Query 031772
Match_columns 153
No_of_seqs 166 out of 787
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 05:08:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031772.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031772hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3339 Uncharacterized conser 99.7 3.2E-16 7E-21 114.3 10.1 87 40-140 6-92 (116)
2 KOG2164 Predicted E3 ubiquitin 99.6 2.6E-16 5.7E-21 137.6 5.3 145 1-149 214-363 (513)
3 PF06803 DUF1232: Protein of u 99.5 2.6E-14 5.6E-19 86.2 2.9 39 95-134 2-40 (40)
4 KOG4604 Uncharacterized conser 93.7 0.048 1E-06 38.2 2.0 88 26-118 2-89 (91)
5 PF13920 zf-C3HC4_3: Zinc fing 86.7 0.3 6.5E-06 29.8 0.8 14 11-24 36-49 (50)
6 PF09237 GAGA: GAGA factor; I 84.4 0.37 8E-06 30.6 0.4 22 2-23 14-35 (54)
7 TIGR02652 conserved hypothetic 80.4 0.61 1.3E-05 35.5 0.4 13 12-24 9-21 (163)
8 PF09654 DUF2396: Protein of u 79.9 0.66 1.4E-05 35.3 0.4 13 12-24 6-18 (161)
9 PF04423 Rad50_zn_hook: Rad50 69.9 1.4 3.1E-05 27.4 -0.0 10 14-23 22-31 (54)
10 KOG4172 Predicted E3 ubiquitin 69.4 1.6 3.4E-05 28.2 0.1 12 13-24 44-55 (62)
11 PLN03208 E3 ubiquitin-protein 59.4 5 0.00011 32.0 1.2 18 11-28 67-86 (193)
12 PF14255 Cys_rich_CPXG: Cystei 56.3 5 0.00011 25.3 0.6 14 13-26 1-14 (52)
13 KOG1039 Predicted E3 ubiquitin 56.2 8.1 0.00018 33.4 2.1 20 12-31 210-230 (344)
14 PF12907 zf-met2: Zinc-binding 56.1 3.4 7.3E-05 24.7 -0.2 14 13-26 2-15 (40)
15 PF11793 FANCL_C: FANCL C-term 53.4 4.4 9.5E-05 26.7 -0.0 12 13-24 56-67 (70)
16 PF13639 zf-RING_2: Ring finge 52.1 5.2 0.00011 23.4 0.2 6 14-19 39-44 (44)
17 PF03716 WCCH: WCCH motif ; I 51.6 7.6 0.00016 20.8 0.7 12 11-22 4-15 (25)
18 KOG1785 Tyrosine kinase negati 51.3 7.4 0.00016 34.6 1.0 21 2-24 397-417 (563)
19 PF14634 zf-RING_5: zinc-RING 50.2 8 0.00017 22.8 0.8 10 11-20 35-44 (44)
20 smart00734 ZnF_Rad18 Rad18-lik 49.5 7.6 0.00017 20.8 0.6 10 13-22 2-11 (26)
21 cd00162 RING RING-finger (Real 48.4 9.2 0.0002 21.2 0.9 12 11-22 34-45 (45)
22 KOG0824 Predicted E3 ubiquitin 48.0 8.3 0.00018 32.9 0.8 18 7-24 37-54 (324)
23 PF10571 UPF0547: Uncharacteri 47.6 8.1 0.00018 20.8 0.5 11 14-24 2-12 (26)
24 PF11672 DUF3268: Protein of u 44.8 10 0.00022 27.2 0.7 14 11-24 1-14 (102)
25 COG4589 Predicted CDP-diglycer 44.4 45 0.00098 28.0 4.6 36 97-132 221-260 (303)
26 PF04564 U-box: U-box domain; 44.1 22 0.00048 23.2 2.3 31 11-53 38-70 (73)
27 KOG0748 Predicted membrane pro 43.9 86 0.0019 26.2 6.3 51 94-150 216-275 (286)
28 PF07800 DUF1644: Protein of u 43.3 9.5 0.00021 29.5 0.5 16 11-26 79-94 (162)
29 PF13913 zf-C2HC_2: zinc-finge 40.4 13 0.00029 19.6 0.6 11 13-23 3-13 (25)
30 PRK04949 putative sulfate tran 40.1 2.1E+02 0.0045 23.4 10.3 42 37-81 99-141 (251)
31 PRK01343 zinc-binding protein; 40.0 18 0.00039 23.3 1.3 15 9-23 6-20 (57)
32 PF05605 zf-Di19: Drought indu 39.8 17 0.00036 22.4 1.1 16 6-21 25-40 (54)
33 PRK00418 DNA gyrase inhibitor; 39.7 13 0.00029 24.3 0.7 13 11-23 5-17 (62)
34 PF07787 DUF1625: Protein of u 38.5 45 0.00098 26.9 3.7 36 88-124 182-217 (248)
35 PF10122 Mu-like_Com: Mu-like 38.0 11 0.00024 23.7 0.1 15 11-26 23-37 (51)
36 PF10601 zf-LITAF-like: LITAF- 36.7 14 0.0003 24.2 0.4 19 8-26 3-21 (73)
37 TIGR00570 cdk7 CDK-activating 36.4 55 0.0012 28.0 4.0 66 11-78 42-110 (309)
38 PF13451 zf-trcl: Probable zin 36.1 11 0.00024 23.5 -0.2 19 3-21 23-42 (49)
39 PF03884 DUF329: Domain of unk 35.7 11 0.00023 24.3 -0.3 12 13-24 3-14 (57)
40 KOG1583 UDP-N-acetylglucosamin 35.6 56 0.0012 27.9 3.9 26 128-153 168-193 (330)
