 257 (281)
-+|+.|+-.+..... ...+|+++|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~-~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRA-VVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchh-hhcCCceecccccccc
Confidence 578889887744333 3689999999999754
No 55
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=37.33 E-value=29 Score=23.46 Aligned_cols=28 Identities=25% Similarity=0.617 Sum_probs=18.2
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCC
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKT 131 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~ 131 (281)
.+.|..|+.+|.+.+.. .-|.|-.|+..
T Consensus 7 ~~~CtSCg~~i~~~~~~---------~~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREKA---------VKFLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCcc---------CEeeCCCCCCe
Confidence 35689999888654422 13677777765
No 56
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=34.90 E-value=15 Score=27.47 Aligned_cols=29 Identities=21% Similarity=0.505 Sum_probs=17.3
Q ss_pred ceeccccCCCCCCCCeeeCCCCcccCccc
Q psy16551 122 CFKCRDCNKTLDSINACDGPDKDIYCKTC 150 (281)
Q Consensus 122 CF~C~~C~~~L~~~~~~~~~~g~~~C~~c 150 (281)
=|+|+.|-.----.......+|.++|.+|
T Consensus 70 EFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEechhhhccccCCCEecccc
Confidence 38888884322112222247899999887
No 57
>KOG2462|consensus
Probab=32.66 E-value=33 Score=30.63 Aligned_cols=37 Identities=24% Similarity=0.394 Sum_probs=21.9
Q ss_pred CCCCCCCcccccceeeecCccccc--ccccccccCCCCCC
Q psy16551 200 GCPRCGGAVFAAEQQLAKGTMWHK--QCFSCNVCKRPLDS 237 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~~~g~~~H~--~Cf~C~~C~~~L~~ 237 (281)
.|..|+|.+..-.++. .--..|- .=|.|..|++.+.+
T Consensus 189 ~C~iCGKaFSRPWLLQ-GHiRTHTGEKPF~C~hC~kAFAD 227 (279)
T KOG2462|consen 189 ECGICGKAFSRPWLLQ-GHIRTHTGEKPFSCPHCGKAFAD 227 (279)
T ss_pred ccccccccccchHHhh-cccccccCCCCccCCcccchhcc
Confidence 7899998874332221 1111222 25889999998865
No 58
>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=32.54 E-value=30 Score=33.66 Aligned_cols=37 Identities=30% Similarity=0.669 Sum_probs=22.5
Q ss_pred CCCCCCCcccccceeeecCcccccccccccccCCCCCC
Q psy16551 200 GCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLDS 237 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~~ 237 (281)
-|+.|...+...+ +...+....++||.|-.|...|..
T Consensus 28 yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 28 YCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred ECccccccCChhh-heeccceeccccccCCCCCCccee
Confidence 4777766553332 223344445588888888888853
No 59
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=32.01 E-value=32 Score=18.86 Aligned_cols=9 Identities=44% Similarity=1.327 Sum_probs=6.3
Q ss_pred CCCCCCCcc
Q psy16551 200 GCPRCGGAV 208 (281)
Q Consensus 200 ~C~~C~~~I 208 (281)
.|+.|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 677777755
No 60
>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=31.98 E-value=30 Score=22.77 Aligned_cols=27 Identities=26% Similarity=0.669 Sum_probs=13.9
Q ss_pred ccccCCCCCCCCeeeCCCCcccCc-cchh
Q psy16551 125 CRDCNKTLDSINACDGPDKDIYCK-TCYG 152 (281)
Q Consensus 125 C~~C~~~L~~~~~~~~~~g~~~C~-~cy~ 152 (281)
|..|...+.....+ .+||+.||- .|..
T Consensus 10 C~~C~C~V~~~~Ai-~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 10 CPSCSCVVSEEEAI-QKDGKYYCSEACAN 37 (52)
T ss_dssp STT----B-TTTSE-ESSS-EESSHHHHH
T ss_pred CCCCEeEECchHhH-HhCCEeeecHHHhc
Confidence 56677777755555 499999994 5544
No 61
>KOG1813|consensus
Probab=31.76 E-value=27 Score=31.44 Aligned_cols=33 Identities=24% Similarity=0.411 Sum_probs=20.5
Q ss_pred eeccccCCCCCCCCeeeCCCCcccCccchhhccCC
Q psy16551 123 FKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGP 157 (281)
Q Consensus 123 F~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~ 157 (281)
|.|..|++.+-..- ...-+..||+.|..+.|..
