Query psy327
Match_columns 168
No_of_seqs 163 out of 1167
Neff 7.8
Searched_HMMs 46136
Date Fri Aug 16 20:44:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy327.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/327hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 2.9E-26 6.3E-31 190.5 0.3 120 7-149 291-411 (468)
2 KOG1701|consensus 99.9 2.2E-23 4.7E-28 173.5 5.1 113 7-134 349-466 (468)
3 KOG2272|consensus 99.8 2.8E-22 6.1E-27 157.3 -1.0 133 8-143 30-265 (332)
4 KOG4577|consensus 99.7 8.3E-20 1.8E-24 145.7 -2.6 102 8-129 50-153 (383)
5 KOG2272|consensus 99.7 1.6E-18 3.6E-23 136.2 -1.4 104 7-132 210-314 (332)
6 KOG1703|consensus 99.7 1.1E-17 2.5E-22 145.2 2.6 116 6-143 318-433 (479)
7 KOG1044|consensus 99.6 1.8E-16 3.9E-21 136.4 2.9 101 6-129 148-249 (670)
8 KOG1703|consensus 99.6 3.2E-16 7E-21 136.1 2.2 102 6-127 377-478 (479)
9 KOG1044|consensus 99.5 8.1E-15 1.8E-19 126.3 3.0 122 5-142 78-202 (670)
10 PF00412 LIM: LIM domain; Int 99.4 4.4E-13 9.4E-18 84.0 2.9 55 73-130 1-57 (58)
11 KOG1700|consensus 99.3 1E-12 2.2E-17 102.3 2.1 130 5-136 21-173 (200)
12 PF00412 LIM: LIM domain; Int 99.2 6.7E-12 1.4E-16 78.5 1.6 43 8-50 16-58 (58)
13 KOG4577|consensus 98.6 1.6E-09 3.5E-14 87.2 -4.3 72 71-146 34-106 (383)
14 smart00132 LIM Zinc-binding do 98.4 1.5E-07 3.2E-12 53.5 2.2 35 73-109 2-38 (39)
15 smart00132 LIM Zinc-binding do 97.6 3.1E-05 6.7E-10 43.7 1.3 23 7-29 16-38 (39)
16 KOG1700|consensus 97.1 0.00024 5.1E-09 55.4 1.5 67 72-141 9-76 (200)
17 KOG0490|consensus 97.0 0.00016 3.4E-09 56.8 -0.6 98 8-126 13-116 (235)
18 KOG1702|consensus 96.5 0.00026 5.7E-09 55.0 -2.1 59 72-133 6-65 (264)
19 KOG1702|consensus 96.1 0.00054 1.2E-08 53.2 -2.5 44 7-50 20-63 (264)
20 PF08394 Arc_trans_TRASH: Arch 88.0 0.19 4E-06 28.5 0.4 29 75-108 3-33 (37)
21 KOG2462|consensus 84.1 0.75 1.6E-05 37.5 2.1 96 14-111 126-228 (279)
22 KOG0490|consensus 83.6 0.31 6.7E-06 38.0 -0.3 55 85-142 12-69 (235)
23 PF02069 Metallothio_Pro: Prok 81.9 0.8 1.7E-05 27.9 1.2 32 100-131 9-40 (52)
24 PF07191 zinc-ribbons_6: zinc- 79.2 2.8 6.1E-05 27.2 3.1 38 20-62 3-41 (70)
25 PF05502 Dynactin_p62: Dynacti 79.1 1.4 3E-05 39.0 2.2 59 39-109 5-63 (483)
26 PF07754 DUF1610: Domain of un 78.2 1.6 3.4E-05 22.4 1.3 8 55-62 2-9 (24)
27 COG1645 Uncharacterized Zn-fin 77.2 1.6 3.4E-05 31.8 1.6 22 20-46 30-51 (131)
28 PF14471 DUF4428: Domain of un 74.9 1.8 3.8E-05 26.3 1.2 29 20-49 1-30 (51)
29 PF14835 zf-RING_6: zf-RING of 74.6 2.7 5.8E-05 26.8 2.0 44 19-62 8-51 (65)
30 PF10367 Vps39_2: Vacuolar sor 71.6 2.7 5.8E-05 28.5 1.6 28 20-47 80-108 (109)
31 PF11781 RRN7: RNA polymerase 68.4 3.4 7.3E-05 23.1 1.3 24 20-47 10-33 (36)
32 PF06677 Auto_anti-p27: Sjogre 68.1 3.4 7.5E-05 23.9 1.3 22 20-45 19-40 (41)
33 PF13248 zf-ribbon_3: zinc-rib 67.5 3.8 8.2E-05 21.0 1.3 9 53-61 4-12 (26)
34 PRK00807 50S ribosomal protein 67.2 2.2 4.8E-05 25.9 0.4 36 53-108 3-38 (52)
35 PF10235 Cript: Microtubule-as 66.4 3.1 6.7E-05 28.3 1.0 42 14-63 40-81 (90)
36 smart00504 Ubox Modified RING 65.9 6 0.00013 24.1 2.3 43 19-62 2-46 (63)
37 PF12773 DZR: Double zinc ribb 64.5 7.2 0.00016 22.9 2.3 23 54-81 1-23 (50)
38 PRK14890 putative Zn-ribbon RN 63.6 4.6 0.0001 25.3 1.3 12 52-63 8-19 (59)
39 PF04570 DUF581: Protein of un 62.1 4.1 8.9E-05 25.4 0.9 29 100-128 18-48 (58)
40 COG2191 Formylmethanofuran deh 62.1 4.8 0.0001 31.5 1.5 31 99-130 173-203 (206)
41 COG1645 Uncharacterized Zn-fin 61.8 3.4 7.4E-05 30.1 0.6 24 100-129 30-53 (131)
42 PF01258 zf-dskA_traR: Prokary 60.9 1 2.2E-05 25.0 -1.8 29 21-49 6-34 (36)
43 PF13920 zf-C3HC4_3: Zinc fing 58.7 14 0.0003 21.7 2.8 43 19-62 3-48 (50)
44 PRK14559 putative protein seri 57.8 7.2 0.00016 35.8 2.1 49 20-80 3-51 (645)
45 PF06906 DUF1272: Protein of u 57.1 8.9 0.00019 23.7 1.8 46 100-146 7-55 (57)
46 PRK14873 primosome assembly pr 56.2 13 0.00028 34.2 3.5 38 100-141 394-431 (665)
47 cd00162 RING RING-finger (Real 56.1 8.7 0.00019 20.9 1.6 40 20-59 1-43 (45)
48 PF13834 DUF4193: Domain of un 52.6 5.5 0.00012 27.6 0.4 30 97-127 69-99 (99)
49 PF10080 DUF2318: Predicted me 51.7 13 0.00029 25.8 2.2 48 88-143 27-79 (102)
50 PF10083 DUF2321: Uncharacteri 50.3 9.7 0.00021 28.5 1.4 52 38-108 27-78 (158)
51 TIGR03826 YvyF flagellar opero 50.2 8.3 0.00018 28.3 1.0 24 98-130 81-104 (137)
52 PF14803 Nudix_N_2: Nudix N-te 49.4 7.1 0.00015 21.6 0.4 7 99-105 23-29 (34)
53 KOG1813|consensus 49.0 8 0.00017 32.0 0.9 44 19-63 242-287 (313)
54 PF13923 zf-C3HC4_2: Zinc fing 48.6 11 0.00024 20.9 1.2 31 21-51 1-31 (39)
55 PF14446 Prok-RING_1: Prokaryo 48.4 9.5 0.00021 23.4 0.9 9 89-99 28-36 (54)
56 COG4416 Com Mu-like prophage p 48.3 4.1 8.9E-05 25.0 -0.7 26 52-77 5-31 (60)
57 PF12855 Ecl1: Life-span regul 47.5 5.7 0.00012 23.2 -0.2 26 101-130 9-34 (43)
58 COG1198 PriA Primosomal protei 46.3 23 0.00051 33.0 3.5 39 99-141 445-484 (730)
59 PRK00420 hypothetical protein; 45.7 12 0.00025 26.6 1.2 24 19-46 24-47 (112)
60 KOG0320|consensus 43.5 13 0.00028 28.6 1.2 47 16-62 129-178 (187)
61 cd02340 ZZ_NBR1_like Zinc fing 42.6 13 0.00029 21.4 0.9 10 53-62 2-11 (43)
62 smart00659 RPOLCX RNA polymera 41.9 21 0.00046 20.8 1.7 26 99-129 3-28 (44)
63 PF09723 Zn-ribbon_8: Zinc rib 41.3 11 0.00023 21.7 0.3 29 99-128 6-34 (42)
64 cd02336 ZZ_RSC8 Zinc finger, Z 40.6 14 0.0003 21.7 0.8 31 19-49 1-33 (45)
65 PF14634 zf-RING_5: zinc-RING 40.4 21 0.00044 20.4 1.5 38 21-58 2-43 (44)
66 cd02334 ZZ_dystrophin Zinc fin 39.5 13 0.00029 22.2 0.6 7 71-77 25-31 (49)
67 smart00291 ZnF_ZZ Zinc-binding 38.7 14 0.00031 21.2 0.6 15 19-33 5-19 (44)
68 smart00834 CxxC_CXXC_SSSS Puta 38.3 13 0.00028 20.6 0.4 29 99-128 6-34 (41)
69 TIGR02605 CxxC_CxxC_SSSS putat 38.1 14 0.0003 21.8 0.5 29 99-128 6-34 (52)
70 COG5152 Uncharacterized conser 37.7 9.7 0.00021 29.9 -0.3 45 18-63 196-242 (259)
71 TIGR00595 priA primosomal prot 37.4 36 0.00079 30.2 3.2 42 99-141 214-262 (505)
72 PRK14873 primosome assembly pr 36.5 21 0.00045 33.0 1.6 39 19-60 393-431 (665)
73 COG4847 Uncharacterized protei 36.5 15 0.00033 25.2 0.6 19 98-116 6-25 (103)
74 KOG3476|consensus 35.4 5.9 0.00013 26.7 -1.5 37 19-63 55-91 (100)
75 cd02338 ZZ_PCMF_like Zinc fing 35.3 19 0.00042 21.3 0.8 9 54-62 3-12 (49)
76 cd02249 ZZ Zinc finger, ZZ typ 34.6 21 0.00045 20.7 0.9 30 100-130 2-33 (46)
77 PF13719 zinc_ribbon_5: zinc-r 32.8 24 0.00051 19.6 0.9 10 99-108 26-35 (37)
78 cd02344 ZZ_HERC2 Zinc finger, 31.2 25 0.00053 20.7 0.8 10 53-62 2-12 (45)
79 PRK14891 50S ribosomal protein 31.1 18 0.00039 26.3 0.2 37 52-108 5-41 (131)
80 PF12674 Zn_ribbon_2: Putative 31.1 15 0.00032 24.4 -0.2 29 20-48 2-35 (81)
81 PF04945 YHS: YHS domain; Int 30.2 14 0.0003 21.5 -0.4 30 74-108 4-36 (47)
82 PF09845 DUF2072: Zn-ribbon co 30.2 54 0.0012 23.9 2.6 31 100-134 3-33 (131)
83 KOG4443|consensus 30.2 24 0.00051 32.4 0.9 20 89-110 108-127 (694)
84 PF09943 DUF2175: Uncharacteri 30.2 30 0.00064 24.1 1.2 33 19-51 3-36 (101)
85 PLN03086 PRLI-interacting fact 30.1 11 0.00024 34.0 -1.2 78 19-108 408-487 (567)
86 PRK00398 rpoP DNA-directed RNA 30.0 27 0.00057 20.2 0.8 10 99-108 4-13 (46)
87 PF00096 zf-C2H2: Zinc finger, 29.2 28 0.00061 16.5 0.7 12 99-110 1-12 (23)
88 TIGR00595 priA primosomal prot 28.8 35 0.00075 30.3 1.7 39 19-60 223-262 (505)
89 PF15135 UPF0515: Uncharacteri 28.7 1E+02 0.0022 25.0 4.1 21 88-110 147-167 (278)
90 COG2888 Predicted Zn-ribbon RN 27.8 57 0.0012 20.5 2.0 12 51-62 9-20 (61)
91 PF04502 DUF572: Family of unk 27.6 51 0.0011 27.5 2.4 11 98-108 77-87 (324)
92 cd00472 Ribosomal_L24e_L24 Rib 27.1 54 0.0012 20.0 1.8 27 52-93 4-30 (54)
93 cd02342 ZZ_UBA_plant Zinc fing 26.1 30 0.00066 20.2 0.6 10 53-62 2-12 (43)
94 PF10764 Gin: Inhibitor of sig 25.9 60 0.0013 19.1 1.8 28 20-49 1-28 (46)
95 smart00746 TRASH metallochaper 25.8 52 0.0011 16.3 1.5 8 86-93 18-25 (39)
96 COG2075 RPL24A Ribosomal prote 25.1 49 0.0011 21.2 1.4 29 100-128 5-38 (66)
97 PF08792 A2L_zn_ribbon: A2L zi 24.3 63 0.0014 17.6 1.6 23 20-45 5-27 (33)
98 TIGR02098 MJ0042_CXXC MJ0042 f 24.0 28 0.00061 19.0 0.2 10 99-108 26-35 (38)
99 PF07503 zf-HYPF: HypF finger; 23.8 68 0.0015 17.7 1.7 22 8-29 11-32 (35)
100 PF07649 C1_3: C1-like domain; 23.6 46 0.00099 17.3 0.9 12 19-30 1-12 (30)
101 COG1545 Predicted nucleic-acid 23.1 53 0.0011 24.0 1.5 28 49-81 27-54 (140)
102 KOG2893|consensus 22.9 31 0.00068 27.9 0.3 12 97-108 33-44 (341)
103 PF06827 zf-FPG_IleRS: Zinc fi 22.9 19 0.00041 18.8 -0.7 6 100-105 23-28 (30)
104 PF00569 ZZ: Zinc finger, ZZ t 22.6 29 0.00062 20.2 0.0 30 19-48 5-37 (46)
105 COG4393 Predicted membrane pro 21.9 60 0.0013 27.6 1.7 32 110-142 342-376 (405)
106 PLN03208 E3 ubiquitin-protein 21.5 68 0.0015 24.9 1.9 31 17-48 17-47 (193)
107 PRK12495 hypothetical protein; 21.4 45 0.00097 26.5 0.9 24 17-45 41-64 (226)
108 PF13894 zf-C2H2_4: C2H2-type 21.3 51 0.0011 15.2 0.8 11 99-109 1-11 (24)
109 TIGR03830 CxxCG_CxxCG_HTH puta 21.3 89 0.0019 21.6 2.4 22 85-108 18-41 (127)
110 COG3813 Uncharacterized protei 21.0 56 0.0012 21.4 1.1 45 100-145 7-54 (84)
111 PF09538 FYDLN_acid: Protein o 20.8 79 0.0017 22.1 1.9 26 100-131 11-37 (108)
112 COG1198 PriA Primosomal protei 20.8 57 0.0012 30.5 1.6 39 19-60 445-484 (730)
113 COG4357 Zinc finger domain con 20.5 10 0.00022 26.1 -2.5 35 87-123 53-87 (105)
114 PF00320 GATA: GATA zinc finge 20.4 72 0.0016 17.4 1.4 28 21-48 1-29 (36)
115 PF07975 C1_4: TFIIH C1-like d 20.2 37 0.00081 20.5 0.2 12 97-108 20-31 (51)
116 KOG3002|consensus 20.1 76 0.0016 26.4 2.0 45 17-62 47-91 (299)
No 1
>KOG1701|consensus
Probab=99.91 E-value=2.9e-26 Score=190.53 Aligned_cols=120 Identities=23% Similarity=0.522 Sum_probs=112.2
Q ss_pred ccCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCcccccccCCccccCCcccccCCCCCCcee
Q psy327 7 RAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMS 86 (168)
Q Consensus 7 ~~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v~ 86 (168)
..||++.||.+||+|..|++.|.++.||..|+++||+.||... ..+|..|+++|++. +|.