41 COG4357 Zinc finger domain con 35.1 16 0.00035 26.1 0.5 13 12-24 80-92 (105)
42 PF03604 DNA_RNApol_7kD: DNA d 35.0 22 0.00047 20.1 1.0 14 9-22 14-27 (32)
43 COG0343 Tgt Queuine/archaeosin 35.0 15 0.00033 32.0 0.5 19 11-29 297-319 (372)
44 TIGR02605 CxxC_CxxC_SSSS putat 34.7 25 0.00054 21.2 1.3 24 3-26 17-41 (52)
45 PRK10877 protein disulfide iso 34.5 12 0.00027 30.0 -0.2 10 12-21 116-125 (232)
46 PRK02975 putative common antig 34.2 3.4E+02 0.0073 24.2 9.5 88 43-147 138-225 (450)
47 PF15176 LRR19-TM: Leucine-ric 33.8 7.2 0.00016 28.0 -1.4 13 12-24 37-49 (102)
48 PRK11657 dsbG disulfide isomer 33.7 14 0.0003 30.1 -0.0 9 13-21 127-135 (251)
49 PF10041 DUF2277: Uncharacteri 33.5 54 0.0012 22.4 2.8 35 17-58 1-35 (78)
50 smart00659 RPOLCX RNA polymera 33.5 16 0.00036 22.0 0.3 15 9-23 16-30 (44)
51 PF15227 zf-C3HC4_4: zinc fing 32.2 22 0.00047 20.9 0.7 16 2-18 27-42 (42)
52 PF11023 DUF2614: Protein of u 32.0 19 0.0004 26.4 0.4 13 12-24 85-97 (114)
53 PRK10824 glutaredoxin-4; Provi 31.1 17 0.00037 26.4 0.1 17 11-27 26-42 (115)
54 PF02891 zf-MIZ: MIZ/SP-RING z 30.6 19 0.00041 22.1 0.3 9 13-21 42-50 (50)
55 smart00504 Ubox Modified RING 30.2 23 0.00049 21.8 0.6 12 13-24 36-47 (63)
56 PF09986 DUF2225: Uncharacteri 29.4 22 0.00047 28.4 0.5 14 11-24 4-17 (214)
57 COG1996 RPC10 DNA-directed RNA 28.9 23 0.0005 22.1 0.4 15 10-24 22-36 (49)
58 PRK00398 rpoP DNA-directed RNA 28.6 21 0.00045 21.3 0.2 13 12-24 21-33 (46)
59 PF13465 zf-H2C2_2: Zinc-finge 27.6 16 0.00036 19.1 -0.4 13 11-23 13-25 (26)
60 PTZ00062 glutaredoxin; Provisi 27.5 21 0.00045 28.5 0.0 15 13-27 126-140 (204)
61 PF04134 DUF393: Protein of un 27.5 16 0.00035 25.3 -0.5 16 14-29 6-21 (114)
62 cd03020 DsbA_DsbC_DsbG DsbA fa 27.3 23 0.00051 27.1 0.3 15 12-26 86-100 (197)
63 COG3305 Predicted membrane pro 27.0 1.7E+02 0.0036 22.2 4.7 26 87-114 88-113 (152)
64 COG5243 HRD1 HRD ubiquitin lig 27.0 24 0.00053 31.2 0.4 12 12-23 334-345 (491)
65 cd02066 GRX_family Glutaredoxi 25.7 25 0.00054 21.2 0.2 16 13-28 8-23 (72)
66 PRK05208 hypothetical protein; 25.7 84 0.0018 24.4 3.1 33 116-148 56-88 (168)
67 PF10276 zf-CHCC: Zinc-finger 25.6 16 0.00034 21.8 -0.7 12 11-22 28-39 (40)
68 TIGR02189 GlrX-like_plant Glut 25.4 42 0.00092 23.2 1.3 17 10-26 13-29 (99)
69 PRK00464 nrdR transcriptional 24.9 30 0.00064 26.5 0.5 10 15-24 31-40 (154)
70 PF14348 DUF4400: Domain of un 24.9 2.6E+02 0.0057 21.6 5.9 22 97-118 156-178 (198)
71 TIGR02194 GlrX_NrdH Glutaredox 24.9 18 0.00039 23.1 -0.6 16 12-27 6-21 (72)
72 PRK07668 hypothetical protein; 24.8 4E+02 0.0087 22.0 7.8 46 97-145 79-131 (254)
73 KOG1752 Glutaredoxin and relat 24.6 19 0.00042 25.7 -0.5 46 10-58 19-66 (104)
74 PRK01008 queuine tRNA-ribosylt 24.3 83 0.0018 27.4 3.2 14 10-23 316-329 (372)
75 cd03027 GRX_DEP Glutaredoxin ( 24.2 34 0.00074 21.7 0.6 16 12-27 8-23 (73)
76 TIGR00365 monothiol glutaredox 24.1 28 0.0006 24.0 0.2 17 11-27 23-39 (97)
77 COG5194 APC11 Component of SCF 23.8 32 0.00069 23.8 0.4 13 12-24 70-82 (88)
78 PRK14351 ligA NAD-dependent DN 23.7 64 0.0014 30.4 2.5 59 10-69 6-64 (689)
79 PF06750 DiS_P_DiS: Bacterial 23.7 28 0.0006 24.2 0.1 13 11-23 32-44 (92)
80 KOG4628 Predicted E3 ubiquitin 23.5 37 0.00079 29.5 0.8 21 8-28 261-283 (348)
81 TIGR00432 arcsn_tRNA_tgt tRNA- 23.4 33 0.00072 31.4 0.6 10 11-20 171-180 (540)
82 TIGR01206 lysW lysine biosynth 23.3 35 0.00076 21.6 0.5 11 14-24 4-14 (54)
83 PRK10638 glutaredoxin 3; Provi 23.2 34 0.00074 22.4 0.5 17 11-27 8-24 (83)
84 PRK13533 7-cyano-7-deazaguanin 22.7 35 0.00075 30.8 0.5 10 11-20 273-282 (487)