T Consensus 242 f~c~icr~~f~~pV--vt~c~h~fc~~ca~~~~qk 274 (313)
T KOG1813|consen 242 FKCFICRKYFYRPV--VTKCGHYFCEVCALKPYQK 274 (313)
T ss_pred ccccccccccccch--hhcCCceeehhhhcccccc
Confidence 67777777664311 1245667888888776643
No 62
>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=31.55 E-value=38 Score=22.64 Aligned_cols=22 Identities=14% Similarity=0.274 Sum_probs=15.2
Q ss_pred ccChhhhccccCCCCCcCCCCC
Q psy16551 248 IYCKACYGKNFGPKGFGYGHSP 269 (281)
Q Consensus 248 ~~C~~c~~~~f~~~c~~c~~~~ 269 (281)
-||..|...++...|-.||+..
T Consensus 30 TFC~~C~e~~l~~~CPNCgGel 51 (57)
T PF06906_consen 30 TFCADCAETMLNGVCPNCGGEL 51 (57)
T ss_pred cccHHHHHHHhcCcCcCCCCcc
Confidence 3577777777777777776643
No 63
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=31.42 E-value=33 Score=31.43 Aligned_cols=45 Identities=18% Similarity=0.421 Sum_probs=31.5
Q ss_pred ccCCCCCCCCcCCCccccccceeec-----cC-----cccccCceeccccCCCCC
Q psy16551 89 KIKAAPGKGCPRCGGVVFAAEQVLA-----KG-----SEWHRKCFKCRDCNKTLD 133 (281)
Q Consensus 89 ~~~~~~~~~C~~C~~~I~~~~~~~~-----~~-----~~~H~~CF~C~~C~~~L~ 133 (281)
-+..++...|..|+..|+-|.++.+ .+ ....+--++|..|...+.
T Consensus 34 Rf~~Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~ 88 (324)
T PF04502_consen 34 RFMMPFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIE 88 (324)
T ss_pred EEcCCccCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEe
Confidence 4456677889999999987776644 22 223344688999987764
No 64
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=31.26 E-value=28 Score=23.52 Aligned_cols=29 Identities=24% Similarity=0.631 Sum_probs=19.0
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCCC
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 132 (281)
.+.|..|+..|..++... -|.|-.|+..+
T Consensus 9 ~~~CtSCg~~i~p~e~~v---------~F~CPnCGe~~ 37 (61)
T COG2888 9 PPVCTSCGREIAPGETAV---------KFPCPNCGEVE 37 (61)
T ss_pred CceeccCCCEeccCCcee---------EeeCCCCCcee
Confidence 467999998885544332 27777777443
No 65
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=31.25 E-value=29 Score=25.00 Aligned_cols=29 Identities=38% Similarity=0.810 Sum_probs=15.3
Q ss_pred ccccCCCCCCCc-cc---cCCCCcccChhhhcc
Q psy16551 228 CNVCKRPLDSVL-AC---DGPDKEIYCKACYGK 256 (281)
Q Consensus 228 C~~C~~~L~~~~-~~---~~~~g~~~C~~c~~~ 256 (281)
|..|+.+|.... +- ...-+.-||.-||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 667777774322 11 122334478777743
No 66
>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=29.97 E-value=26 Score=20.72 Aligned_cols=8 Identities=38% Similarity=0.883 Sum_probs=4.3
Q ss_pred CcCCCccc
Q psy16551 98 CPRCGGVV 105 (281)
Q Consensus 98 C~~C~~~I 105 (281)
|..|...+
T Consensus 2 C~iC~~~~ 9 (45)
T cd00162 2 CPICLEEF 9 (45)
T ss_pred CCcCchhh
Confidence 55555554
No 67
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=28.99 E-value=36 Score=22.91 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=19.0
Q ss_pred ccccCCCCC-CCCeeeCCCCcccCc-cchhh
Q psy16551 125 CRDCNKTLD-SINACDGPDKDIYCK-TCYGK 153 (281)
Q Consensus 125 C~~C~~~L~-~~~~~~~~~g~~~C~-~cy~~ 153 (281)
|..|++.|. +...+..++++.+|. +|-.+
T Consensus 19 C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~ 49 (58)
T PF04570_consen 19 CYLCKKKLDPGKDIYMYRGDKAFCSEECRSQ 49 (58)
T ss_pred HHccCCCCCCCCCeeeeccccccccHHHHHH
Confidence 567788888 444444488899994 55443
No 68
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=28.48 E-value=25 Score=21.78 Aligned_cols=29 Identities=17% Similarity=0.749 Sum_probs=15.3
Q ss_pred eeccccCCCCCCCCeeeCCCCcccCccchh
Q psy16551 123 FKCRDCNKTLDSINACDGPDKDIYCKTCYG 152 (281)
Q Consensus 123 F~C~~C~~~L~~~~~~~~~~g~~~C~~cy~ 152 (281)
|+|..|+..+....... .+....|..|-.