T Consensus 291 c~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~d~-------------------iLr 350 (468)
T KOG1701|consen 291 VEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIMDR-------------------ILR 350 (468)
T ss_pred HHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHHHH-------------------HHH
Confidence 5899999999999999999999999999999999999999987 67999999999853 699
Q ss_pred eCCceeeCCCCceecCCCCccCCCCCceec-CCeeeecccccCCCCCCCCCCCCCCCCCCCCcc
Q psy327 87 HEGQHWHATDSCFCCATCSLSLLGRPFLPR-AGVIFCSIACSKGEPPTPSDSSGPGLRPQRPRK 149 (168)
Q Consensus 87 ~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~-dg~~~C~~~C~~~~~~~~~~~~~~~~~~~~~~~ 149 (168)
|+|+.||+ .||+|..|.+.|+|..|+++ ++++||.+ +|.++|+.+|..|+++|+|..-..
T Consensus 351 A~GkayHp--~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~-dfh~kfAPrCs~C~~PI~P~~G~~ 411 (468)
T KOG1701|consen 351 ALGKAYHP--GCFTCVVCARCLDGIPFTVDSQNNVYCVP-DFHKKFAPRCSVCGNPILPRDGKD 411 (468)
T ss_pred hcccccCC--CceEEEEeccccCCccccccCCCceeeeh-hhhhhcCcchhhccCCccCCCCCc
Confidence 99999999 99999999999999999975 99999996 888999999999999999986654
No 2
>KOG1701|consensus
Probab=99.88 E-value=2.2e-23 Score=173.46 Aligned_cols=113 Identities=26% Similarity=0.636 Sum_probs=101.3
Q ss_pred ccCCCCCCCCCCccccccccccCCCceE-EECCeeccccchHhhhccccccCcccccccCCccccCCcccccCCCCCCce
Q psy327 7 RAGPNSCWHPGCFTCSVCNELLVDLIYF-YRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQM 85 (168)
Q Consensus 7 ~~a~~~~~H~~Cf~C~~C~~~L~~~~~~-~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v 85 (168)
+.|+|+.||++||+|..|++.|++..|. ..++++||.+||++.|+++|+.|+++|++.+|... ...|
T Consensus 349 LrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~e------------tvRv 416 (468)
T KOG1701|consen 349 LRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDE------------TVRV 416 (468)
T ss_pred HHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcc------------eEEE
Confidence 5799999999999999999999999996 48999999999999999999999999999888752 3358
Q ss_pred eeCCceeeCCCCceecCCCCccCC----CCCceecCCeeeecccccCCCCCCC
Q psy327 86 SHEGQHWHATDSCFCCATCSLSLL----GRPFLPRAGVIFCSIACSKGEPPTP 134 (168)
Q Consensus 86 ~~~~~~~H~~~~CF~C~~C~~~l~----~~~f~~~dg~~~C~~~C~~~~~~~~ 134 (168)
+++|+.||. +||+|.+|+..|+ ++..|..||.++|+. |+.+.....
T Consensus 417 vamdr~fHv--~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~-Ch~~Rl~~~ 466 (468)
T KOG1701|consen 417 VAMDRDFHV--NCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKT-CHLKRLQAG 466 (468)
T ss_pred EEccccccc--cceehhhcCccccccCCCCcceeccCceeech-hhhhhhccc
Confidence 999999999 9999999999994 778999999999997 987765443
No 3
>KOG2272|consensus
Probab=99.83 E-value=2.8e-22 Score=157.33 Aligned_cols=133 Identities=20% Similarity=0.454 Sum_probs=116.2
Q ss_pred cCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCcccccc------------------------
Q psy327 8 AGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQ------------------------ 63 (168)
Q Consensus 8 ~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~------------------------ 63 (168)
...|..||.+||+|+.|=.|+.++.||+.+|+.||+.||..+|+|.|.+|++.|.+
T Consensus 30 ns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~L 109 (332)
T KOG2272|consen 30 NSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHL 109 (332)
T ss_pred ccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHHhhccccCcccchhHHHHHHH
Confidence 45788999999999999999999999999999999999999999999999999871
Q ss_pred --------------------------------------------cCCccc------------------------------
Q psy327 64 --------------------------------------------VGGHRT------------------------------ 69 (168)
Q Consensus 64 --------------------------------------------~~g~~~------------------------------ 69 (168)
..|+.|
T Consensus 110 ad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrC 189 (332)
T KOG2272|consen 110 ADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRC 189 (332)
T ss_pred hhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccchhhhhccceecccc
Confidence 011111
Q ss_pred -----cCCcccccCCCCCCceeeCCceeeCCCCceecCCCCccCCCCCceecCCeeeecccccCCCCCCCCCCCCCCCC
Q psy327 70 -----RDLNINYFSSLPAGQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTPSDSSGPGLR 143 (168)
Q Consensus 70 -----~~~C~~C~~~i~~~~v~~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~~~~~~~~~~~ 143 (168)
.|+|..|.++|++++|.++|++||. ++|+|+.|.+++-|-..|++.|.+||.+ -|.+++...|-.|+.++-
T Consensus 190 hD~mgipiCgaC~rpIeervi~amgKhWHv--eHFvCa~CekPFlGHrHYEkkGlaYCe~-h~~qLfG~~CF~C~~~i~ 265 (332)
T KOG2272|consen 190 HDKMGIPICGACRRPIEERVIFAMGKHWHV--EHFVCAKCEKPFLGHRHYEKKGLAYCET-HYHQLFGNLCFICNRVIG 265 (332)
T ss_pred ccccCCcccccccCchHHHHHHHhccccch--hheeehhcCCcccchhhhhhcCchhHHH-HHHHHhhhhheecCCccC
Confidence 3567777788999999999999999 9999999999999999999999999997 678888888887777664
No 4
>KOG4577|consensus
Probab=99.74 E-value=8.3e-20 Score=145.71 Aligned_cols=102 Identities=25% Similarity=0.569 Sum_probs=89.3
Q ss_pred cCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCcccccccCCccccCCcccccCCCCCCceee
Q psy327 8 AGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMSH 87 (168)
Q Consensus 8 ~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v~~ 87 (168)
..+++.||..|++|+.|..+|.. ..|.++|.+||+++|.++|+.+|..|++.|.+..- +-.|
T Consensus 50 Kvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqV-----------------VRkA 111 (383)
T KOG4577|consen 50 KVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQV-----------------VRKA 111 (383)
T ss_pred HHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHH-----------------HHHh
Confidence 56799999999999999999977 56889999999999999999999999999987421 3457
Q ss_pred CCceeeCCCCceecCCCCccC-CCCCcee-cCCeeeecccccCC
Q psy327 88 EGQHWHATDSCFCCATCSLSL-LGRPFLP-RAGVIFCSIACSKG 129 (168)
Q Consensus 88 ~~~~~H~~~~CF~C~~C~~~l-~~~~f~~-~dg~~~C~~~C~~~ 129 (168)
.+..||. .||.|..|.+.| .|+.||+ .|+++.|+.|+...
T Consensus 112 qd~VYHl--~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~A 153 (383)
T KOG4577|consen 112 QDFVYHL--HCFACFICKRQLATGDEFYLMEDARLVCKDDYETA 153 (383)
T ss_pred hcceeeh--hhhhhHhhhcccccCCeeEEeccceeehhhhHHHH
Confidence 8999999 999999999999 7888885 59999999876543
No 5
>KOG2272|consensus
Probab=99.69 E-value=1.6e-18 Score=136.20 Aligned_cols=104 Identities=22% Similarity=0.474 Sum_probs=95.3
Q ss_pred ccCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCcccccccCCccccCCcccccCCCCCCcee
Q psy327 7 RAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMS 86 (168)
Q Consensus 7 ~~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v~ 86 (168)
+.|||+.||.+.|+|+.|.+|+-+-.-|++.|..||+.+|.++|+..|..|+.+|.+ ++++
T Consensus 210 i~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G-------------------~vv~ 270 (332)
T KOG2272|consen 210 IFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGG-------------------DVVS 270 (332)
T ss_pred HHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCc-------------------cHHH
Confidence 478999999999999999999988788999999999999999999999999999973 3689
Q ss_pred eCCceeeCCCCceecCCCCccC-CCCCceecCCeeeecccccCCCCC
Q psy327 87 HEGQHWHATDSCFCCATCSLSL-LGRPFLPRAGVIFCSIACSKGEPP 132 (168)
Q Consensus 87 ~~~~~~H~~~~CF~C~~C~~~l-~~~~f~~~dg~~~C~~~C~~~~~~ 132 (168)
++++.|-+ +||.|+.|++.| ....|++.|-+|.|++ ||.+.+.
T Consensus 271 al~KawCv--~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKk-Cy~rfp~ 314 (332)
T KOG2272|consen 271 ALNKAWCV--ECFSCSTCDKKLTQKNKFYEFDMKPVCKK-CYDRFPL 314 (332)
T ss_pred Hhhhhhcc--ccccccccccccccccceeeeccchHHHH-HHhhccH
Confidence 99999999 999999999999 5778999999999997 9987653
No 6
>KOG1703|consensus
Probab=99.68 E-value=1.1e-17 Score=145.18 Aligned_cols=116 Identities=24% Similarity=0.489 Sum_probs=107.0
Q ss_pred eccCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCcccccccCCccccCCcccccCCCCCCce
Q psy327 6 SRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQM 85 (168)
Q Consensus 6 ~~~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v 85 (168)
.++++++.||+.+|.|..|+..+....|...+|.+||.+|+.+.+.++|.+|+.+|.+. .|
T Consensus 318 ~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~-------------------~v 378 (479)
T KOG1703|consen 318 VIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEE-------------------GV 378 (479)
T ss_pred eEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHh-------------------Hh
Confidence 46899999999999999999999888888999999999999999999999999999842 58
Q ss_pred eeCCceeeCCCCceecCCCCccCCCCCceecCCeeeecccccCCCCCCCCCCCCCCCC
Q psy327 86 SHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTPSDSSGPGLR 143 (168)
Q Consensus 86 ~~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~~~~~~~~~~~ 143 (168)
.++++.||+ +||.|..|+++|.+..|+..||.+||.. ++.+++.+.|..|...++
T Consensus 379 ~a~~~~wH~--~cf~C~~C~~~~~~~~~~~~~~~pyce~-~~~~~~~~~~~~~~~p~~ 433 (479)
T KOG1703|consen 379 CALGRLWHP--ECFVCADCGKPLKNSSFFESDGEPYCED-HYKKLFTTKCDYCKKPVE 433 (479)
T ss_pred hhccCeech--hceeeecccCCCCCCcccccCCccchhh-hHhhhccccchhccchhH
Confidence 888999999 9999999999999999999999999996 999999989888876654
No 7
>KOG1044|consensus
Probab=99.61 E-value=1.8e-16 Score=136.41 Aligned_cols=101 Identities=20% Similarity=0.592 Sum_probs=92.4
Q ss_pred eccCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCcccccccCCccccCCcccccCCCCCCce
Q psy327 6 SRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQM 85 (168)
Q Consensus 6 ~~~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v 85 (168)
.++|+++.||..||+|..|+..|.+ .|..+||.+||+.||.+.|+.+|..|.+.|.+ ++|
T Consensus 148 ~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisg-------------------kvL 207 (670)
T KOG1044|consen 148 ALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISG-------------------KVL 207 (670)
T ss_pred eeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhh-------------------hhh
Confidence 4689999999999999999999965 78999999999999999999999999999984 379
Q ss_pred eeCCceeeCCCCceecCCCCccC-CCCCceecCCeeeecccccCC
Q psy327 86 SHEGQHWHATDSCFCCATCSLSL-LGRPFLPRAGVIFCSIACSKG 129 (168)
Q Consensus 86 ~~~~~~~H~~~~CF~C~~C~~~l-~~~~f~~~dg~~~C~~~C~~~ 129 (168)
.|.|++||| .|-+|++|+..+ +|+.-|+.+..+|=. +|...