85 PF08209 Sgf11: Sgf11 (transcr 22.7 25 0.00053 20.1 -0.3 13 11-23 3-15 (33)
86 TIGR02183 GRXA Glutaredoxin, G 22.0 27 0.00059 23.3 -0.2 16 12-27 7-22 (86)
87 COG2835 Uncharacterized conser 22.0 36 0.00077 22.2 0.4 14 10-23 6-19 (60)
88 smart00834 CxxC_CXXC_SSSS Puta 21.6 62 0.0013 18.2 1.3 13 11-23 25-37 (41)
89 PF04186 FxsA: FxsA cytoplasmi 21.4 3.2E+02 0.007 19.7 8.1 27 123-149 84-110 (119)
90 TIGR00645 HI0507 conserved hyp 21.4 89 0.0019 24.3 2.5 33 115-147 51-83 (167)
91 PHA03050 glutaredoxin; Provisi 21.3 25 0.00055 24.9 -0.5 15 11-25 19-33 (108)
92 cd01283 cytidine_deaminase Cyt 20.8 28 0.00061 24.4 -0.4 17 13-29 78-94 (112)
93 COG4338 Uncharacterized protei 20.8 31 0.00068 21.6 -0.1 13 11-23 11-23 (54)
94 PRK06386 replication factor A; 20.7 39 0.00084 29.4 0.4 17 13-29 237-254 (358)
95 PF09723 Zn-ribbon_8: Zinc rib 20.7 54 0.0012 19.2 0.9 16 10-25 24-40 (42)
96 PRK09783 copper/silver efflux 20.7 53 0.0012 28.5 1.3 19 1-19 42-65 (409)
97 PRK10144 formate-dependent nit 20.5 1.2E+02 0.0026 22.5 3.0 30 11-49 39-68 (126)
98 PRK00112 tgt queuine tRNA-ribo 20.5 57 0.0012 28.2 1.4 11 10-20 301-311 (366)
99 PF13098 Thioredoxin_2: Thiore 20.4 25 0.00054 23.8 -0.7 14 12-25 14-27 (112)
100 PF13453 zf-TFIIB: Transcripti 20.2 44 0.00095 19.4 0.5 10 14-23 1-10 (41)
101 COG2260 Predicted Zn-ribbon RN 20.0 1E+02 0.0022 20.0 2.2 19 13-31 18-36 (59)
No 1
>COG3339 Uncharacterized conserved protein [Function unknown]
Probab=99.68 E-value=3.2e-16 Score=114.28 Aligned_cols=87 Identities=23% Similarity=0.331 Sum_probs=67.7
Q ss_pred HHHHHHHHHHHHHHhCCCCCCchhHHHHhhHHHHHHHHHHHHcCCCCChhHHHHHHHHHHHHHHHHHhhccCCcCCccch
Q 031772 40 VGDILQKVESYNRIFGGPTTANGLFQRIQDLPFLLRRLVRELVDPHRSLPLVIRARVYIAMIFSAVYIFSPIDIIPEALL 119 (153)
Q Consensus 40 ~~~v~~~i~~YNr~fs~~~~~~~~~~~l~~~p~l~~~l~~~~~~~~~~~~~~~~~r~~~~i~~al~Y~isP~D~IPd~i~ 119 (153)
+....+..++||+.+ +.+..++...-.++.. +....++++ +++.++++.++++|++||+|+|||++
T Consensus 6 ~~~~~~~~~~~~~~~------rr~~~~~~~~~~~l~~-~~~~~~~~~------p~~~~l~i~aal~Y~V~PiDiIPD~l- 71 (116)
T COG3339 6 RDREGEVLERFRKKY------RRAKRYIPFLFDLLAA-WYAARDPET------PKYAKLIILAALGYFVSPIDIIPDFL- 71 (116)
T ss_pred HHHHHHHHHHHHHHH------HHHHHHhhHHHHHHHH-HHHhhcccc------hHHHHHHHHHHHHHHHchhhhchhhh-
Confidence 556667788888877 7777777644444333 333445543 36778899999999999999999986
Q ss_pred hhhhhhHHHHHHHHHHHHHHH
Q 031772 120 GIVGLLDDLLIALLCFLHVAA 140 (153)
Q Consensus 120 g~lG~lDD~~v~~~~l~~v~~ 140 (153)
|++|++||++|+.+++..+++
T Consensus 72 p~iG~iDDi~V~~~~v~~i~~ 92 (116)
T COG3339 72 PVIGFIDDIAVLTLAVTAISK 92 (116)
T ss_pred hccchHHHHHHHHHHHHHHHH
Confidence 889999999999999999888
No 2
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.63 E-value=2.6e-16 Score=137.63 Aligned_cols=145 Identities=23% Similarity=0.402 Sum_probs=123.9
Q ss_pred CcccccCCCCCCCCCCcccccccc--cccCCCcccccCChHHHHHHHHHH---HHHHHhCCCCCCchhHHHHhhHHHHHH
Q 031772 1 MLVWDHGSTLQACRCPLCRRRITL--LIPNDDSLRQRHDPAVGDILQKVE---SYNRIFGGPTTANGLFQRIQDLPFLLR 75 (153)
Q Consensus 1 ~~yW~~~~~~~~~~CP~CR~~i~~--L~p~~~~~~~~~d~~~~~v~~~i~---~YNr~fs~~~~~~~~~~~l~~~p~l~~ 75 (153)
+|||++|++.++|+||+||+.|++ |.|+.+... +..+. .+...+-+ .||++|++.++ +..-+.+.++|.+++
T Consensus 214 Lqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~e~~-qkke~-l~~~~~~ng~~~~~r~F~~d~~-r~~p~fl~dl~~~a~ 290 (513)
T KOG2164|consen 214 LQYWNYSAIKGPCSCPICRSTITLKDLLPVFIEDD-QKKEE-LKLHQDPNGIPDYNRRFSGDPA-RFVPDFLMDLPTYAR 290 (513)
T ss_pred HHHHhhhcccCCccCCchhhhccccceeeeeeccc-cccHH-HHHHhcccCCCccccceecCcc-cccHHHHHhHHHHHH
Confidence 589999999999999999999999 999987743 22233 34444444 89999999985 889999999999999