T Consensus 6 y~C~~Cg~~fe~~~~~~-~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSIS-EDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcC-CCCCCcCCCCCC
Confidence 56667766555433332 245556666543
No 69
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=28.07 E-value=18 Score=30.62 Aligned_cols=32 Identities=25% Similarity=0.513 Sum_probs=18.9
Q ss_pred eeccccCCCCCCCCeeeCCCCcccCccchhhccC
Q psy16551 123 FKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWG 156 (281)
Q Consensus 123 F~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~ 156 (281)
|.|..|.+......- -.=|.-||..|+.+.+.
T Consensus 197 F~C~iCKkdy~spvv--t~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 197 FLCGICKKDYESPVV--TECGHSFCSLCAIRKYQ 228 (259)
T ss_pred eeehhchhhccchhh--hhcchhHHHHHHHHHhc
Confidence 677777665543111 13466677777777664
No 70
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=27.86 E-value=17 Score=22.81 Aligned_cols=13 Identities=23% Similarity=0.713 Sum_probs=5.3
Q ss_pred CcCCCccccccce
Q psy16551 98 CPRCGGVVFAAEQ 110 (281)
Q Consensus 98 C~~C~~~I~~~~~ 110 (281)
|..|++.|..+.+
T Consensus 1 C~~C~~iv~~G~~ 13 (43)
T PF08746_consen 1 CEACKEIVTQGQR 13 (43)
T ss_dssp -TTT-SB-SSSEE
T ss_pred CcccchhHeeecc
Confidence 5566666654433
No 71
>PRK00420 hypothetical protein; Validated
Probab=25.76 E-value=40 Score=25.91 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=16.4
Q ss_pred eeccccCCCCCCCCeeeCCCCcccCccchhh
Q psy16551 123 FKCRDCNKTLDSINACDGPDKDIYCKTCYGK 153 (281)
Q Consensus 123 F~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~ 153 (281)
-.|..|+.+|-. .++|+.||..|-..
T Consensus 24 ~~CP~Cg~pLf~-----lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFE-----LKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCccee-----cCCCceECCCCCCe
Confidence 346677766622 26778888877653
No 72
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=25.32 E-value=61 Score=27.46 Aligned_cols=16 Identities=31% Similarity=0.501 Sum_probs=10.3
Q ss_pred CCCCCCCcccccceee
Q psy16551 200 GCPRCGGAVFAAEQQL 215 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~ 215 (281)
.|+.|+..|.....+.
T Consensus 70 ~CPvCR~~Is~~~LvP 85 (193)
T PLN03208 70 KCPVCKSDVSEATLVP 85 (193)
T ss_pred cCCCCCCcCChhcEEE
Confidence 6777777776554443
No 73
>KOG3579|consensus
Probab=25.20 E-value=43 Score=30.05 Aligned_cols=48 Identities=21% Similarity=0.483 Sum_probs=33.1
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCCeeeCCCCcccCc
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSINACDGPDKDIYCK 148 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~~g~~~C~ 148 (281)
...|.-|++++.+..+|....-.-|+-||-|+.= .+... ...|.+||.
T Consensus 268 pLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRe--sIK~Q----g~sgevYCP 315 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRE--SIKQQ----GASGEVYCP 315 (352)
T ss_pred ceeehhhhhhhccCceeecCCCcccceecccCHH--HHHhh----cCCCceeCC
Confidence 3568889998888778888888888889888632 22221 245577774
No 74
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=24.70 E-value=23 Score=28.86 Aligned_cols=32 Identities=25% Similarity=0.282 Sum_probs=22.4
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCCCCC
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDS 134 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~ 134 (281)
.=+|..|+..+...+.+. .=|.|..||..|..