T Consensus 208 qag~kh~HP--tCARCsRCgqmF~eGEEMYlQGs~iWHP-~C~qa 249 (670)
T KOG1044|consen 208 QAGDKHFHP--TCARCSRCGQMFGEGEEMYLQGSEIWHP-DCKQA 249 (670)
T ss_pred hccCcccCc--chhhhhhhccccccchheeeccccccCC-ccccc
Confidence 999999999 899999999999 899999999999976 47754
No 8
>KOG1703|consensus
Probab=99.59 E-value=3.2e-16 Score=136.14 Aligned_cols=102 Identities=26% Similarity=0.654 Sum_probs=92.9
Q ss_pred eccCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCcccccccCCccccCCcccccCCCCCCce
Q psy327 6 SRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQM 85 (168)
Q Consensus 6 ~~~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v 85 (168)
.+.|+++.||++||+|..|+++|.+..|+..++.+||+.||.+++..+|..|..++.- +.+ .+
T Consensus 377 ~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~--~~~---------------~i 439 (479)
T KOG1703|consen 377 GVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEF--GSR---------------QI 439 (479)
T ss_pred HhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHh--hhh---------------Hh
Confidence 3578899999999999999999999999999999999999999999999999998762 222 48
Q ss_pred eeCCceeeCCCCceecCCCCccCCCCCceecCCeeeeccccc
Q psy327 86 SHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACS 127 (168)
Q Consensus 86 ~~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~ 127 (168)
.+++..||. .||+|+.|.+.|.++.|+...++|+|.. ++
T Consensus 440 e~~~~~~h~--~~F~c~~c~~~l~~~~~~~~~~~p~c~~-~~ 478 (479)
T KOG1703|consen 440 EADGSPFHG--DCFRCANCMKKLTKKTFFETLDKPLCQK-HF 478 (479)
T ss_pred hccCccccc--cceehhhhhccccCCceeecCCcccccc-CC
Confidence 999999999 9999999999999999999999999996 43
No 9
>KOG1044|consensus
Probab=99.50 E-value=8.1e-15 Score=126.33 Aligned_cols=122 Identities=19% Similarity=0.399 Sum_probs=91.0
Q ss_pred eeccCCCCCCCCCCccccccccccCCCceE-EECCeeccccchHhhhccccccCcccccccCCccc-cCCcccccCCC-C
Q psy327 5 ASRAGPNSCWHPGCFTCSVCNELLVDLIYF-YRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRT-RDLNINYFSSL-P 81 (168)
Q Consensus 5 ~~~~a~~~~~H~~Cf~C~~C~~~L~~~~~~-~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~-~~~C~~C~~~i-~ 81 (168)
.-+.++|+.||++||.|+.|+.++....-. .......|..| .++.....+..+ ...|++|+..| .
T Consensus 78 evvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c------------~~~~~~~p~~~~~ps~cagc~~~lk~ 145 (670)
T KOG1044|consen 78 EVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTC------------SQPMPVSPAESYGPSTCAGCGEELKN 145 (670)
T ss_pred eeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhh------------cCcccCCcccccCCccccchhhhhhc
Confidence 346899999999999999999999554333 33344555554 333222222333 45688888877 4
Q ss_pred CCceeeCCceeeCCCCceecCCCCccCCCCCceecCCeeeecccccCCCCCCCCCCCCCCC
Q psy327 82 AGQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTPSDSSGPGL 142 (168)
Q Consensus 82 ~~~v~~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~~~~~~~~~~ 142 (168)
++.+.|+++.||+ .||+|..|...|.|+ |+..||.+||.. +|.+.|..+|..|..-|
T Consensus 146 gq~llald~qwhv--~cfkc~~c~~vL~ge-y~skdg~pyce~-dy~~~fgvkc~~c~~fi 202 (670)
T KOG1044|consen 146 GQALLALDKQWHV--SCFKCKSCSAVLNGE-YMSKDGVPYCEK-DYQAKFGVKCEECEKFI 202 (670)
T ss_pred cceeeeeccceee--eeeehhhhcccccce-eeccCCCcchhh-hhhhhcCeehHHhhhhh
Confidence 5679999999999 999999999999876 888999999997 78788888877665544
No 10
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.35 E-value=4.4e-13 Score=83.96 Aligned_cols=55 Identities=22% Similarity=0.572 Sum_probs=43.8
Q ss_pred cccccCCCCCCc--eeeCCceeeCCCCceecCCCCccCCCCCceecCCeeeecccccCCC
Q psy327 73 NINYFSSLPAGQ--MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSKGE 130 (168)
Q Consensus 73 C~~C~~~i~~~~--v~~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~ 130 (168)
|..|.++|.+.. +.++|+.||+ +||+|..|+++|.+..|+..||++||.. |+.++
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~--~Cf~C~~C~~~l~~~~~~~~~~~~~C~~-c~~~~ 57 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHP--ECFKCSKCGKPLNDGDFYEKDGKPYCKD-CYQKR 57 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEET--TTSBETTTTCBTTTSSEEEETTEEEEHH-HHHHH
T ss_pred CCCCCCCccCcEEEEEeCCcEEEc--cccccCCCCCccCCCeeEeECCEEECHH-HHhhh
Confidence 444555554333 3599999999 9999999999998888999999999996 77543
No 11
>KOG1700|consensus
Probab=99.29 E-value=1e-12 Score=102.33 Aligned_cols=130 Identities=17% Similarity=0.352 Sum_probs=102.5
Q ss_pred eeccCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCccc---ccc-------cCC----c--c
Q psy327 5 ASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEV---RVQ-------VGG----H--R 68 (168)
Q Consensus 5 ~~~~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~---I~~-------~~g----~--~ 68 (168)
+.+...|..||+.||.|..|.+.|....+...++.+||+.+|...++++=..=++. +.. ... . .
T Consensus 21 e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (200)
T KOG1700|consen 21 EKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKDGKSLNESKPNQSAK 100 (200)
T ss_pred HHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcccccccccccccchh
Confidence 34568899999999999999999999999999999999998777766654443332 110 000 0 0
Q ss_pred c------cCCcccccCCCCC-CceeeCCceeeCCCCceecCCCCccCCCCCceecCCeeeecccccCCCCCCCCC
Q psy327 69 T------RDLNINYFSSLPA-GQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTPSD 136 (168)
Q Consensus 69 ~------~~~C~~C~~~i~~-~~v~~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~~~~ 136 (168)
+ ...|..|.+.++. +.+...+..||. .||+|+.|+..|....+...+|.+||..+++..++...-.
T Consensus 101 ~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk--~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~ 173 (200)
T KOG1700|consen 101 FQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHK--SCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNY 173 (200)
T ss_pred HHhhhccccccccccceeeehHHHhhhhhhhhh--hheeecccccccCCcchhhcCCccccchhhheeecCCCcc
Confidence 0 6789999999874 668899999999 9999999999999999999999999998777666554433
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=99.18 E-value=6.7e-12 Score=78.52 Aligned_cols=43 Identities=30% Similarity=0.718 Sum_probs=40.5
Q ss_pred cCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhh
Q psy327 8 AGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL 50 (168)
Q Consensus 8 ~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~ 50 (168)
.++|+.||++||+|..|+++|.+..|+..||++||..||.++|
T Consensus 16 ~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 16 KAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp EETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred EeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 5899999999999999999998888999999999999999875
No 13
>KOG4577|consensus
Probab=98.58 E-value=1.6e-09 Score=87.19 Aligned_cols=72 Identities=19% Similarity=0.420 Sum_probs=57.9
Q ss_pred CCcccccCCCCCC-ceeeCCceeeCCCCceecCCCCccCCCCCceecCCeeeecccccCCCCCCCCCCCCCCCCCCC
Q psy327 71 DLNINYFSSLPAG-QMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTPSDSSGPGLRPQR 146 (168)
Q Consensus 71 ~~C~~C~~~i~~~-~v~~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~~~~~~~~~~~~~~ 146 (168)
|.|.+|.+.|.+. ++.+++++||. .|++|+.|+.+|.. ..+.++|.+||+.| +-+.+.+.|..|..+|+|..
T Consensus 34 p~CagC~q~IlDrFilKvl~R~wHs--~CLkCs~C~~qL~d-rCFsR~~s~yCked-FfKrfGTKCsaC~~GIpPtq 106 (383)
T KOG4577|consen 34 PICAGCDQHILDRFILKVLDRHWHS--SCLKCSDCHDQLAD-RCFSREGSVYCKED-FFKRFGTKCSACQEGIPPTQ 106 (383)
T ss_pred ccccchHHHHHHHHHHHHHhhhhhh--hhcchhhhhhHHHH-HHhhcCCceeehHH-HHHHhCCcchhhcCCCChHH
Confidence 4444444444433 58899999999 99999999999965 47779999999975 55778999999999999863
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=98.42 E-value=1.5e-07 Score=53.51 Aligned_cols=35 Identities=23% Similarity=0.507 Sum_probs=27.1
Q ss_pred cccccCCCCC--CceeeCCceeeCCCCceecCCCCccCC
Q psy327 73 NINYFSSLPA--GQMSHEGQHWHATDSCFCCATCSLSLL 109 (168)
Q Consensus 73 C~~C~~~i~~--~~v~~~~~~~H~~~~CF~C~~C~~~l~ 109 (168)
|..|.+.|.+ ..+.+.++.||+ +||+|..|+++|.
T Consensus 2 C~~C~~~i~~~~~~~~~~~~~~H~--~Cf~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRALGKVWHP--ECFKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEeCCccccc--cCCCCcccCCcCc
Confidence 4445555443 358889999999 9999999999985
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=97.58 E-value=3.1e-05 Score=43.69 Aligned_cols=23 Identities=39% Similarity=0.941 Sum_probs=20.8
Q ss_pred ccCCCCCCCCCCccccccccccC
Q psy327 7 RAGPNSCWHPGCFTCSVCNELLV 29 (168)
Q Consensus 7 ~~a~~~~~H~~Cf~C~~C~~~L~ 29 (168)
+.++++.||++||+|..|+++|.
T Consensus 16 ~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 16 LRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred EEeCCccccccCCCCcccCCcCc
Confidence 56789999999999999999985
No 16
>KOG1700|consensus
Probab=97.08 E-value=0.00024 Score=55.43 Aligned_cols=67 Identities=19% Similarity=0.420 Sum_probs=51.3
Q ss_pred CcccccCCCC-CCceeeCCceeeCCCCceecCCCCccCCCCCceecCCeeeecccccCCCCCCCCCCCCCC
Q psy327 72 LNINYFSSLP-AGQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTPSDSSGPG 141 (168)
Q Consensus 72 ~C~~C~~~i~-~~~v~~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~~~~~~~~~ 141 (168)
.|..|++.|+ .+.+...|..||+ .||+|..|.+.|....+...++.+||.. |+-..+.+...+=+..
T Consensus 9 kc~~c~k~vy~~e~~~~~g~~~hk--~c~~c~~~~k~l~~~~~~~~e~~~yc~~-~~~~~~~~~~~~~~~~ 76 (200)
T KOG1700|consen 9 KCNACGKTVYFVEKVQKDGVDFHK--ECFKCEKCKKTLTLSGYSEHEGVPYCKN-CHVAQFGPKGGGFGKG 76 (200)
T ss_pred hhhhccCcchHHHHHhccCcchhh--hHHhcccccccccccccccccccccccc-chHhhhCccccccccc
Confidence 4555555554 3456788999999 9999999999998888999999999996 7666666555544443
No 17
>KOG0490|consensus
Probab=96.95 E-value=0.00016 Score=56.77 Aligned_cols=98 Identities=22% Similarity=0.458 Sum_probs=77.0
Q ss_pred cCCCCCCCCCCccccccccccC--CCceEEECCeeccccchHh--hhccccccCcccccccCCccccCCcccccCCCCCC
Q psy327 8 AGPNSCWHPGCFTCSVCNELLV--DLIYFYRGDKLYCGRHHAE--TLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAG 83 (168)
Q Consensus 8 ~a~~~~~H~~Cf~C~~C~~~L~--~~~~~~~~g~~yC~~cy~~--~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~ 83 (168)
..++..||..|+.|..|...|. ...|.. +|..||..+|.. .+..+|..|...|..++ .
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~-----------------~ 74 (235)
T KOG0490|consen 13 RVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLD-----------------E 74 (235)
T ss_pred hcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHH-----------------H
Confidence 3447889999999999999997 555555 999999999998 77789999998886432 1
Q ss_pred ceeeCCceeeCCCCceecCCCCccC-CCCCceecCC-eeeecccc
Q psy327 84 QMSHEGQHWHATDSCFCCATCSLSL-LGRPFLPRAG-VIFCSIAC 126 (168)
Q Consensus 84 ~v~~~~~~~H~~~~CF~C~~C~~~l-~~~~f~~~dg-~~~C~~~C 126 (168)
+..+..++ |. .||.|..|...+ .+..+.+.+. +..|.++.