Q ss_pred HHHHHHcCCCCChhHHHHHHHHHHHHHHHHHhhccCCcCCccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 031772 76 RLVRELVDPHRSLPLVIRARVYIAMIFSAVYIFSPIDIIPEALLGIVGLLDDLLIALLCFLHVAALYRAVLYNR 149 (153)
Q Consensus 76 ~l~~~~~~~~~~~~~~~~~r~~~~i~~al~Y~isP~D~IPd~i~g~lG~lDD~~v~~~~l~~v~~~yr~~~~~r 149 (153)
.+++.++... .+.++...++.+..++..+|+..|.+.+|+.+.|.+|++||..+-..++...+.+++++.+.|
T Consensus 291 ~~i~~~~~~~-~l~i~~~~~i~~v~i~~~~~~~~~~~~~~q~~~~~is~lde~~~~~l~ls~~s~~dne~n~s~ 363 (513)
T KOG2164|consen 291 INIRNMFNNH-ILTIVDQVCIAAVFICQYLSFLLPRRMVPQAIKGRISFLDECTNDQLILSEMSRIDNEYNASR 363 (513)
T ss_pred HHHHHhhccc-ceeehhhHhHHHHHHHHHhcccchhhhcchhhcCccCchhhhcchhhhhhhhhhhhhhhhhhh
Confidence 9999977653 577777788888999999999999999999999999999999999999999999999776654
No 3
>PF06803 DUF1232: Protein of unknown function (DUF1232); InterPro: IPR010652 This family represents a conserved region of approximately 60 residues within a number of hypothetical bacterial and archaeal proteins of unknown function.
Probab=99.47 E-value=2.6e-14 Score=86.24 Aligned_cols=39 Identities=28% Similarity=0.651 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHhhccCCcCCccchhhhhhhHHHHHHHHH
Q 031772 95 RVYIAMIFSAVYIFSPIDIIPEALLGIVGLLDDLLIALLC 134 (153)
Q Consensus 95 r~~~~i~~al~Y~isP~D~IPd~i~g~lG~lDD~~v~~~~ 134 (153)
|.++.++++++|++||+|+|||++ |++|++||++++.++
T Consensus 2 ~~~~~~~~al~Y~isP~D~iPD~~-p~~G~lDD~~v~~~v 40 (40)
T PF06803_consen 2 KAKLLILAALAYFISPIDLIPDFI-PVIGYLDDAAVLAFV 40 (40)
T ss_pred hHHHHHHHHHHHHhchhhhCCCcc-ccccHHHHHHHHHhC
Confidence 556789999999999999999975 999999999998763
No 4
>KOG4604 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.65 E-value=0.048 Score=38.23 Aligned_cols=88 Identities=22% Similarity=0.219 Sum_probs=58.0
Q ss_pred ccCCCcccccCChHHHHHHHHHHHHHHHhCCCCCCchhHHHHhhHHHHHHHHHHHHcCCCCChhHHHHHHHHHHHHHHHH
Q 031772 26 IPNDDSLRQRHDPAVGDILQKVESYNRIFGGPTTANGLFQRIQDLPFLLRRLVRELVDPHRSLPLVIRARVYIAMIFSAV 105 (153)
Q Consensus 26 ~p~~~~~~~~~d~~~~~v~~~i~~YNr~fs~~~~~~~~~~~l~~~p~l~~~l~~~~~~~~~~~~~~~~~r~~~~i~~al~ 105 (153)
.|+.....++.+++..+..-|..-||+.+.+.. ...+.-+-.+|++.++.+=...+. +..+-... .-.-......
T Consensus 2 ~p~~sa~~~~~~e~~~~~~~d~clad~l~kg~s--g~~ig~v~s~~ffr~~~wpiw~gt--gvglGvay-~~cq~~l~a~ 76 (91)
T KOG4604|consen 2 HPSHSAIRSRNSESELGRKWDRCLADSLVKGGS--GLGIGIVVSLLFFRRREWPIWLGT--GVGLGVAY-SNCQARLNAV 76 (91)
T ss_pred CccccccccCCcHhhhhhhhhHHHHHHHhccCc--ceeeehhhhhhhhcceeeeeecCc--ccccchhh-HHHHHHhccc
Confidence 355545556677788888889999999999987 566666666777766654333322 11111111 1134556778
Q ss_pred HhhccCCcCCccc
Q 031772 106 YIFSPIDIIPEAL 118 (153)
Q Consensus 106 Y~isP~D~IPd~i 118 (153)
|+++|+|++|+..
T Consensus 77 y~i~~~~~~~~~~ 89 (91)
T KOG4604|consen 77 YIIHGIDIIPEGV 89 (91)
T ss_pred eeecCCCCCcccc
Confidence 9999999999975
No 5
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=86.74 E-value=0.3 Score=29.81 Aligned_cols=14 Identities=36% Similarity=0.987 Sum_probs=10.9
Q ss_pred CCCCCCcccccccc
Q 031772 11 QACRCPLCRRRITL 24 (153)
Q Consensus 11 ~~~~CP~CR~~i~~ 24 (153)
+.-+||+||++|+.
T Consensus 36 ~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 36 RKKKCPICRQPIES 49 (50)
T ss_dssp TTSBBTTTTBB-SE
T ss_pred cCCCCCcCChhhcC
Confidence 56799999999873
No 6
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=84.39 E-value=0.37 Score=30.57 Aligned_cols=22 Identities=23% Similarity=0.454 Sum_probs=12.7
Q ss_pred cccccCCCCCCCCCCccccccc
Q 031772 2 LVWDHGSTLQACRCPLCRRRIT 23 (153)
Q Consensus 2 ~yW~~~~~~~~~~CP~CR~~i~ 23 (153)
+-|.++....|-.||.|...+.