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAME--------LNFTCPRCGAMLDY 140 (158)
T ss_pred eEECCCCCcEeeHHHHHH--------cCCcCCCCCCEeee
Confidence 346999998775444442 24999999998853
No 75
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.20 E-value=40 Score=22.15 Aligned_cols=29 Identities=28% Similarity=0.575 Sum_probs=18.0
Q ss_pred CCcCCCccccccceeeccCcccccCceec
Q psy16551 97 GCPRCGGVVFAAEQVLAKGSEWHRKCFKC 125 (281)
Q Consensus 97 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C 125 (281)
.|..||..|...--....++.|=.+|-.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhc
Confidence 48888888743222345567787777444
No 76
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=24.02 E-value=46 Score=19.86 Aligned_cols=10 Identities=30% Similarity=0.900 Sum_probs=3.6
Q ss_pred CCcCCCcccc
Q psy16551 97 GCPRCGGVVF 106 (281)
Q Consensus 97 ~C~~C~~~I~ 106 (281)
.|..|+++..
T Consensus 5 ~C~eC~~~f~ 14 (34)
T PF01286_consen 5 KCDECGKPFM 14 (34)
T ss_dssp E-TTT--EES
T ss_pred hHhHhCCHHH
Confidence 4555555543
No 77
>KOG3039|consensus
Probab=23.79 E-value=1.1e+02 Score=27.09 Aligned_cols=84 Identities=15% Similarity=0.099 Sum_probs=59.1
Q ss_pred CCCCCCCcCCCccccccceeec----cC-------cccccCceeccccCCCCCCC--CeeeCCCCcccCccchhhccCCC
Q psy16551 92 AAPGKGCPRCGGVVFAAEQVLA----KG-------SEWHRKCFKCRDCNKTLDSI--NACDGPDKDIYCKTCYGKKWGPH 158 (281)
Q Consensus 92 ~~~~~~C~~C~~~I~~~~~~~~----~~-------~~~H~~CF~C~~C~~~L~~~--~~~~~~~g~~~C~~cy~~~~~~~ 158 (281)
+.....|..=+++|...+.+.+ ++ ..-|..-|.|..|+..|... ..+....|.++|.+|.++++...
T Consensus 180 P~~~v~CP~s~kplklkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D 259 (303)
T KOG3039|consen 180 PSTTVVCPVSGKPLKLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD 259 (303)
T ss_pred CCceeeccCCCCccchhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc
Confidence 3345678888888865443321 11 13566789999999999853 33444688999999999877542
Q ss_pred CCCcccCCcccccCCCccccccCCCCCcCCCCccccCCCCCCCCCCCCcccccceee
Q psy16551 159 GYGFAAGSGFLQTDGLTEDEISANRPFYNPNTTSIMARKGEGCPRCGGAVFAAEQQL 215 (281)
Q Consensus 159 ~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~ 215 (281)
.+|+.|.+++.+.++|.
T Consensus 260 ----------------------------------------~v~pv~d~plkdrdiI~ 276 (303)
T KOG3039|consen 260 ----------------------------------------MVDPVTDKPLKDRDIIG 276 (303)
T ss_pred ----------------------------------------ccccCCCCcCcccceEe
Confidence 18999999998887664
No 78
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=23.64 E-value=50 Score=29.58 Aligned_cols=29 Identities=31% Similarity=0.655 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCcccccceeeecCccccccc
Q psy16551 196 RKGEGCPRCGGAVFAAEQQLAKGTMWHKQC 225 (281)
Q Consensus 196 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~C 225 (281)
..+.-|.+|+.+|. ...+.-++..|++.|
T Consensus 243 R~GepC~~CGt~I~-k~~~~gR~t~~CP~C 271 (273)
T COG0266 243 RAGEPCRRCGTPIE-KIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCCCccCCEeE-EEEEcCCcCEeCCCC
Confidence 45668999999883 433445566666655
No 79
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.10 E-value=31 Score=28.75 Aligned_cols=31 Identities=26% Similarity=0.544 Sum_probs=22.0
Q ss_pred CCCcCCCccccccceeeccCcccccCceeccccCCCCCC
Q psy16551 96 KGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDS 134 (281)
Q Consensus 96 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~ 134 (281)
=+|..|+......+.+ . .=|.|..|+..|..