T Consensus 75 ler~f~~~-h~--Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r 116 (235)
T KOG0490|consen 75 LERAFEKV-HL--PCFACRECLALLLTGDEFRVQVWFQNRRAKDR 116 (235)
T ss_pred HHHhhcCC-Cc--CccchHHHHhhcCCCCeeeeehhhhhhcHhhh
Confidence 34555666 87 899999999876 6777776644 99998743
No 18
>KOG1702|consensus
Probab=96.53 E-value=0.00026 Score=54.99 Aligned_cols=59 Identities=15% Similarity=0.335 Sum_probs=46.1
Q ss_pred CcccccCCCCC-CceeeCCceeeCCCCceecCCCCccCCCCCceecCCeeeecccccCCCCCC
Q psy327 72 LNINYFSSLPA-GQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPT 133 (168)
Q Consensus 72 ~C~~C~~~i~~-~~v~~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~ 133 (168)
.|..|++.++. +.|.-+++.||. .||+|..|+.+|.-..|--.|.++||.. .|.+..++
T Consensus 6 n~~~cgk~vYPvE~v~cldk~whk--~cfkce~c~mtlnmKnyKgy~kkpycn~-hYpkq~at 65 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEVKCLDKVWHK--QCFKCEVCGMTLNMKNYKGYDKKPYCNP-HYPKQVAT 65 (264)
T ss_pred hhhhhccccccHHHHhhHHHHHHH--HhheeeeccCChhhhhccccccCCCcCc-ccccceee
Confidence 45566666543 458889999999 9999999999998888877899999997 55554433
No 19
>KOG1702|consensus
Probab=96.06 E-value=0.00054 Score=53.25 Aligned_cols=44 Identities=30% Similarity=0.580 Sum_probs=38.5
Q ss_pred ccCCCCCCCCCCccccccccccCCCceEEECCeeccccchHhhh
Q psy327 7 RAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL 50 (168)
Q Consensus 7 ~~a~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~ 50 (168)
+.-+++.||..||+|..|+-+|.-.+|-..|.++||..+|-+..
T Consensus 20 v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 20 VKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred HhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 34578899999999999999998888888999999999997653
No 20
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=88.01 E-value=0.19 Score=28.54 Aligned_cols=29 Identities=17% Similarity=0.431 Sum_probs=18.9
Q ss_pred cccCCCCCC--ceeeCCceeeCCCCceecCCCCccC
Q psy327 75 NYFSSLPAG--QMSHEGQHWHATDSCFCCATCSLSL 108 (168)
Q Consensus 75 ~C~~~i~~~--~v~~~~~~~H~~~~CF~C~~C~~~l 108 (168)
-|++.|.++ ++...++.|| |.|..|...|
T Consensus 3 ~CG~~I~~eP~~~k~~~~~y~-----fCC~tC~~~f 33 (37)
T PF08394_consen 3 YCGGEITGEPIVVKIGNKVYY-----FCCPTCLSQF 33 (37)
T ss_pred ccCCcccCCEEEEEECCeEEE-----EECHHHHHHH
Confidence 344444443 3566789999 6888887655
No 21
>KOG2462|consensus
Probab=84.08 E-value=0.75 Score=37.47 Aligned_cols=96 Identities=13% Similarity=0.155 Sum_probs=55.7
Q ss_pred CCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCcccccccCCccc-------cCCcccccCCCCCCcee
Q psy327 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRT-------RDLNINYFSSLPAGQMS 86 (168)
Q Consensus 14 ~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~-------~~~C~~C~~~i~~~~v~ 86 (168)
--...++|..|++.+.+..-..+-.+..|..+- .-+..|..|++..+.++...- .-.|..|+|...---|.
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s--~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLL 203 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDS--KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLL 203 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccc--cccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHh
Confidence 345688999999999776555666677666553 225678888877664321111 23577777653210011
Q ss_pred eCCceeeCCCCceecCCCCccCCCC
Q psy327 87 HEGQHWHATDSCFCCATCSLSLLGR 111 (168)
Q Consensus 87 ~~~~~~H~~~~CF~C~~C~~~l~~~ 111 (168)
-.--.-|..+.-|.|..|++.|.++
T Consensus 204 QGHiRTHTGEKPF~C~hC~kAFADR 228 (279)
T KOG2462|consen 204 QGHIRTHTGEKPFSCPHCGKAFADR 228 (279)
T ss_pred hcccccccCCCCccCCcccchhcch
Confidence 1112234445678888888777433
No 22
>KOG0490|consensus
Probab=83.57 E-value=0.31 Score=37.96 Aligned_cols=55 Identities=24% Similarity=0.429 Sum_probs=41.1
Q ss_pred eeeCCceeeCCCCceecCCCCccCC--CCCceecCCeeeecccccC-CCCCCCCCCCCCCC
Q psy327 85 MSHEGQHWHATDSCFCCATCSLSLL--GRPFLPRAGVIFCSIACSK-GEPPTPSDSSGPGL 142 (168)
Q Consensus 85 v~~~~~~~H~~~~CF~C~~C~~~l~--~~~f~~~dg~~~C~~~C~~-~~~~~~~~~~~~~~ 142 (168)
+.+.+..||. .|..|..|...|. ...|.. +|.+||..+... ..+...+..|...+
T Consensus 12 l~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~ 69 (235)
T KOG0490|consen 12 LRVLDRYWHA--SCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTI 69 (235)
T ss_pred hhcccHHHHH--HHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCc
Confidence 5666999998 9999999999996 555666 999999986554 14455566555554
No 23
>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=81.94 E-value=0.8 Score=27.95 Aligned_cols=32 Identities=31% Similarity=0.804 Sum_probs=21.9
Q ss_pred ecCCCCccCCCCCceecCCeeeecccccCCCC
Q psy327 100 CCATCSLSLLGRPFLPRAGVIFCSIACSKGEP 131 (168)
Q Consensus 100 ~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~ 131 (168)
-|..|...+....-+..||+.||...|....+
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~gH~ 40 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACANGHP 40 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHHTSS
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhccCC
Confidence 47788888887888999999999999988763
No 24
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=79.19 E-value=2.8 Score=27.16 Aligned_cols=38 Identities=21% Similarity=0.465 Sum_probs=21.0
Q ss_pred cccccccccCCCceEEECCeeccccchHhh-hccccccCccccc
Q psy327 20 TCSVCNELLVDLIYFYRGDKLYCGRHHAET-LKPRCSACDEVRV 62 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~-~~~~C~~C~~~I~ 62 (168)
.|..|+.+|.. .++..+|..|.... ....|..|++++.
T Consensus 3 ~CP~C~~~L~~-----~~~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 3 TCPKCQQELEW-----QGGHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp B-SSS-SBEEE-----ETTEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred cCCCCCCccEE-----eCCEEECccccccceecccCCCcccHHH
Confidence 57788888743 45888888886532 1367777877775
No 25
>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=79.15 E-value=1.4 Score=38.96 Aligned_cols=59 Identities=22% Similarity=0.500 Sum_probs=39.2
Q ss_pred eeccccchHhhhccccccCcccccccCCccccCCcccccCCCCCCceeeCCceeeCCCCceecCCCCccCC
Q psy327 39 KLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMSHEGQHWHATDSCFCCATCSLSLL 109 (168)
Q Consensus 39 ~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v~~~~~~~H~~~~CF~C~~C~~~l~ 109 (168)
-+||+.|.. .+|..|-..-.. --||+.|-..+....+...+..--. +||.|..|..+|.
T Consensus 5 L~fC~~C~~----irc~~c~~~Ei~------~~yCp~CL~~~p~~e~~~~~nrC~r--~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 5 LYFCEHCHK----IRCPRCVSEEID------SYYCPNCLFEVPSSEARSEKNRCSR--NCFDCPICFSPLS 63 (483)
T ss_pred ceecccccc----cCChhhcccccc------eeECccccccCChhhheeccceecc--ccccCCCCCCcce
Confidence 467888854 456665543221 2378888887765555555554444 8999999999993
No 26
>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=78.21 E-value=1.6 Score=22.35 Aligned_cols=8 Identities=13% Similarity=0.439 Sum_probs=3.7
Q ss_pred ccCccccc
Q psy327 55 SACDEVRV 62 (168)
Q Consensus 55 ~~C~~~I~ 62 (168)
..|+..|.
T Consensus 2 ~sC~~~i~ 9 (24)
T PF07754_consen 2 TSCGRPIA 9 (24)
T ss_pred ccCCCccc
Confidence 34444444
No 27
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=77.16 E-value=1.6 Score=31.82 Aligned_cols=22 Identities=23% Similarity=0.679 Sum_probs=18.4
Q ss_pred cccccccccCCCceEEECCeeccccch
Q psy327 20 TCSVCNELLVDLIYFYRGDKLYCGRHH 46 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~~~~g~~yC~~cy 46 (168)
.|..|+.|| |.+||.+||.-|-
T Consensus 30 hCp~Cg~PL-----F~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL-----FRKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc-----eeeCCeEECCCCC
Confidence 478899988 5599999999884
No 28
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=74.90 E-value=1.8 Score=26.26 Aligned_cols=29 Identities=10% Similarity=0.368 Sum_probs=22.7
Q ss_pred cccccccccCCCc-eEEECCeeccccchHhh
Q psy327 20 TCSVCNELLVDLI-YFYRGDKLYCGRHHAET 49 (168)
Q Consensus 20 ~C~~C~~~L~~~~-~~~~~g~~yC~~cy~~~ 49 (168)
.|..|+..+.--. +-..|| ..|..|+.+.
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 4899999985533 557788 7999999876
No 29
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=74.58 E-value=2.7 Score=26.82 Aligned_cols=44 Identities=16% Similarity=0.570 Sum_probs=22.9
Q ss_pred ccccccccccCCCceEEECCeeccccchHhhhccccccCccccc
Q psy327 19 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRV 62 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~ 62 (168)
++|+.|...|...-....=..+||..|-.+.++..|..|..|..
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw 51 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAW 51 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHH
Confidence 57899988886643344556789999988888888988888765
No 30
>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=71.63 E-value=2.7 Score=28.54 Aligned_cols=28 Identities=18% Similarity=0.374 Sum_probs=22.4
Q ss_pred cccccccccCCCceE-EECCeeccccchH
Q psy327 20 TCSVCNELLVDLIYF-YRGDKLYCGRHHA 47 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~-~~~g~~yC~~cy~ 47 (168)
.|..|+++|.+..|. ..+|.++...|..
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 599999999887775 4678888877753
No 31
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=68.36 E-value=3.4 Score=23.14 Aligned_cols=24 Identities=25% Similarity=0.681 Sum_probs=17.7
Q ss_pred cccccccccCCCceEEECCeeccccchH
Q psy327 20 TCSVCNELLVDLIYFYRGDKLYCGRHHA 47 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~~~~g~~yC~~cy~ 47 (168)
.|..|+.. .|...||..||..|..
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCce
Confidence 46777654 4678899999987743
No 32
>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=68.05 E-value=3.4 Score=23.86 Aligned_cols=22 Identities=27% Similarity=0.625 Sum_probs=15.8
Q ss_pred cccccccccCCCceEEECCeeccccc
Q psy327 20 TCSVCNELLVDLIYFYRGDKLYCGRH 45 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~~~~g~~yC~~c 45 (168)
.|..|+.+|- -.++|+.||..|
T Consensus 19 ~Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeE----EecCCCEECCCC
Confidence 4667888773 247889998766
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=67.49 E-value=3.8 Score=21.01 Aligned_cols=9 Identities=22% Similarity=0.582 Sum_probs=4.5
Q ss_pred ccccCcccc
Q psy327 53 RCSACDEVR 61 (168)
Q Consensus 53 ~C~~C~~~I 61 (168)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 455555544
No 34
>PRK00807 50S ribosomal protein L24e; Validated
Probab=67.18 E-value=2.2 Score=25.93 Aligned_cols=36 Identities=22% Similarity=0.497 Sum_probs=25.7
Q ss_pred ccccCcccccccCCccccCCcccccCCCCCCceeeCCceeeCCCCceecCCCCccC
Q psy327 53 RCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMSHEGQHWHATDSCFCCATCSLSL 108 (168)
Q Consensus 53 ~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v~~~~~~~H~~~~CF~C~~C~~~l 108 (168)
.|.-|+..|.+..|..| |...|+.|. |.+..|.+.+
T Consensus 3 ~C~fcG~~I~pg~G~~~---------------vr~Dgkv~~-----Fcs~KC~~~f 38 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMY---------------VKKDGTILY-----FCSSKCEKNY 38 (52)
T ss_pred ccCCCCCeEcCCCCeEE---------------EEeCCcEEE-----EeCHHHHHHH
Confidence 57777777776555543 677899998 6777886654
No 35
>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=66.36 E-value=3.1 Score=28.34 Aligned_cols=42 Identities=17% Similarity=0.479 Sum_probs=28.2
Q ss_pred CCCCCccccccccccCCCceEEECCeeccccchHhhhccccccCcccccc
Q psy327 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQ 63 (168)
Q Consensus 14 ~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~ 63 (168)
|-+.=-+|.+|...+.. .|.-||..|..+. ..|+.|++.|.+
T Consensus 40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred ccccCcccccccccccc------CCCccChhhhccc--CcccccCCeecc
Confidence 43434467788776633 3567899986654 578888888864
No 36
>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=65.87 E-value=6 Score=24.07 Aligned_cols=43 Identities=16% Similarity=0.188 Sum_probs=31.6
Q ss_pred ccccccccccCCCceEEECCeeccccchHhhhc--cccccCccccc
Q psy327 19 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLK--PRCSACDEVRV 62 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~--~~C~~C~~~I~ 62 (168)
|.|..|+..+.+ ......|..||+.+..+.+. ..|..|++++.