T Consensus 14 ~~k~~~~S~~PatCP~C~a~~~ 35 (54)
T PF09237_consen 14 KPKSKSQSEQPATCPICGAVIR 35 (54)
T ss_dssp --CCCCTTS--EE-TTT--EES
T ss_pred HHHHhhccCCCCCCCcchhhcc
Confidence 4588888889999999997764
No 7
>TIGR02652 conserved hypothetical protein TIGR02652, cyanobacterial. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end.
Probab=80.44 E-value=0.61 Score=35.50 Aligned_cols=13 Identities=46% Similarity=1.068 Sum_probs=11.3
Q ss_pred CCCCCcccccccc
Q 031772 12 ACRCPLCRRRITL 24 (153)
Q Consensus 12 ~~~CP~CR~~i~~ 24 (153)
-+.||.|||+|.-
T Consensus 9 ei~CPhCRQ~ipA 21 (163)
T TIGR02652 9 EIRCPHCRQNIPA 21 (163)
T ss_pred cCcCchhhcccch
Confidence 4799999999974
No 8
>PF09654 DUF2396: Protein of unknown function (DUF2396); InterPro: IPR013472 These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N terminus.
Probab=79.94 E-value=0.66 Score=35.28 Aligned_cols=13 Identities=38% Similarity=0.974 Sum_probs=11.2
Q ss_pred CCCCCcccccccc
Q 031772 12 ACRCPLCRRRITL 24 (153)
Q Consensus 12 ~~~CP~CR~~i~~ 24 (153)
-+.||.|||+|.-
T Consensus 6 ei~CPhCRq~ipA 18 (161)
T PF09654_consen 6 EIQCPHCRQTIPA 18 (161)
T ss_pred cCcCchhhcccch
Confidence 4789999999974
No 9
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=69.89 E-value=1.4 Score=27.40 Aligned_cols=10 Identities=50% Similarity=1.265 Sum_probs=5.3
Q ss_pred CCCccccccc
Q 031772 14 RCPLCRRRIT 23 (153)
Q Consensus 14 ~CP~CR~~i~ 23 (153)
.||+|.++++
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 8999998865
No 10
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.42 E-value=1.6 Score=28.18 Aligned_cols=12 Identities=42% Similarity=0.902 Sum_probs=9.5
Q ss_pred CCCCcccccccc
Q 031772 13 CRCPLCRRRITL 24 (153)
Q Consensus 13 ~~CP~CR~~i~~ 24 (153)
-.||+||.+|.-
T Consensus 44 g~CPiCRapi~d 55 (62)
T KOG4172|consen 44 GCCPICRAPIKD 55 (62)
T ss_pred CcCcchhhHHHH
Confidence 469999998753
No 11
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=59.36 E-value=5 Score=31.97 Aligned_cols=18 Identities=28% Similarity=0.923 Sum_probs=14.4
Q ss_pred CCCCCCcccccccc--cccC
Q 031772 11 QACRCPLCRRRITL--LIPN 28 (153)
Q Consensus 11 ~~~~CP~CR~~i~~--L~p~ 28 (153)
++.+||+||.+|+. |+|.
T Consensus 67 ~~~~CPvCR~~Is~~~LvPi 86 (193)
T PLN03208 67 EPPKCPVCKSDVSEATLVPI 86 (193)
T ss_pred CCCcCCCCCCcCChhcEEEe
Confidence 46799999999985 5654
No 12
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=56.29 E-value=5 Score=25.27 Aligned_cols=14 Identities=43% Similarity=1.051 Sum_probs=12.3
Q ss_pred CCCCcccccccccc
Q 031772 13 CRCPLCRRRITLLI 26 (153)
Q Consensus 13 ~~CP~CR~~i~~L~ 26 (153)
+.||+|-.++.+++
T Consensus 1 i~CPyCge~~~~~i 14 (52)
T PF14255_consen 1 IQCPYCGEPIEILI 14 (52)
T ss_pred CCCCCCCCeeEEEE
Confidence 47999999999977
No 13
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.21 E-value=8.1 Score=33.36 Aligned_cols=20 Identities=25% Similarity=0.601 Sum_probs=16.6
Q ss_pred CCCCCcccccccccccCC-Cc
Q 031772 12 ACRCPLCRRRITLLIPND-DS 31 (153)
Q Consensus 12 ~~~CP~CR~~i~~L~p~~-~~ 31 (153)
--+||.||.+.+...|+. |.
T Consensus 210 sksCP~CRv~s~~v~pS~~Wv 230 (344)
T KOG1039|consen 210 SKSCPFCRVPSSFVNPSSFWV 230 (344)
T ss_pred ccCCCcccCccccccccceee
Confidence 468999999999999984 44
No 14
>PF12907 zf-met2: Zinc-binding
Probab=56.07 E-value=3.4 Score=24.74 Aligned_cols=14 Identities=21% Similarity=0.586 Sum_probs=10.8
Q ss_pred CCCCcccccccccc
Q 031772 13 CRCPLCRRRITLLI 26 (153)
Q Consensus 13 ~~CP~CR~~i~~L~ 26 (153)
+.|++|||++-...
T Consensus 2 i~C~iC~qtF~~t~ 15 (40)
T PF12907_consen 2 IICKICRQTFMQTT 15 (40)
T ss_pred cCcHHhhHHHHhcC
Confidence 68999999876543
No 15
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=53.38 E-value=4.4 Score=26.73 Aligned_cols=12 Identities=33% Similarity=0.902 Sum_probs=8.1
Q ss_pred CCCCcccccccc
Q 031772 13 CRCPLCRRRITL 24 (153)
Q Consensus 13 ~~CP~CR~~i~~ 24 (153)
-+||+|+.+|+.