T Consensus 118 Y~Cp~C~~rytf~eA~---~-----~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 118 FFCPNCHIRFTFDEAM---E-----YGFRCPQCGEMLEE 148 (178)
T ss_pred EECCCCCcEEeHHHHh---h-----cCCcCCCCCCCCee
Confidence 4599999877544333 2 25999999998854
No 80
>PRK00807 50S ribosomal protein L24e; Validated
Probab=22.99 E-value=63 Score=21.13 Aligned_cols=31 Identities=19% Similarity=0.518 Sum_probs=21.0
Q ss_pred CCCCCCCcccccceee---ecCcccccccccccccCC
Q psy16551 200 GCPRCGGAVFAAEQQL---AKGTMWHKQCFSCNVCKR 233 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~---~~g~~~H~~Cf~C~~C~~ 233 (281)
.|..|+..|.++.... ..|++|.- -+..|.+
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~~F---cs~KC~~ 36 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTILYF---CSSKCEK 36 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEEEE---eCHHHHH
Confidence 7999999998776333 57887763 3345544
No 81
>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=22.41 E-value=60 Score=20.34 Aligned_cols=9 Identities=44% Similarity=1.335 Sum_probs=6.0
Q ss_pred cChhhhccc
Q psy16551 249 YCKACYGKN 257 (281)
Q Consensus 249 ~C~~c~~~~ 257 (281)
+|..||...
T Consensus 25 LC~~Cf~~~ 33 (46)
T cd02249 25 LCSSCYAKG 33 (46)
T ss_pred CHHHHHCcC
Confidence 577777653
No 82
>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=22.29 E-value=22 Score=21.29 Aligned_cols=30 Identities=17% Similarity=0.499 Sum_probs=17.2
Q ss_pred CcCCCccccccceeeccCcccccCceeccccCCCC
Q psy16551 98 CPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132 (281)
Q Consensus 98 C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 132 (281)
|..|.+++ ....++.||-.=..|..||-.+
T Consensus 2 C~~C~~Ey-----~~p~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 2 CDDCLKEY-----FDPSNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp -HHHHHHH-----CSTTSTTTT-TT--BTTCC-SC
T ss_pred CHHHHHHH-----cCCCCCcccCcCccCCCCCCCE
Confidence 55665544 3345788999888999998655
No 83
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.28 E-value=35 Score=27.40 Aligned_cols=37 Identities=22% Similarity=0.407 Sum_probs=24.0
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCCCCC
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDS 134 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~ 134 (281)
.-.|..|+..+...+.+...+. ..=|.|..|+..|..
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELEE 135 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEEE
Confidence 3459999987754444433332 233999999998853
No 84
>PHA02929 N1R/p28-like protein; Provisional
Probab=22.09 E-value=51 Score=28.89 Aligned_cols=39 Identities=21% Similarity=0.457 Sum_probs=24.5
Q ss_pred CCCCcCCCccccccc-------eeeccCcccccCce--------eccccCCCCC
Q psy16551 95 GKGCPRCGGVVFAAE-------QVLAKGSEWHRKCF--------KCRDCNKTLD 133 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~-------~~~~~~~~~H~~CF--------~C~~C~~~L~ 133 (281)
...|+-|...+.+.+ .+..-+..||..|+ .|..|+..+.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 467999999876543 12234666777776 5666665554
No 85
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=21.94 E-value=65 Score=19.63 Aligned_cols=29 Identities=31% Similarity=0.640 Sum_probs=13.5
Q ss_pred CCCCCCCcccccceeeecCcccccccccccccCC
Q psy16551 200 GCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKR 233 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~ 233 (281)
+|..|+--|.+--.+...++.| .|..|+.