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 678999998866 45667899999999776543 45666666653
No 37
>PF12773 DZR: Double zinc ribbon
Probab=64.55 E-value=7.2 Score=22.87 Aligned_cols=23 Identities=17% Similarity=0.346 Sum_probs=11.1
Q ss_pred cccCcccccccCCccccCCcccccCCCC
Q psy327 54 CSACDEVRVQVGGHRTRDLNINYFSSLP 81 (168)
Q Consensus 54 C~~C~~~I~~~~g~~~~~~C~~C~~~i~ 81 (168)
|..|+.+|... ..+|..|+.++.
T Consensus 1 Cp~Cg~~~~~~-----~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDD-----AKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCcc-----ccCChhhcCChh
Confidence 34455555421 234666665554
No 38
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=63.65 E-value=4.6 Score=25.26 Aligned_cols=12 Identities=25% Similarity=0.803 Sum_probs=7.1
Q ss_pred cccccCcccccc
Q psy327 52 PRCSACDEVRVQ 63 (168)
Q Consensus 52 ~~C~~C~~~I~~ 63 (168)
+.|..|+..|.+
T Consensus 8 ~~CtSCg~~i~~ 19 (59)
T PRK14890 8 PKCTSCGIEIAP 19 (59)
T ss_pred ccccCCCCcccC
Confidence 456666666654
No 39
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=62.07 E-value=4.1 Score=25.43 Aligned_cols=29 Identities=31% Similarity=0.695 Sum_probs=22.1
Q ss_pred ecCCCCccCC-CC-CceecCCeeeecccccC
Q psy327 100 CCATCSLSLL-GR-PFLPRAGVIFCSIACSK 128 (168)
Q Consensus 100 ~C~~C~~~l~-~~-~f~~~dg~~~C~~~C~~ 128 (168)
.|.-|++.|. +. -|..++.+.+|..+|..
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~ 48 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECRS 48 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHHH
Confidence 4888999995 44 45568899999987764
No 40
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=62.06 E-value=4.8 Score=31.47 Aligned_cols=31 Identities=16% Similarity=0.434 Sum_probs=26.0
Q ss_pred eecCCCCccCCCCCceecCCeeeecccccCCC
Q psy327 99 FCCATCSLSLLGRPFLPRAGVIFCSIACSKGE 130 (168)
Q Consensus 99 F~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~ 130 (168)
-+|..|+..+-...-...+|++.|.. |+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~-C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKP-CAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceeccc-ccccc
Confidence 58999999987777788999999997 87643
No 41
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=61.84 E-value=3.4 Score=30.06 Aligned_cols=24 Identities=33% Similarity=0.991 Sum_probs=19.1
Q ss_pred ecCCCCccCCCCCceecCCeeeecccccCC
Q psy327 100 CCATCSLSLLGRPFLPRAGVIFCSIACSKG 129 (168)
Q Consensus 100 ~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~ 129 (168)
.|..|+.+| |- .||.+||+. |...
T Consensus 30 hCp~Cg~PL----F~-KdG~v~CPv-C~~~ 53 (131)
T COG1645 30 HCPKCGTPL----FR-KDGEVFCPV-CGYR 53 (131)
T ss_pred hCcccCCcc----ee-eCCeEECCC-CCce
Confidence 588998887 33 899999997 8843
No 42
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=60.90 E-value=1 Score=25.03 Aligned_cols=29 Identities=14% Similarity=0.253 Sum_probs=21.1
Q ss_pred ccccccccCCCceEEECCeeccccchHhh
Q psy327 21 CSVCNELLVDLIYFYRGDKLYCGRHHAET 49 (168)
Q Consensus 21 C~~C~~~L~~~~~~~~~g~~yC~~cy~~~ 49 (168)
|..|+.++........++..+|..|....
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 88999988776666678889998887643
No 43
>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=58.68 E-value=14 Score=21.66 Aligned_cols=43 Identities=23% Similarity=0.517 Sum_probs=29.6
Q ss_pred ccccccccccCCCceEEECCee-ccccchHhhh--ccccccCccccc
Q psy327 19 FTCSVCNELLVDLIYFYRGDKL-YCGRHHAETL--KPRCSACDEVRV 62 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~-yC~~cy~~~~--~~~C~~C~~~I~ 62 (168)
+.|..|...... ..+..=|.. +|..|+.+.. ..+|..|.++|.
T Consensus 3 ~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp SB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 357777776644 345566777 9999998774 478888888875
No 44
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=57.76 E-value=7.2 Score=35.76 Aligned_cols=49 Identities=12% Similarity=0.224 Sum_probs=34.9
Q ss_pred cccccccccCCCceEEECCeeccccchHhhhccccccCcccccccCCccccCCcccccCCC
Q psy327 20 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSL 80 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i 80 (168)
+|..|+.... ++.-||..|-..+-...|..|+..+.. |. .+|..|+.++
T Consensus 3 ~Cp~Cg~~n~-------~~akFC~~CG~~l~~~~Cp~CG~~~~~--~~---~fC~~CG~~~ 51 (645)
T PRK14559 3 ICPQCQFENP-------NNNRFCQKCGTSLTHKPCPQCGTEVPV--DE---AHCPNCGAET 51 (645)
T ss_pred cCCCCCCcCC-------CCCccccccCCCCCCCcCCCCCCCCCc--cc---ccccccCCcc
Confidence 5778877653 345578888766545789999998763 33 4699999774
No 45
>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=57.14 E-value=8.9 Score=23.75 Aligned_cols=46 Identities=17% Similarity=0.364 Sum_probs=28.4
Q ss_pred ecCCCCccCC--C-CCceecCCeeeecccccCCCCCCCCCCCCCCCCCCC
Q psy327 100 CCATCSLSLL--G-RPFLPRAGVIFCSIACSKGEPPTPSDSSGPGLRPQR 146 (168)
Q Consensus 100 ~C~~C~~~l~--~-~~f~~~dg~~~C~~~C~~~~~~~~~~~~~~~~~~~~ 146 (168)
.|..|++.|. + +.++-.-.=-||.+ |...+....|-.||..+.+..
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~-C~e~~l~~~CPNCgGelv~RP 55 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCAD-CAETMLNGVCPNCGGELVRRP 55 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHH-HHHHHhcCcCcCCCCccccCC
Confidence 4566666662 1 23333444556774 887777777888888776543
No 46
>PRK14873 primosome assembly protein PriA; Provisional
Probab=56.15 E-value=13 Score=34.23 Aligned_cols=38 Identities=21% Similarity=0.435 Sum_probs=26.5
Q ss_pred ecCCCCccCCCCCceecCCeeeecccccCCCCCCCCCCCCCC
Q psy327 100 CCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTPSDSSGPG 141 (168)
Q Consensus 100 ~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~~~~~~~~~ 141 (168)
+|..|+.+|. |...++.+.|. .|.....+..|-.|+..
T Consensus 394 ~C~~C~~~L~---~h~~~~~l~Ch-~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 394 RCRHCTGPLG---LPSAGGTPRCR-WCGRAAPDWRCPRCGSD 431 (665)
T ss_pred ECCCCCCcee---EecCCCeeECC-CCcCCCcCccCCCCcCC
Confidence 4555555542 33356789999 49887777889999886
No 47
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=56.07 E-value=8.7 Score=20.94 Aligned_cols=40 Identities=20% Similarity=0.546 Sum_probs=23.2
Q ss_pred cccccccccCCCceEEECCeeccccchHhhhc---cccccCcc
Q psy327 20 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLK---PRCSACDE 59 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~---~~C~~C~~ 59 (168)
.|..|...+........=|..||..|....+. .+|..|..
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~ 43 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCC
Confidence 36777777633222333677788888765543 35655554
No 48
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=52.58 E-value=5.5 Score=27.56 Aligned_cols=30 Identities=23% Similarity=0.519 Sum_probs=20.7
Q ss_pred CceecCCCCccCC-CCCceecCCeeeeccccc
Q psy327 97 SCFCCATCSLSLL-GRPFLPRAGVIFCSIACS 127 (168)
Q Consensus 97 ~CF~C~~C~~~l~-~~~f~~~dg~~~C~~~C~ 127 (168)
+=|+|+.|-..-. ++--...+|+++|.. |.
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~D-Ca 99 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRD-CA 99 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEeccc-cC
Confidence 4599999965553 333345689999994 73
No 49
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=51.67 E-value=13 Score=25.79 Aligned_cols=48 Identities=15% Similarity=0.315 Sum_probs=34.0
Q ss_pred CCceeeCCCCcee-cCCCCccCCCCCceecCCeeeecccccCCCCCCC----CCCCCCCCC
Q psy327 88 EGQHWHATDSCFC-CATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTP----SDSSGPGLR 143 (168)
Q Consensus 88 ~~~~~H~~~~CF~-C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~~----~~~~~~~~~ 143 (168)
.+..+.. -|. |..| .+..|+..++.+.|.. |...++... .-+|++...
T Consensus 27 ~dg~~~v---a~daCeiC----~~~GY~q~g~~lvC~~-C~~~~~~~~ig~~~GGCNP~P~ 79 (102)
T PF10080_consen 27 PDGSYRV---AFDACEIC----GPKGYYQEGDQLVCKN-CGVRFNLPTIGGKSGGCNPIPL 79 (102)
T ss_pred CCCCEEE---EEEecccc----CCCceEEECCEEEEec-CCCEEehhhcccccCCCCccCC
Confidence 3445553 233 7777 5778999999999995 999876544 447777655
No 50
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=50.35 E-value=9.7 Score=28.54 Aligned_cols=52 Identities=21% Similarity=0.411 Sum_probs=30.9
Q ss_pred CeeccccchHhhhccccccCcccccccCCccccCCcccccCCCCCCceeeCCceeeCCCCceecCCCCccC
Q psy327 38 DKLYCGRHHAETLKPRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMSHEGQHWHATDSCFCCATCSLSL 108 (168)
Q Consensus 38 g~~yC~~cy~~~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v~~~~~~~H~~~~CF~C~~C~~~l 108 (168)
.+-||..|-.+. -..|..|+.+|.+. -+ ..+ +...+..|++ ---|..|++++
T Consensus 27 ~~~fC~kCG~~t-I~~Cp~C~~~IrG~---y~-----------v~g-v~~~g~~~~~---PsYC~~CGkpy 78 (158)
T PF10083_consen 27 REKFCSKCGAKT-ITSCPNCSTPIRGD---YH-----------VEG-VFGLGGHYEA---PSYCHNCGKPY 78 (158)
T ss_pred HHHHHHHhhHHH-HHHCcCCCCCCCCc---ee-----------cCC-eeeeCCCCCC---ChhHHhCCCCC
Confidence 345777776665 35677777777631 11 112 3344677775 45688888876
No 51
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=50.18 E-value=8.3 Score=28.28 Aligned_cols=24 Identities=21% Similarity=0.564 Sum_probs=17.2
Q ss_pred ceecCCCCccCCCCCceecCCeeeecccccCCC
Q psy327 98 CFCCATCSLSLLGRPFLPRAGVIFCSIACSKGE 130 (168)
Q Consensus 98 CF~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~ 130 (168)
=+.|..||.+|..+ -||.. |...+
T Consensus 81 ~~~CE~CG~~I~~G--------r~C~~-C~~~l 104 (137)
T TIGR03826 81 GYPCERCGTSIREG--------RLCDS-CAGEL 104 (137)
T ss_pred cCcccccCCcCCCC--------CccHH-HHHHH
Confidence 46899999999433 37775 77655
No 52
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=49.44 E-value=7.1 Score=21.58 Aligned_cols=7 Identities=29% Similarity=1.251 Sum_probs=4.4
Q ss_pred eecCCCC
Q psy327 99 FCCATCS 105 (168)
Q Consensus 99 F~C~~C~ 105 (168)
+.|..|+
T Consensus 23 ~vC~~Cg 29 (34)
T PF14803_consen 23 LVCPACG 29 (34)
T ss_dssp EEETTTT
T ss_pred eECCCCC
Confidence 4666665
No 53
>KOG1813|consensus
Probab=48.97 E-value=8 Score=31.98 Aligned_cols=44 Identities=14% Similarity=0.475 Sum_probs=34.5
Q ss_pred ccccccccccCCCceEEECCeeccccchHhhhc--cccccCcccccc
Q psy327 19 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLK--PRCSACDEVRVQ 63 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~--~~C~~C~~~I~~ 63 (168)
|.|.+|++.... .....=+..+|+.|..+.|. ++|..|++.+.+
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccccCCcceeccccccc
Confidence 788899887754 23456778899999887765 689999999875
No 54
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=48.59 E-value=11 Score=20.89 Aligned_cols=31 Identities=19% Similarity=0.438 Sum_probs=20.9
Q ss_pred ccccccccCCCceEEECCeeccccchHhhhc
Q psy327 21 CSVCNELLVDLIYFYRGDKLYCGRHHAETLK 51 (168)
Q Consensus 21 C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~ 51 (168)
|.+|...+.+......=|..||.+|..+.+.