T Consensus 56 G~CP~C~~~i~~ 67 (70)
T PF11793_consen 56 GECPYCSSPISW 67 (70)
T ss_dssp EE-TTT-SEEEG
T ss_pred cCCcCCCCeeeE
Confidence 379999999874
No 16
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=52.10 E-value=5.2 Score=23.40 Aligned_cols=6 Identities=67% Similarity=2.045 Sum_probs=4.6
Q ss_pred CCCccc
Q 031772 14 RCPLCR 19 (153)
Q Consensus 14 ~CP~CR 19 (153)
+||+||
T Consensus 39 ~CP~CR 44 (44)
T PF13639_consen 39 SCPVCR 44 (44)
T ss_dssp B-TTTH
T ss_pred cCCccC
Confidence 999998
No 17
>PF03716 WCCH: WCCH motif ; InterPro: IPR005159 The WCCH motif is found in a retrotransposons and Gemini viruses. A specific function has not been associated to this motif [].
Probab=51.55 E-value=7.6 Score=20.81 Aligned_cols=12 Identities=50% Similarity=1.201 Sum_probs=10.1
Q ss_pred CCCCCCcccccc
Q 031772 11 QACRCPLCRRRI 22 (153)
Q Consensus 11 ~~~~CP~CR~~i 22 (153)
.+|.||.|.+--
T Consensus 4 ~pC~cphCprHk 15 (25)
T PF03716_consen 4 QPCCCPHCPRHK 15 (25)
T ss_pred cccCCCCCcccc
Confidence 799999998763
No 18
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=51.35 E-value=7.4 Score=34.61 Aligned_cols=21 Identities=29% Similarity=0.767 Sum_probs=16.2
Q ss_pred cccccCCCCCCCCCCcccccccc
Q 031772 2 LVWDHGSTLQACRCPLCRRRITL 24 (153)
Q Consensus 2 ~yW~~~~~~~~~~CP~CR~~i~~ 24 (153)
.-|++|.- --.||.||+.|.=
T Consensus 397 a~WQ~sd~--gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 397 AAWQDSDE--GQTCPFCRCEIKG 417 (563)
T ss_pred HhhcccCC--CCCCCceeeEecc
Confidence 45998874 4579999999873
No 19
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=50.21 E-value=8 Score=22.79 Aligned_cols=10 Identities=40% Similarity=1.534 Sum_probs=8.3
Q ss_pred CCCCCCcccc
Q 031772 11 QACRCPLCRR 20 (153)
Q Consensus 11 ~~~~CP~CR~ 20 (153)
...+||.||+
T Consensus 35 ~~~~CP~C~k 44 (44)
T PF14634_consen 35 KSVKCPICRK 44 (44)
T ss_pred CCCCCcCCCC
Confidence 4789999985
No 20
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=49.46 E-value=7.6 Score=20.79 Aligned_cols=10 Identities=40% Similarity=1.295 Sum_probs=8.5
Q ss_pred CCCCcccccc
Q 031772 13 CRCPLCRRRI 22 (153)
Q Consensus 13 ~~CP~CR~~i 22 (153)
..||+|-+.+
T Consensus 2 v~CPiC~~~v 11 (26)
T smart00734 2 VQCPVCFREV 11 (26)
T ss_pred CcCCCCcCcc
Confidence 4799999887
No 21
>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=48.44 E-value=9.2 Score=21.22 Aligned_cols=12 Identities=50% Similarity=1.077 Sum_probs=8.9
Q ss_pred CCCCCCcccccc
Q 031772 11 QACRCPLCRRRI 22 (153)
Q Consensus 11 ~~~~CP~CR~~i 22 (153)
+..+||.||..+
T Consensus 34 ~~~~Cp~C~~~~ 45 (45)
T cd00162 34 GKNTCPLCRTPI 45 (45)
T ss_pred CcCCCCCCCCcC
Confidence 356799999764
No 22
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.01 E-value=8.3 Score=32.87 Aligned_cols=18 Identities=22% Similarity=0.385 Sum_probs=14.1
Q ss_pred CCCCCCCCCCcccccccc
Q 031772 7 GSTLQACRCPLCRRRITL 24 (153)
Q Consensus 7 ~~~~~~~~CP~CR~~i~~ 24 (153)
+.+.+--.||+||++|.-
T Consensus 37 sy~ndk~~CavCR~pids 54 (324)
T KOG0824|consen 37 SYKNDKKTCAVCRFPIDS 54 (324)
T ss_pred hhhcCCCCCceecCCCCc
Confidence 455666779999999983
No 23
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=47.65 E-value=8.1 Score=20.80 Aligned_cols=11 Identities=27% Similarity=0.812 Sum_probs=9.2
Q ss_pred CCCcccccccc
Q 031772 14 RCPLCRRRITL 24 (153)
Q Consensus 14 ~CP~CR~~i~~ 24 (153)
+||-|++.|..