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred ccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 7888877765544444455555 5566654
No 86
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=21.70 E-value=16 Score=26.13 Aligned_cols=32 Identities=28% Similarity=0.669 Sum_probs=11.4
Q ss_pred CCCCCCCCCCCCcccccceeeecCcccccccccccccCCC
Q psy16551 195 ARKGEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRP 234 (281)
Q Consensus 195 ~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~ 234 (281)
...+.+|..|+..|. +.+.|..| ..|..|.-+
T Consensus 6 ~~~~qiCqiCGD~VG----l~~~Ge~F----VAC~eC~fP 37 (80)
T PF14569_consen 6 NLNGQICQICGDDVG----LTENGEVF----VACHECAFP 37 (80)
T ss_dssp --SS-B-SSS--B------B-SSSSB------S-SSS---
T ss_pred hcCCcccccccCccc----cCCCCCEE----EEEcccCCc
Confidence 345569999998883 44566665 235555433
No 87
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=21.36 E-value=59 Score=26.02 Aligned_cols=43 Identities=19% Similarity=0.323 Sum_probs=27.2
Q ss_pred CCCCcCCCccccccceee------ccCcccccCceeccccCCCCCCCCe
Q psy16551 95 GKGCPRCGGVVFAAEQVL------AKGSEWHRKCFKCRDCNKTLDSINA 137 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~------~~~~~~H~~CF~C~~C~~~L~~~~~ 137 (281)
...|..|+..+.....-. ..-...+....+|..|++-...+..
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSH 139 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEeccccc
Confidence 467999999775422211 1222245668999999987765543
No 88
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=21.32 E-value=42 Score=19.94 Aligned_cols=32 Identities=22% Similarity=0.493 Sum_probs=16.0
Q ss_pred CCCCCCCcccccceeeecCcccccccccccccCCCC
Q psy16551 200 GCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPL 235 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L 235 (281)
.|+.|+..+...+.....+.. -++|..|+..|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~----~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGG----KVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCC----EEECCCCCCEE
Confidence 688888765433211111111 25567776654
No 89
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=21.10 E-value=84 Score=27.92 Aligned_cols=14 Identities=21% Similarity=0.477 Sum_probs=9.9
Q ss_pred CCCCCCCCcCCCcc
Q psy16551 91 KAAPGKGCPRCGGV 104 (281)
Q Consensus 91 ~~~~~~~C~~C~~~ 104 (281)
.....|+|+.|++.
T Consensus 59 s~qrlp~Ca~Cgk~ 72 (314)
T PF06524_consen 59 SVQRLPMCAHCGKT 72 (314)
T ss_pred hhhcCchhhhcCCe
Confidence 34446889999885
No 90
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=20.99 E-value=47 Score=24.45 Aligned_cols=40 Identities=20% Similarity=0.352 Sum_probs=28.8
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCCCCCCC
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTLDSIN 136 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L~~~~ 136 (281)
...|..|++++.--+.+-+.+-.+.+ -+|..|+.++...+
T Consensus 33 rS~C~~C~~~L~~~~lIPi~S~l~lr--GrCr~C~~~I~~~y 72 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIPILSYLLLR--GRCRYCGAPIPPRY 72 (92)
T ss_pred CCcCcCCCCcCcccccchHHHHHHhC--CCCcccCCCCChHH
Confidence 35799999998766666666555554 67888888886543
No 91
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.98 E-value=41 Score=22.09 Aligned_cols=35 Identities=20% Similarity=0.417 Sum_probs=19.5
Q ss_pred CCCCcCCCccccccceeeccCcccccCceeccccCCCC
Q psy16551 95 GKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132 (281)
Q Consensus 95 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 132 (281)
...|.+|+-.|.......+... .+=..|..|++-|
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~---~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKG---DEIVFCPNCGRIL 56 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcC---CCeEECcCCCccC
Confidence 4578888888854333332222 2336667776543
No 92
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.92 E-value=85 Score=31.87 Aligned_cols=39 Identities=28% Similarity=0.625 Sum_probs=0.0
Q ss_pred eeccccCCCCCCCCeeeCCCCcccCccchhhccCCCCCCcccCCcccccCCCccccccCCCCCcCCCCccccCCCCCCCC
Q psy16551 123 FKCRDCNKTLDSINACDGPDKDIYCKTCYGKKWGPHGYGFAAGSGFLQTDGLTEDEISANRPFYNPNTTSIMARKGEGCP 202 (281)
Q Consensus 123 F~C~~C~~~L~~~~~~~~~~g~~~C~~cy~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ 202 (281)
++|..|+.+| .++...+.+.|..|-...... .|+
T Consensus 393 ~~C~~C~~~L----~~h~~~~~l~Ch~CG~~~~p~------------------------------------------~Cp 426 (665)
T PRK14873 393 ARCRHCTGPL----GLPSAGGTPRCRWCGRAAPDW------------------------------------------RCP 426 (665)
T ss_pred eECCCCCCce----eEecCCCeeECCCCcCCCcCc------------------------------------------cCC
Q ss_pred CCCCc
Q psy16551 203 RCGGA 207 (281)
Q Consensus 203 ~C~~~ 207 (281)
.|+..