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHH
Confidence 5567776665334567889999999876543
No 55
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=48.43 E-value=9.5 Score=23.43 Aligned_cols=9 Identities=33% Similarity=1.125 Sum_probs=6.9
Q ss_pred CceeeCCCCce
Q psy327 89 GQHWHATDSCF 99 (168)
Q Consensus 89 ~~~~H~~~~CF 99 (168)
+..||. +|+
T Consensus 28 gapyHR--~C~ 36 (54)
T PF14446_consen 28 GAPYHR--DCW 36 (54)
T ss_pred CCcccH--HHH
Confidence 678887 777
No 56
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=48.26 E-value=4.1 Score=25.02 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=14.0
Q ss_pred cccccCcccccccCCccc-cCCccccc
Q psy327 52 PRCSACDEVRVQVGGHRT-RDLNINYF 77 (168)
Q Consensus 52 ~~C~~C~~~I~~~~g~~~-~~~C~~C~ 77 (168)
.+|..|++.+...+|+.| ...|+.|.
T Consensus 5 iRC~~CnKlLa~a~~~~yle~KCPrCK 31 (60)
T COG4416 5 IRCAKCNKLLAEAEGQAYLEKKCPRCK 31 (60)
T ss_pred eehHHHhHHHHhcccceeeeecCCccc
Confidence 456666666665555544 33444443
No 57
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=47.53 E-value=5.7 Score=23.21 Aligned_cols=26 Identities=27% Similarity=0.773 Sum_probs=19.3
Q ss_pred cCCCCccCCCCCceecCCeeeecccccCCC
Q psy327 101 CATCSLSLLGRPFLPRAGVIFCSIACSKGE 130 (168)
Q Consensus 101 C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~ 130 (168)
|..|++.+.. ..++.+||...|..+-
T Consensus 9 C~~Cdk~~~~----~~~~~lYCSe~Cr~~D 34 (43)
T PF12855_consen 9 CIVCDKQIDP----PDDGSLYCSEECRLKD 34 (43)
T ss_pred HHHhhccccC----CCCCccccCHHHHhHh
Confidence 6677777744 5789999998887643
No 58
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=46.29 E-value=23 Score=33.00 Aligned_cols=39 Identities=21% Similarity=0.453 Sum_probs=26.7
Q ss_pred eecCCCCccCCCCCceecCCeeeecccccCC-CCCCCCCCCCCC
Q psy327 99 FCCATCSLSLLGRPFLPRAGVIFCSIACSKG-EPPTPSDSSGPG 141 (168)
Q Consensus 99 F~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~-~~~~~~~~~~~~ 141 (168)
+.|..|+..|. |....+.+.|+ .|... ..+..|..|++.
T Consensus 445 ~~Cp~Cd~~lt---~H~~~~~L~CH-~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLT---LHKATGQLRCH-YCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceE---EecCCCeeEeC-CCCCCCCCCCCCCCCCCC
Confidence 34555555542 34457999999 59887 456779999887
No 59
>PRK00420 hypothetical protein; Validated
Probab=45.74 E-value=12 Score=26.58 Aligned_cols=24 Identities=25% Similarity=0.501 Sum_probs=16.1
Q ss_pred ccccccccccCCCceEEECCeeccccch
Q psy327 19 FTCSVCNELLVDLIYFYRGDKLYCGRHH 46 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~yC~~cy 46 (168)
-.|..|+.+|. -.++|+.||..|-
T Consensus 24 ~~CP~Cg~pLf----~lk~g~~~Cp~Cg 47 (112)
T PRK00420 24 KHCPVCGLPLF----ELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCCcce----ecCCCceECCCCC
Confidence 35677887762 2378888887763
No 60
>KOG0320|consensus
Probab=43.52 E-value=13 Score=28.56 Aligned_cols=47 Identities=15% Similarity=0.578 Sum_probs=34.4
Q ss_pred CCCccccccccccCCCc-eEEECCeeccccchHhhh--ccccccCccccc
Q psy327 16 PGCFTCSVCNELLVDLI-YFYRGDKLYCGRHHAETL--KPRCSACDEVRV 62 (168)
Q Consensus 16 ~~Cf~C~~C~~~L~~~~-~~~~~g~~yC~~cy~~~~--~~~C~~C~~~I~ 62 (168)
..+|+|-+|-....... +.-+=|.+||..|-.... +.+|..|.+.|.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 47899999966665443 456789999999987654 367777777665
No 61
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=42.58 E-value=13 Score=21.44 Aligned_cols=10 Identities=30% Similarity=0.697 Sum_probs=5.5
Q ss_pred ccccCccccc
Q psy327 53 RCSACDEVRV 62 (168)
Q Consensus 53 ~C~~C~~~I~ 62 (168)
.|..|+++|.
T Consensus 2 ~Cd~C~~~i~ 11 (43)
T cd02340 2 ICDGCQGPIV 11 (43)
T ss_pred CCCCCCCcCc
Confidence 3556666554
No 62
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=41.93 E-value=21 Score=20.77 Aligned_cols=26 Identities=19% Similarity=0.493 Sum_probs=16.0
Q ss_pred eecCCCCccCCCCCceecCCeeeecccccCC
Q psy327 99 FCCATCSLSLLGRPFLPRAGVIFCSIACSKG 129 (168)
Q Consensus 99 F~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~ 129 (168)
|.|..|+..+.-. ..+.+-|+. |..+
T Consensus 3 Y~C~~Cg~~~~~~----~~~~irC~~-CG~r 28 (44)
T smart00659 3 YICGECGRENEIK----SKDVVRCRE-CGYR 28 (44)
T ss_pred EECCCCCCEeecC----CCCceECCC-CCce
Confidence 6788887765422 456677774 5543
No 63
>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=41.29 E-value=11 Score=21.66 Aligned_cols=29 Identities=14% Similarity=0.430 Sum_probs=17.4
Q ss_pred eecCCCCccCCCCCceecCCeeeecccccC
Q psy327 99 FCCATCSLSLLGRPFLPRAGVIFCSIACSK 128 (168)
Q Consensus 99 F~C~~C~~~l~~~~f~~~dg~~~C~~~C~~ 128 (168)
|+|..|+..+.-..-...+..+-|.. |..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~-Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPE-CGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCC-CCC
Confidence 78888887773222222256677774 654
No 64
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=40.57 E-value=14 Score=21.74 Aligned_cols=31 Identities=16% Similarity=0.296 Sum_probs=20.1
Q ss_pred ccccccccccCCCceEE--ECCeeccccchHhh
Q psy327 19 FTCSVCNELLVDLIYFY--RGDKLYCGRHHAET 49 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~--~~g~~yC~~cy~~~ 49 (168)
+.|..|+..+....|.- ..+..+|.+||.+-
T Consensus 1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G 33 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEG 33 (45)
T ss_pred CcccCCCCccCceEEEecCCCccccChHHHhCc
Confidence 35788888886544421 23467888888764
No 65
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=40.44 E-value=21 Score=20.38 Aligned_cols=38 Identities=16% Similarity=0.509 Sum_probs=23.9
Q ss_pred ccccccccC-C-CceEEECCeeccccchHhhh--ccccccCc
Q psy327 21 CSVCNELLV-D-LIYFYRGDKLYCGRHHAETL--KPRCSACD 58 (168)
Q Consensus 21 C~~C~~~L~-~-~~~~~~~g~~yC~~cy~~~~--~~~C~~C~ 58 (168)
|..|...+. . ..+...=|.++|..|..+.. ...|..|+
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~ 43 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICR 43 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCC
Confidence 567777662 2 22344667889999988776 34555554
No 66
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=39.54 E-value=13 Score=22.16 Aligned_cols=7 Identities=43% Similarity=0.591 Sum_probs=3.5
Q ss_pred CCccccc
Q psy327 71 DLNINYF 77 (168)
Q Consensus 71 ~~C~~C~ 77 (168)
++|..|+
T Consensus 25 DLC~~Cf 31 (49)
T cd02334 25 DLCQSCF 31 (49)
T ss_pred CchHHHH
Confidence 3455555
No 67
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=38.73 E-value=14 Score=21.23 Aligned_cols=15 Identities=27% Similarity=0.952 Sum_probs=8.4
Q ss_pred ccccccccccCCCce
Q psy327 19 FTCSVCNELLVDLIY 33 (168)
Q Consensus 19 f~C~~C~~~L~~~~~ 33 (168)
+.|..|++++.+..|
T Consensus 5 ~~C~~C~~~i~g~ry 19 (44)
T smart00291 5 YSCDTCGKPIVGVRY 19 (44)
T ss_pred cCCCCCCCCCcCCEE
Confidence 346667666655443
No 68
>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=38.34 E-value=13 Score=20.60 Aligned_cols=29 Identities=14% Similarity=0.414 Sum_probs=15.1
Q ss_pred eecCCCCccCCCCCceecCCeeeecccccC
Q psy327 99 FCCATCSLSLLGRPFLPRAGVIFCSIACSK 128 (168)
Q Consensus 99 F~C~~C~~~l~~~~f~~~dg~~~C~~~C~~ 128 (168)
|+|..|+..+....-...+..+-|.. |..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~-Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPE-CGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCC-CCC
Confidence 67888887663221112244555663 543
No 69
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=38.12 E-value=14 Score=21.83 Aligned_cols=29 Identities=14% Similarity=0.408 Sum_probs=16.6
Q ss_pred eecCCCCccCCCCCceecCCeeeecccccC
Q psy327 99 FCCATCSLSLLGRPFLPRAGVIFCSIACSK 128 (168)
Q Consensus 99 F~C~~C~~~l~~~~f~~~dg~~~C~~~C~~ 128 (168)
|+|..|+..+........+..+-|.. |..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~-Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPE-CGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCC-CCC
Confidence 78889988764322222245556774 553
No 70
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=37.66 E-value=9.7 Score=29.85 Aligned_cols=45 Identities=13% Similarity=0.397 Sum_probs=32.4
Q ss_pred CccccccccccCCCceEEECCeeccccchHhhhc--cccccCcccccc
Q psy327 18 CFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLK--PRCSACDEVRVQ 63 (168)
Q Consensus 18 Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~--~~C~~C~~~I~~ 63 (168)
=|.|.+|.+.... .....=|..+|..|+...+. +.|..|++...+
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 3788888887644 33445678899999887764 788888876653
No 71
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.45 E-value=36 Score=30.18 Aligned_cols=42 Identities=24% Similarity=0.619 Sum_probs=27.4
Q ss_pred eecCCCCccCC------CCCceecCCeeeecccccCCCC-CCCCCCCCCC
Q psy327 99 FCCATCSLSLL------GRPFLPRAGVIFCSIACSKGEP-PTPSDSSGPG 141 (168)
Q Consensus 99 F~C~~C~~~l~------~~~f~~~dg~~~C~~~C~~~~~-~~~~~~~~~~ 141 (168)
..|..|+..+. .-.|...++.+.|.- |..... +..|..|+..
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~-Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTYHKKEGKLRCHY-CGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eEhhhCcCccCCCCCCCceEEecCCCeEEcCC-CcCcCCCCCCCCCCCCC
Confidence 44555555542 112445688999995 988765 6678889875
No 72
>PRK14873 primosome assembly protein PriA; Provisional
Probab=36.52 E-value=21 Score=32.95 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=26.1
Q ss_pred ccccccccccCCCceEEECCeeccccchHhhhccccccCccc
Q psy327 19 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEV 60 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~ 60 (168)
++|..|+.+|. |...++.+.|..|-......+|..|+..
T Consensus 393 ~~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 45666666662 3345667888888665556688888765
No 73
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.46 E-value=15 Score=25.21 Aligned_cols=19 Identities=21% Similarity=0.445 Sum_probs=15.8
Q ss_pred ceecCCCCccC-CCCCceec
Q psy327 98 CFCCATCSLSL-LGRPFLPR 116 (168)
Q Consensus 98 CF~C~~C~~~l-~~~~f~~~ 116 (168)
=|+|..|+.++ .|+.|++.
T Consensus 6 ewkC~VCg~~iieGqkFTF~ 25 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFT 25 (103)
T ss_pred eeeEeeeCCEeeeccEEEEe
Confidence 37899999998 89998764
No 74
>KOG3476|consensus
Probab=35.41 E-value=5.9 Score=26.75 Aligned_cols=37 Identities=19% Similarity=0.557 Sum_probs=26.4
Q ss_pred ccccccccccCCCceEEECCeeccccchHhhhccccccCcccccc
Q psy327 19 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRVQ 63 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~ 63 (168)
-+|.+|...+-. .|.-||..|..+. ..|+.|++.|..
T Consensus 55 ~kC~iCk~~vHQ------~GshYC~tCAY~K--giCAMCGKki~n 91 (100)
T KOG3476|consen 55 AKCRICKQLVHQ------PGSHYCQTCAYKK--GICAMCGKKILN 91 (100)
T ss_pred chhHHHHHHhcC------CcchhHhHhhhhh--hHHHHhhhHhhc
Confidence 467778665532 5677899886654 578888888874
No 75
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=35.25 E-value=19 Score=21.32 Aligned_cols=9 Identities=22% Similarity=0.700 Sum_probs=4.3
Q ss_pred cccCc-cccc
Q psy327 54 CSACD-EVRV 62 (168)
Q Consensus 54 C~~C~-~~I~ 62 (168)
|..|+ .+|.