T Consensus 2 ~CP~C~~~V~~ 12 (26)
T PF10571_consen 2 TCPECGAEVPE 12 (26)
T ss_pred cCCCCcCCchh
Confidence 69999998864
No 24
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=44.84 E-value=10 Score=27.21 Aligned_cols=14 Identities=29% Similarity=0.693 Sum_probs=12.2
Q ss_pred CCCCCCcccccccc
Q 031772 11 QACRCPLCRRRITL 24 (153)
Q Consensus 11 ~~~~CP~CR~~i~~ 24 (153)
+|..||+|-.++.+
T Consensus 1 ~p~~CpYCg~~~~l 14 (102)
T PF11672_consen 1 KPIICPYCGGPAEL 14 (102)
T ss_pred CCcccCCCCCeeEE
Confidence 48899999998876
No 25
>COG4589 Predicted CDP-diglyceride synthetase/phosphatidate cytidylyltransferase [General function prediction only]
Probab=44.43 E-value=45 Score=28.00 Aligned_cols=36 Identities=17% Similarity=0.450 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhhccCCcC----CccchhhhhhhHHHHHHH
Q 031772 97 YIAMIFSAVYIFSPIDII----PEALLGIVGLLDDLLIAL 132 (153)
Q Consensus 97 ~~~i~~al~Y~isP~D~I----Pd~i~g~lG~lDD~~v~~ 132 (153)
...+++++++.++|+|.. +-.+.+..|++-|+++.+
T Consensus 221 t~~~~~~~l~~lTp~~~lqa~~~~~~I~l~GF~GdlvmSa 260 (303)
T COG4589 221 TTMIASAILGLLTPLNTLQALLAGLLIGLSGFCGDLVMSA 260 (303)
T ss_pred HHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhhhHHHHHH
Confidence 356788888899999965 444557889999987643
No 26
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=44.10 E-value=22 Score=23.23 Aligned_cols=31 Identities=23% Similarity=0.398 Sum_probs=18.1
Q ss_pred CCCCCCcccccccc--cccCCCcccccCChHHHHHHHHHHHHHHH
Q 031772 11 QACRCPLCRRRITL--LIPNDDSLRQRHDPAVGDILQKVESYNRI 53 (153)
Q Consensus 11 ~~~~CP~CR~~i~~--L~p~~~~~~~~~d~~~~~v~~~i~~YNr~ 53 (153)
+.-.||.|+++++. |.|+. .+.+.|++|.++
T Consensus 38 ~~~~~P~t~~~l~~~~l~pn~------------~Lk~~I~~~~~~ 70 (73)
T PF04564_consen 38 NGGTDPFTRQPLSESDLIPNR------------ALKSAIEEWCAE 70 (73)
T ss_dssp TSSB-TTT-SB-SGGGSEE-H------------HHHHHHHHHHHH
T ss_pred CCCCCCCCCCcCCcccceECH------------HHHHHHHHHHHH
Confidence 46789999998885 44432 366677777654
No 27
>KOG0748 consensus Predicted membrane proteins, contain hemolysin III domain [General function prediction only; Signal transduction mechanisms]
Probab=43.90 E-value=86 Score=26.23 Aligned_cols=51 Identities=20% Similarity=0.329 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHhhccCCcCCccchhhhhhhHH---------HHHHHHHHHHHHHHHHHHHHHhc
Q 031772 94 ARVYIAMIFSAVYIFSPIDIIPEALLGIVGLLDD---------LLIALLCFLHVAALYRAVLYNRH 150 (153)
Q Consensus 94 ~r~~~~i~~al~Y~isP~D~IPd~i~g~lG~lDD---------~~v~~~~l~~v~~~yr~~~~~r~ 150 (153)
+...+.++++++|..- |||-.+| |-.|. +++++.++.+...+.+.+-..+.
T Consensus 216 ~~~~~yi~ga~fY~~r----iPER~~P--GkfD~~G~SHQifHv~vv~~a~~~~~a~~~~~~~~~~ 275 (286)
T KOG0748|consen 216 LMAVLYLLGALFYATR----IPERWFP--GKFDIWGHSHQIFHVLVVLAALFHLEAVLLDYEWRHS 275 (286)
T ss_pred HHHHHHHHHHHHhhcC----CCcccCC--CccceeCChhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4567789999999987 9999877 99998 55777777777776666555443
No 28
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=43.33 E-value=9.5 Score=29.54 Aligned_cols=16 Identities=31% Similarity=0.706 Sum_probs=12.7
Q ss_pred CCCCCCcccccccccc
Q 031772 11 QACRCPLCRRRITLLI 26 (153)
Q Consensus 11 ~~~~CP~CR~~i~~L~ 26 (153)
....||+||.+|.=-.
T Consensus 79 ~~L~CPLCRG~V~GWt 94 (162)
T PF07800_consen 79 PELACPLCRGEVKGWT 94 (162)
T ss_pred ccccCccccCceeceE
Confidence 3678999999998543
No 29
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=40.35 E-value=13 Score=19.55 Aligned_cols=11 Identities=36% Similarity=1.223 Sum_probs=9.1
Q ss_pred CCCCccccccc
Q 031772 13 CRCPLCRRRIT 23 (153)
Q Consensus 13 ~~CP~CR~~i~ 23 (153)
..||.|-++++
T Consensus 3 ~~C~~CgR~F~ 13 (25)
T PF13913_consen 3 VPCPICGRKFN 13 (25)
T ss_pred CcCCCCCCEEC
Confidence 57999999875
No 30
>PRK04949 putative sulfate transport protein CysZ; Validated
Probab=40.14 E-value=2.1e+02 Score=23.43 Aligned_cols=42 Identities=31% Similarity=0.500 Sum_probs=27.6
Q ss_pred ChHHHHHHHHHHHHHHHhCCCC-CCchhHHHHhhHHHHHHHHHHHH
Q 031772 37 DPAVGDILQKVESYNRIFGGPT-TANGLFQRIQDLPFLLRRLVREL 81 (153)
Q Consensus 37 d~~~~~v~~~i~~YNr~fs~~~-~~~~~~~~l~~~p~l~~~l~~~~ 81 (153)
+++.+.+-|++|+. +.|++ ...++.+-++|.+..+++-++.+
T Consensus 99 aPF~~~lAE~VE~~---l~g~~~~~~~~~~~~~~~~r~l~~el~kl 141 (251)
T PRK04949 99 APFNGLLAEKVEAR---LTGETLPDTGIAGLVKDVPRILKREWQKL 141 (251)
T ss_pred HHHhHHHHHHHHHH---cCCCCCCCCchHHHHHHHHHHHHHHHHHH
Confidence 46777888888875 44432 11456888888887777655543
No 31
>PRK01343 zinc-binding protein; Provisional
Probab=40.02 E-value=18 Score=23.29 Aligned_cols=15 Identities=27% Similarity=0.514 Sum_probs=11.8
Q ss_pred CCCCCCCCccccccc
Q 031772 9 TLQACRCPLCRRRIT 23 (153)
Q Consensus 9 ~~~~~~CP~CR~~i~ 23 (153)
.....+||.|.+++.