T Consensus 427 ~Cgs~ 431 (665)
T PRK14873 427 RCGSD 431 (665)
T ss_pred CCcCC
No 93
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=20.54 E-value=1.4e+02 Score=18.59 Aligned_cols=33 Identities=33% Similarity=0.769 Sum_probs=18.2
Q ss_pred cCCCCCCCCcCCCccccccceeeccCcccccCceeccccCC
Q psy16551 90 IKAAPGKGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNK 130 (281)
Q Consensus 90 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~ 130 (281)
+....+.+|..|+..- ...+.+ +.=++|..|+.
T Consensus 13 ~RW~~g~~CP~Cg~~~----~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 13 IRWPDGFVCPHCGSTK----HYRLKT----RGRYRCKACRK 45 (46)
T ss_pred hcCCCCCCCCCCCCee----eEEeCC----CCeEECCCCCC
Confidence 3455667888888641 111111 34467777764
No 94
>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=20.39 E-value=36 Score=20.90 Aligned_cols=28 Identities=25% Similarity=0.649 Sum_probs=16.3
Q ss_pred CCCCCCCcccccceee--ecCccccccccc
Q psy16551 200 GCPRCGGAVFAAEQQL--AKGTMWHKQCFS 227 (281)
Q Consensus 200 ~C~~C~~~I~~~~~v~--~~g~~~H~~Cf~ 227 (281)
.|+.|...+..++.+. .=+..||.+|+.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~ 31 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIK 31 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHH
Confidence 5788888775544443 234456666543
No 95
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=20.30 E-value=46 Score=19.91 Aligned_cols=11 Identities=36% Similarity=1.334 Sum_probs=5.3
Q ss_pred eeccccCCCCC
Q psy16551 123 FKCRDCNKTLD 133 (281)
Q Consensus 123 F~C~~C~~~L~ 133 (281)
|+|..|+..+.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 44555555443
No 96
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=20.19 E-value=79 Score=33.73 Aligned_cols=53 Identities=25% Similarity=0.557 Sum_probs=32.0
Q ss_pred cCCCCCCCCCCCCcccccceeeecCcccccccccccccCCCCC-CCccccCCCCcccChhhh
Q psy16551 194 MARKGEGCPRCGGAVFAAEQQLAKGTMWHKQCFSCNVCKRPLD-SVLACDGPDKEIYCKACY 254 (281)
Q Consensus 194 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~L~-~~~~~~~~~g~~~C~~c~ 254 (281)
....+++|..|+..|. +.+.|..| -.|..|+-++- .-+-+..++|.-.|..|-
T Consensus 13 ~~~~~qiCqICGD~vg----~~~~Ge~F----VAC~eC~FPVCrpCYEYEr~eG~q~CPqCk 66 (1079)
T PLN02638 13 KHGGGQVCQICGDNVG----KTVDGEPF----VACDVCAFPVCRPCYEYERKDGNQSCPQCK 66 (1079)
T ss_pred cccCCceeeecccccC----cCCCCCEE----EEeccCCCccccchhhhhhhcCCccCCccC
Confidence 3445669999999883 55777777 45666655541 112223456665666654
No 97
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=20.11 E-value=39 Score=21.65 Aligned_cols=35 Identities=14% Similarity=0.423 Sum_probs=20.7
Q ss_pred CCCcCCCccccccceeeccCcccccCceeccccCCCC
Q psy16551 96 KGCPRCGGVVFAAEQVLAKGSEWHRKCFKCRDCNKTL 132 (281)
Q Consensus 96 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~L 132 (281)
.+|..|.+-+.....+....+..++ ++|..|...|
T Consensus 7 v~C~~C~~lLqlP~~~~~~~k~~~k--lrCGaCs~vl 41 (46)
T PF11331_consen 7 VVCSSCFELLQLPAKFSLSKKNQQK--LRCGACSEVL 41 (46)
T ss_pred eECccHHHHHcCCCccCCCccceeE--EeCCCCceeE
Confidence 4577887766544444444444443 6777776654
Done!