T Consensus 3 C~~C~~~~i~ 12 (49)
T cd02338 3 CDGCGKSNFT 12 (49)
T ss_pred CCCCcCCCcE
Confidence 45555 4444
No 76
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=34.64 E-value=21 Score=20.72 Aligned_cols=30 Identities=20% Similarity=0.464 Sum_probs=15.3
Q ss_pred ecCCCCccCCCCCcee--cCCeeeecccccCCC
Q psy327 100 CCATCSLSLLGRPFLP--RAGVIFCSIACSKGE 130 (168)
Q Consensus 100 ~C~~C~~~l~~~~f~~--~dg~~~C~~~C~~~~ 130 (168)
.|..|+++|.|..|.- =.+--+|.+ |+...
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~-Cf~~~ 33 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSS-CYAKG 33 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHH-HHCcC
Confidence 4555555555433321 135566774 77544
No 77
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=32.75 E-value=24 Score=19.59 Aligned_cols=10 Identities=20% Similarity=0.693 Sum_probs=5.8
Q ss_pred eecCCCCccC
Q psy327 99 FCCATCSLSL 108 (168)
Q Consensus 99 F~C~~C~~~l 108 (168)
.+|..|+..+
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 3666666543
No 78
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=31.24 E-value=25 Score=20.68 Aligned_cols=10 Identities=20% Similarity=0.544 Sum_probs=5.2
Q ss_pred ccccCcc-ccc
Q psy327 53 RCSACDE-VRV 62 (168)
Q Consensus 53 ~C~~C~~-~I~ 62 (168)
.|..|+. ||.
T Consensus 2 ~Cd~C~~~pI~ 12 (45)
T cd02344 2 TCDGCQMFPIN 12 (45)
T ss_pred CCCCCCCCCCc
Confidence 3556653 454
No 79
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=31.12 E-value=18 Score=26.25 Aligned_cols=37 Identities=19% Similarity=0.304 Sum_probs=27.9
Q ss_pred cccccCcccccccCCccccCCcccccCCCCCCceeeCCceeeCCCCceecCCCCccC
Q psy327 52 PRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMSHEGQHWHATDSCFCCATCSLSL 108 (168)
Q Consensus 52 ~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v~~~~~~~H~~~~CF~C~~C~~~l 108 (168)
..|.-|+.+|.|-.|..| |...|+.|+ |.=++|.+.+
T Consensus 5 e~CsFcG~kIyPG~G~~f---------------VR~DGkvf~-----FcssKC~k~f 41 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMF---------------VRKDGTVLH-----FVDSKCEKNY 41 (131)
T ss_pred eeecCcCCcccCCCCcEE---------------EecCCCEEE-----EecHHHHHHH
Confidence 468889999998778775 777899998 5556676554
No 80
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=31.11 E-value=15 Score=24.44 Aligned_cols=29 Identities=21% Similarity=0.304 Sum_probs=20.4
Q ss_pred cccccccccCCCceE--EECC---eeccccchHh
Q psy327 20 TCSVCNELLVDLIYF--YRGD---KLYCGRHHAE 48 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~--~~~g---~~yC~~cy~~ 48 (168)
.|..|+-||.....+ ..|| .-||..||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 488999999766532 3444 4689998875
No 81
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=30.22 E-value=14 Score=21.52 Aligned_cols=30 Identities=17% Similarity=0.307 Sum_probs=17.7
Q ss_pred ccccCCC---CCCceeeCCceeeCCCCceecCCCCccC
Q psy327 74 INYFSSL---PAGQMSHEGQHWHATDSCFCCATCSLSL 108 (168)
Q Consensus 74 ~~C~~~i---~~~~v~~~~~~~H~~~~CF~C~~C~~~l 108 (168)
+.|+..| ....+...|+.|| |.+..|...+
T Consensus 4 Pvcg~~v~~~~~~~~~y~G~~Y~-----FCS~~C~~~F 36 (47)
T PF04945_consen 4 PVCGMKVPGNAAYSVEYNGRTYY-----FCSEGCKEKF 36 (47)
T ss_dssp -GGG-BE-----EEEEETTEEEE-----ESSHHHHHHH
T ss_pred CCCCCEEccCccEEEEECCEEEE-----EcCHHHHHHH
Confidence 3455555 2234778899999 6776676555
No 82
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=30.21 E-value=54 Score=23.89 Aligned_cols=31 Identities=16% Similarity=0.302 Sum_probs=19.0
Q ss_pred ecCCCCccCCCCCceecCCeeeecccccCCCCCCC
Q psy327 100 CCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTP 134 (168)
Q Consensus 100 ~C~~C~~~l~~~~f~~~dg~~~C~~~C~~~~~~~~ 134 (168)
+|..|++.+....--+.+| |+. |..++|.-.
T Consensus 3 ~Ct~Cg~~f~dgs~eil~G---CP~-CGg~kF~yv 33 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSG---CPE-CGGNKFQYV 33 (131)
T ss_pred ccCcCCCCcCCCcHHHHcc---Ccc-cCCcceEEc
Confidence 7999999985444334555 552 555555433
No 83
>KOG4443|consensus
Probab=30.17 E-value=24 Score=32.40 Aligned_cols=20 Identities=30% Similarity=0.684 Sum_probs=14.1
Q ss_pred CceeeCCCCceecCCCCccCCC
Q psy327 89 GQHWHATDSCFCCATCSLSLLG 110 (168)
Q Consensus 89 ~~~~H~~~~CF~C~~C~~~l~~ 110 (168)
+..+-+ +||.|..|+..|.|
T Consensus 108 g~~~ck--k~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 108 GPWLCK--KCTRCRQCDSTLPG 127 (694)
T ss_pred cccccH--HHHhhhhccccccc
Confidence 344455 78888888888855
No 84
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=30.17 E-value=30 Score=24.07 Aligned_cols=33 Identities=9% Similarity=0.290 Sum_probs=24.1
Q ss_pred ccccccccccC-CCceEEECCeeccccchHhhhc
Q psy327 19 FTCSVCNELLV-DLIYFYRGDKLYCGRHHAETLK 51 (168)
Q Consensus 19 f~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~~~ 51 (168)
.+|..|+.++. ++.|....+.+..-.|+.+...
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~ 36 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKAS 36 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence 47999999994 4557565667788888876543
No 85
>PLN03086 PRLI-interacting factor K; Provisional
Probab=30.10 E-value=11 Score=34.03 Aligned_cols=78 Identities=18% Similarity=0.379 Sum_probs=37.8
Q ss_pred ccccccccccCCCceEEECCeeccccchHhhhccccc--cCcccccccCCccccCCcccccCCCCCCceeeCCceeeCCC
Q psy327 19 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCS--ACDEVRVQVGGHRTRDLNINYFSSLPAGQMSHEGQHWHATD 96 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~--~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v~~~~~~~H~~~ 96 (168)
-.|..|+..+....+.... .+|.. ....|. .|+..+..... ..+-.|..|++.+....+....+.+|
T Consensus 408 V~C~NC~~~i~l~~l~lHe--~~C~r-----~~V~Cp~~~Cg~v~~r~el-~~H~~C~~Cgk~f~~s~LekH~~~~H--- 476 (567)
T PLN03086 408 VECRNCKHYIPSRSIALHE--AYCSR-----HNVVCPHDGCGIVLRVEEA-KNHVHCEKCGQAFQQGEMEKHMKVFH--- 476 (567)
T ss_pred EECCCCCCccchhHHHHHH--hhCCC-----cceeCCcccccceeecccc-ccCccCCCCCCccchHHHHHHHHhcC---
Confidence 3566666655444333211 22322 123454 47776653211 11446777877664333333334445
Q ss_pred CceecCCCCccC
Q psy327 97 SCFCCATCSLSL 108 (168)
Q Consensus 97 ~CF~C~~C~~~l 108 (168)
.=+.|. |+..+
T Consensus 477 kpv~Cp-Cg~~~ 487 (567)
T PLN03086 477 EPLQCP-CGVVL 487 (567)
T ss_pred CCccCC-CCCCc
Confidence 346777 77655
No 86
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=30.00 E-value=27 Score=20.20 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=5.5
Q ss_pred eecCCCCccC
Q psy327 99 FCCATCSLSL 108 (168)
Q Consensus 99 F~C~~C~~~l 108 (168)
|+|..|+..+
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 4555555554
No 87
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=29.23 E-value=28 Score=16.46 Aligned_cols=12 Identities=25% Similarity=0.717 Sum_probs=8.6
Q ss_pred eecCCCCccCCC
Q psy327 99 FCCATCSLSLLG 110 (168)
Q Consensus 99 F~C~~C~~~l~~ 110 (168)
|.|..|++.+..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 678888877643
No 88
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.80 E-value=35 Score=30.32 Aligned_cols=39 Identities=23% Similarity=0.559 Sum_probs=24.9
Q ss_pred ccccccccccCCCceEEECCeeccccchHhh-hccccccCccc
Q psy327 19 FTCSVCNELLVDLIYFYRGDKLYCGRHHAET-LKPRCSACDEV 60 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~-~~~~C~~C~~~ 60 (168)
.+|..|+.+| .|...++.+.|..|-... +...|..|+..
T Consensus 223 ~~C~~C~~~l---~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSL---TYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCce---EEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 3556666655 345567788888885443 34677777764
No 89
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=28.73 E-value=1e+02 Score=25.05 Aligned_cols=21 Identities=24% Similarity=0.662 Sum_probs=16.4
Q ss_pred CCceeeCCCCceecCCCCccCCC
Q psy327 88 EGQHWHATDSCFCCATCSLSLLG 110 (168)
Q Consensus 88 ~~~~~H~~~~CF~C~~C~~~l~~ 110 (168)
.++.|-. .=|.|..|+..+.|
T Consensus 147 ~dkmwG~--aef~C~~C~h~F~G 167 (278)
T PF15135_consen 147 CDKMWGI--AEFHCPKCRHNFRG 167 (278)
T ss_pred cccccce--eeeecccccccchh
Confidence 4567766 67999999999864
No 90
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=27.81 E-value=57 Score=20.45 Aligned_cols=12 Identities=25% Similarity=0.747 Sum_probs=8.1
Q ss_pred ccccccCccccc
Q psy327 51 KPRCSACDEVRV 62 (168)
Q Consensus 51 ~~~C~~C~~~I~ 62 (168)
.+.|..|+..|.
T Consensus 9 ~~~CtSCg~~i~ 20 (61)
T COG2888 9 PPVCTSCGREIA 20 (61)
T ss_pred CceeccCCCEec
Confidence 356777777774
No 91
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=27.61 E-value=51 Score=27.53 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=9.4
Q ss_pred ceecCCCCccC
Q psy327 98 CFCCATCSLSL 108 (168)
Q Consensus 98 CF~C~~C~~~l 108 (168)
-|+|..|...|
T Consensus 77 ~~kC~~C~~~i 87 (324)
T PF04502_consen 77 YIKCPRCSNEI 87 (324)
T ss_pred EEEcCCCCCEE
Confidence 57899999888
No 92
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=27.11 E-value=54 Score=20.03 Aligned_cols=27 Identities=19% Similarity=0.391 Sum_probs=21.2
Q ss_pred cccccCcccccccCCccccCCcccccCCCCCCceeeCCceee
Q psy327 52 PRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMSHEGQHWH 93 (168)
Q Consensus 52 ~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~~~~v~~~~~~~H 93 (168)
..|.-|+..|.+-.|..| |...|+.++
T Consensus 4 ~~C~f~g~~I~PG~G~~~---------------Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMY---------------VRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEE---------------EecCCCEEE
Confidence 468888889988777775 777788887
No 93
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=26.08 E-value=30 Score=20.18 Aligned_cols=10 Identities=20% Similarity=0.650 Sum_probs=5.2
Q ss_pred ccccCcc-ccc
Q psy327 53 RCSACDE-VRV 62 (168)
Q Consensus 53 ~C~~C~~-~I~ 62 (168)
.|.+|+. ||.
T Consensus 2 ~CDgCg~~PI~ 12 (43)
T cd02342 2 QCDGCGVLPIT 12 (43)
T ss_pred CCCCCCCCccc
Confidence 3556663 454
No 94
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=25.89 E-value=60 Score=19.10 Aligned_cols=28 Identities=18% Similarity=0.332 Sum_probs=18.9
Q ss_pred cccccccccCCCceEEECCeeccccchHhh
Q psy327 20 TCSVCNELLVDLIYFYRGDKLYCGRHHAET 49 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~ 49 (168)
+|..|+++...+ ....|+..|.+|-.+.
T Consensus 1 ~CiiC~~~~~~G--I~I~~~fIC~~CE~~i 28 (46)
T PF10764_consen 1 KCIICGKEKEEG--IHIYGKFICSDCEKEI 28 (46)
T ss_pred CeEeCCCcCCCC--EEEECeEehHHHHHHh
Confidence 477788877653 5667777777775543
No 95
>smart00746 TRASH metallochaperone-like domain.
Probab=25.83 E-value=52 Score=16.33 Aligned_cols=8 Identities=13% Similarity=0.434 Sum_probs=4.0
Q ss_pred eeCCceee
Q psy327 86 SHEGQHWH 93 (168)
Q Consensus 86 ~~~~~~~H 93 (168)
...|+.+|
T Consensus 18 ~~~g~~~~ 25 (39)
T smart00746 18 VNDGKVFY 25 (39)
T ss_pred EECCEEEE
Confidence 34455555
No 96
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=25.13 E-value=49 Score=21.16 Aligned_cols=29 Identities=28% Similarity=0.741 Sum_probs=20.3
Q ss_pred ecCCCCccCC---CCCceecCCeee--ecccccC
Q psy327 100 CCATCSLSLL---GRPFLPRAGVIF--CSIACSK 128 (168)
Q Consensus 100 ~C~~C~~~l~---~~~f~~~dg~~~--C~~~C~~ 128 (168)
+|+-|+..|. |.-|+..||.++ |..-|.+
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k 38 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEK 38 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEEEEechhHHH
Confidence 6889999992 333556688876 7765654
No 97
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=24.26 E-value=63 Score=17.56 Aligned_cols=23 Identities=26% Similarity=0.222 Sum_probs=15.3
Q ss_pred cccccccccCCCceEEECCeeccccc
Q psy327 20 TCSVCNELLVDLIYFYRGDKLYCGRH 45 (168)
Q Consensus 20 ~C~~C~~~L~~~~~~~~~g~~yC~~c 45 (168)
+|..|+..+ -+...++..+|..|
T Consensus 5 ~C~~C~~~~---i~~~~~~~~~C~~C 27 (33)
T PF08792_consen 5 KCSKCGGNG---IVNKEDDYEVCIFC 27 (33)
T ss_pred EcCCCCCCe---EEEecCCeEEcccC
Confidence 466777655 34467777777776
No 98
>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=23.96 E-value=28 Score=19.05 Aligned_cols=10 Identities=20% Similarity=0.611 Sum_probs=5.9
Q ss_pred eecCCCCccC
Q psy327 99 FCCATCSLSL 108 (168)
Q Consensus 99 F~C~~C~~~l 108 (168)
++|..|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4666666554
No 99
>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=23.81 E-value=68 Score=17.72 Aligned_cols=22 Identities=18% Similarity=0.397 Sum_probs=14.6
Q ss_pred cCCCCCCCCCCccccccccccC
Q psy327 8 AGPNSCWHPGCFTCSVCNELLV 29 (168)
Q Consensus 8 ~a~~~~~H~~Cf~C~~C~~~L~ 29 (168)
...++.||-.=..|..||-.+.
T Consensus 11 ~p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 11 DPSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp STTSTTTT-TT--BTTCC-SCC
T ss_pred CCCCCcccCcCccCCCCCCCEE
Confidence 4568999999999999987763
No 100
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=23.56 E-value=46 Score=17.30 Aligned_cols=12 Identities=25% Similarity=0.825 Sum_probs=3.7
Q ss_pred ccccccccccCC
Q psy327 19 FTCSVCNELLVD 30 (168)
Q Consensus 19 f~C~~C~~~L~~ 30 (168)
|+|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 567778777755
No 101
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=23.14 E-value=53 Score=23.96 Aligned_cols=28 Identities=21% Similarity=0.275 Sum_probs=20.0
Q ss_pred hhccccccCcccccccCCccccCCcccccCCCC
Q psy327 49 TLKPRCSACDEVRVQVGGHRTRDLNINYFSSLP 81 (168)
Q Consensus 49 ~~~~~C~~C~~~I~~~~g~~~~~~C~~C~~~i~ 81 (168)
+.+.+|.+|+....+- +..|+.|+....
T Consensus 27 l~g~kC~~CG~v~~PP-----r~~Cp~C~~~~~ 54 (140)
T COG1545 27 LLGTKCKKCGRVYFPP-----RAYCPKCGSETE 54 (140)
T ss_pred EEEEEcCCCCeEEcCC-----cccCCCCCCCCc
Confidence 4578899998766542 457888888753
No 102
>KOG2893|consensus
Probab=22.95 E-value=31 Score=27.90 Aligned_cols=12 Identities=33% Similarity=0.733 Sum_probs=10.8
Q ss_pred CceecCCCCccC
Q psy327 97 SCFCCATCSLSL 108 (168)
Q Consensus 97 ~CF~C~~C~~~l 108 (168)
.+|+|..|++.|
T Consensus 33 khfkchichkkl 44 (341)
T KOG2893|consen 33 KHFKCHICHKKL 44 (341)
T ss_pred ccceeeeehhhh
Confidence 569999999998
No 103
>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=22.91 E-value=19 Score=18.80 Aligned_cols=6 Identities=33% Similarity=1.209 Sum_probs=2.3
Q ss_pred ecCCCC
Q psy327 100 CCATCS 105 (168)
Q Consensus 100 ~C~~C~ 105 (168)
-|..|.
T Consensus 23 ~C~rCq 28 (30)
T PF06827_consen 23 LCPRCQ 28 (30)
T ss_dssp E-TTTC
T ss_pred ECcCCc
Confidence 444443
No 104
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=22.58 E-value=29 Score=20.17 Aligned_cols=30 Identities=20% Similarity=0.489 Sum_probs=13.7
Q ss_pred cccccccc-ccCCCceE--EECCeeccccchHh
Q psy327 19 FTCSVCNE-LLVDLIYF--YRGDKLYCGRHHAE 48 (168)
Q Consensus 19 f~C~~C~~-~L~~~~~~--~~~g~~yC~~cy~~ 48 (168)
++|..|+. ++.+..|- .=.+--+|..||.+
T Consensus 5 ~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 5 YTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp CE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred eECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 46677776 55554432 12334456666654
No 105
>COG4393 Predicted membrane protein [Function unknown]
Probab=21.95 E-value=60 Score=27.59 Aligned_cols=32 Identities=9% Similarity=0.217 Sum_probs=25.1
Q ss_pred CCCceecCCeeeecccccCCCCCCC---CCCCCCCC
Q psy327 110 GRPFLPRAGVIFCSIACSKGEPPTP---SDSSGPGL 142 (168)
Q Consensus 110 ~~~f~~~dg~~~C~~~C~~~~~~~~---~~~~~~~~ 142 (168)
.++|+++++++.|.. |.-.++.+. ..+|++..
T Consensus 342 d~GYv~e~dqvICv~-C~VrmfipSIGk~GGCNPvP 376 (405)
T COG4393 342 DQGYVMEGDQVICVR-CDVRMFIPSIGKKGGCNPVP 376 (405)
T ss_pred ccceEeECCEEEEEE-ccEEEEcccCCCCCCCCCCc
Confidence 568999999999996 998877655 55777654
No 106
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=21.46 E-value=68 Score=24.94 Aligned_cols=31 Identities=23% Similarity=0.470 Sum_probs=23.2
Q ss_pred CCccccccccccCCCceEEECCeeccccchHh
Q psy327 17 GCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 48 (168)
Q Consensus 17 ~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~ 48 (168)
+-|.|.+|...+.+ .....=|..||..|..+
T Consensus 17 ~~~~CpICld~~~d-PVvT~CGH~FC~~CI~~ 47 (193)
T PLN03208 17 GDFDCNICLDQVRD-PVVTLCGHLFCWPCIHK 47 (193)
T ss_pred CccCCccCCCcCCC-cEEcCCCchhHHHHHHH
Confidence 46899999887754 34456788999999764
No 107
>PRK12495 hypothetical protein; Provisional
Probab=21.39 E-value=45 Score=26.52 Aligned_cols=24 Identities=13% Similarity=0.432 Sum_probs=15.3
Q ss_pred CCccccccccccCCCceEEECCeeccccc
Q psy327 17 GCFTCSVCNELLVDLIYFYRGDKLYCGRH 45 (168)
Q Consensus 17 ~Cf~C~~C~~~L~~~~~~~~~g~~yC~~c 45 (168)
.-+.|..|+.+|. ...|..+|..|
T Consensus 41 sa~hC~~CG~PIp-----a~pG~~~Cp~C 64 (226)
T PRK12495 41 TNAHCDECGDPIF-----RHDGQEFCPTC 64 (226)
T ss_pred chhhcccccCccc-----CCCCeeECCCC
Confidence 3456777888885 23666666665
No 108
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=21.32 E-value=51 Score=15.15 Aligned_cols=11 Identities=36% Similarity=0.836 Sum_probs=6.0
Q ss_pred eecCCCCccCC
Q psy327 99 FCCATCSLSLL 109 (168)
Q Consensus 99 F~C~~C~~~l~ 109 (168)
|.|..|+..+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 56777776653
No 109
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=21.28 E-value=89 Score=21.58 Aligned_cols=22 Identities=18% Similarity=0.493 Sum_probs=15.3
Q ss_pred eeeCCce--eeCCCCceecCCCCccC
Q psy327 85 MSHEGQH--WHATDSCFCCATCSLSL 108 (168)
Q Consensus 85 v~~~~~~--~H~~~~CF~C~~C~~~l 108 (168)
+...|.. |.. ..+.|..|+..+
T Consensus 18 ~~~~G~~~~v~~--~~~~C~~CGe~~ 41 (127)
T TIGR03830 18 YTYKGESITIGV--PGWYCPACGEEL 41 (127)
T ss_pred EEEcCEEEEEee--eeeECCCCCCEE
Confidence 4555554 444 789999998776
No 110
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.97 E-value=56 Score=21.39 Aligned_cols=45 Identities=18% Similarity=0.355 Sum_probs=24.5
Q ss_pred ecCCCCccCCCC---CceecCCeeeecccccCCCCCCCCCCCCCCCCCC
Q psy327 100 CCATCSLSLLGR---PFLPRAGVIFCSIACSKGEPPTPSDSSGPGLRPQ 145 (168)
Q Consensus 100 ~C~~C~~~l~~~---~f~~~dg~~~C~~~C~~~~~~~~~~~~~~~~~~~ 145 (168)
.|.-|++-|... .-+-.=.--||. +|........|-.||..+...
T Consensus 7 nCECCDrDLpp~s~dA~ICtfEcTFCa-dCae~~l~g~CPnCGGelv~R 54 (84)
T COG3813 7 NCECCDRDLPPDSTDARICTFECTFCA-DCAENRLHGLCPNCGGELVAR 54 (84)
T ss_pred CCcccCCCCCCCCCceeEEEEeeehhH-hHHHHhhcCcCCCCCchhhcC
Confidence 355566666221 111122344666 477766677777777776543
No 111
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.85 E-value=79 Score=22.14 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=14.3
Q ss_pred ecCCCCccCCCCCceecCCeee-ecccccCCCC
Q psy327 100 CCATCSLSLLGRPFLPRAGVIF-CSIACSKGEP 131 (168)
Q Consensus 100 ~C~~C~~~l~~~~f~~~dg~~~-C~~~C~~~~~ 131 (168)
.|..|+ .+||-++..|. |.. |...+.
T Consensus 11 ~Cp~CG-----~kFYDLnk~PivCP~-CG~~~~ 37 (108)
T PF09538_consen 11 TCPSCG-----AKFYDLNKDPIVCPK-CGTEFP 37 (108)
T ss_pred cCCCCc-----chhccCCCCCccCCC-CCCccC
Confidence 455554 45776655555 775 554443
No 112
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.82 E-value=57 Score=30.52 Aligned_cols=39 Identities=18% Similarity=0.437 Sum_probs=28.7
Q ss_pred ccccccccccCCCceEEECCeeccccchHh-hhccccccCccc
Q psy327 19 FTCSVCNELLVDLIYFYRGDKLYCGRHHAE-TLKPRCSACDEV 60 (168)
Q Consensus 19 f~C~~C~~~L~~~~~~~~~g~~yC~~cy~~-~~~~~C~~C~~~ 60 (168)
++|..|+.+| .|....+.+.|..|-.+ .....|..|+..
T Consensus 445 ~~Cp~Cd~~l---t~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPL---TLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcce---EEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 6788888877 45566788889988665 445678888876
No 113
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=20.55 E-value=10 Score=26.14 Aligned_cols=35 Identities=14% Similarity=0.321 Sum_probs=26.0
Q ss_pred eCCceeeCCCCceecCCCCccCCCCCceecCCeeeec
Q psy327 87 HEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123 (168)
Q Consensus 87 ~~~~~~H~~~~CF~C~~C~~~l~~~~f~~~dg~~~C~ 123 (168)
..-..+++ .+..|..|.+.|+-..|.+...=|||.
T Consensus 53 ~~~~~~~~--~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 53 WGLQEFNP--KAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred CChhhcCC--ccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 33466787 889999999999877777766656655
No 114
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=20.40 E-value=72 Score=17.45 Aligned_cols=28 Identities=14% Similarity=0.109 Sum_probs=14.5
Q ss_pred ccccccccCCCceEEECCee-ccccchHh
Q psy327 21 CSVCNELLVDLIYFYRGDKL-YCGRHHAE 48 (168)
Q Consensus 21 C~~C~~~L~~~~~~~~~g~~-yC~~cy~~ 48 (168)
|..|+..-...-....+|.. +|..|+..
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHH
Confidence 55666655443333456776 89988653
No 115
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=20.15 E-value=37 Score=20.52 Aligned_cols=12 Identities=25% Similarity=0.700 Sum_probs=4.9
Q ss_pred CceecCCCCccC
Q psy327 97 SCFCCATCSLSL 108 (168)
Q Consensus 97 ~CF~C~~C~~~l 108 (168)
.-|.|..|+..+
T Consensus 20 ~~y~C~~C~~~F 31 (51)
T PF07975_consen 20 SRYRCPKCKNHF 31 (51)
T ss_dssp EEE--TTTT--B
T ss_pred CeEECCCCCCcc
Confidence 456777776443
No 116
>KOG3002|consensus
Probab=20.08 E-value=76 Score=26.37 Aligned_cols=45 Identities=20% Similarity=0.443 Sum_probs=37.1
Q ss_pred CCccccccccccCCCceEEECCeeccccchHhhhccccccCccccc
Q psy327 17 GCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEVRV 62 (168)
Q Consensus 17 ~Cf~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~ 62 (168)
+=|.|..|-..|....|.=.+|.+.|..|-.++ ..+|..|..+|.
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~-~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKV-SNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhhhh-cccCCccccccc
Confidence 346788898999777777789999999998655 578999999987
Done!