T Consensus 6 ~~p~~~CP~C~k~~~ 20 (57)
T PRK01343 6 LRPTRPCPECGKPST 20 (57)
T ss_pred CCCCCcCCCCCCcCc
Confidence 345788999999875
No 32
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=39.85 E-value=17 Score=22.40 Aligned_cols=16 Identities=38% Similarity=0.872 Sum_probs=10.9
Q ss_pred cCCCCCCCCCCccccc
Q 031772 6 HGSTLQACRCPLCRRR 21 (153)
Q Consensus 6 ~~~~~~~~~CP~CR~~ 21 (153)
|........||+|...
T Consensus 25 H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 25 HRSESKNVVCPICSSR 40 (54)
T ss_pred CcCCCCCccCCCchhh
Confidence 3444457899999853
No 33
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=39.67 E-value=13 Score=24.26 Aligned_cols=13 Identities=23% Similarity=0.823 Sum_probs=10.6
Q ss_pred CCCCCCccccccc
Q 031772 11 QACRCPLCRRRIT 23 (153)
Q Consensus 11 ~~~~CP~CR~~i~ 23 (153)
...+||.|+.++.
T Consensus 5 ~~v~CP~C~k~~~ 17 (62)
T PRK00418 5 ITVNCPTCGKPVE 17 (62)
T ss_pred ccccCCCCCCccc
Confidence 4589999998864
No 34
>PF07787 DUF1625: Protein of unknown function (DUF1625); InterPro: IPR012430 Sequences making up this family are derived from hypothetical proteins expressed by both prokaryotic and eukaryotic species. The region in question is approximately 250 residues long.
Probab=38.50 E-value=45 Score=26.93 Aligned_cols=36 Identities=19% Similarity=0.415 Sum_probs=23.5
Q ss_pred hhHHHHHHHHHHHHHHHHHhhccCCcCCccchhhhhh
Q 031772 88 LPLVIRARVYIAMIFSAVYIFSPIDIIPEALLGIVGL 124 (153)
Q Consensus 88 ~~~~~~~r~~~~i~~al~Y~isP~D~IPd~i~g~lG~ 124 (153)
..|..|.-..++++.++.-+.+|+..+=+.+ |++|=
T Consensus 182 ~tW~lR~~G~llmf~G~~~~~~~l~~l~~~~-P~lg~ 217 (248)
T PF07787_consen 182 LTWILRFIGWLLMFIGFFLLFSPLYTLVDWI-PLLGN 217 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh-ceeec
Confidence 4455554445667777777788887776775 66663
No 35
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=38.01 E-value=11 Score=23.74 Aligned_cols=15 Identities=27% Similarity=0.731 Sum_probs=11.7
Q ss_pred CCCCCCcccccccccc
Q 031772 11 QACRCPLCRRRITLLI 26 (153)
Q Consensus 11 ~~~~CP~CR~~i~~L~ 26 (153)
-.+|||-|+ ++|.+-
T Consensus 23 leIKCpRC~-tiN~~~ 37 (51)
T PF10122_consen 23 LEIKCPRCK-TINHVR 37 (51)
T ss_pred EEEECCCCC-ccceEe
Confidence 478999999 777753
No 36
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=36.66 E-value=14 Score=24.17 Aligned_cols=19 Identities=16% Similarity=0.541 Sum_probs=14.6
Q ss_pred CCCCCCCCCcccccccccc
Q 031772 8 STLQACRCPLCRRRITLLI 26 (153)
Q Consensus 8 ~~~~~~~CP~CR~~i~~L~ 26 (153)
.....+.||.|++.+..-+
T Consensus 3 ~~p~~~~CP~C~~~~~T~v 21 (73)
T PF10601_consen 3 PEPVRIYCPYCQQQVQTRV 21 (73)
T ss_pred CCceeeECCCCCCEEEEEE
Confidence 3456789999999987655
No 37
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.38 E-value=55 Score=27.97 Aligned_cols=66 Identities=12% Similarity=0.153 Sum_probs=31.7
Q ss_pred CCCCCCcccccccc--cccCCCcccccCChHHHHHHHH-HHHHHHHhCCCCCCchhHHHHhhHHHHHHHHH
Q 031772 11 QACRCPLCRRRITL--LIPNDDSLRQRHDPAVGDILQK-VESYNRIFGGPTTANGLFQRIQDLPFLLRRLV 78 (153)
Q Consensus 11 ~~~~CP~CR~~i~~--L~p~~~~~~~~~d~~~~~v~~~-i~~YNr~fs~~~~~~~~~~~l~~~p~l~~~l~ 78 (153)
++..||.|+.++.. +-|.- . ++..-+.-..+++. ..-||++=..=++.+.+=++|.++-.++-.|.
T Consensus 42 ~~~~CP~C~~~lrk~~fr~q~-F-~D~~vekEV~iRkrv~~i~Nk~e~dF~~l~~yNdYLE~vEdii~nL~ 110 (309)
T TIGR00570 42 GSGSCPECDTPLRKNNFRVQL-F-EDPTVEKEVDIRKRVLKIYNKREEDFPSLREYNDYLEEVEDIVYNLT 110 (309)
T ss_pred CCCCCCCCCCccchhhccccc-c-ccHHHHHHHHHHHHHHHHHccchhccCCHHHHHHHHHHHHHHHHHhh
Confidence 34589999988875 22221 1 11111111223333 34566653332233566666666555555444
No 38
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=36.11 E-value=11 Score=23.52 Aligned_cols=19 Identities=26% Similarity=0.639 Sum_probs=13.9
Q ss_pred ccccCCC-CCCCCCCccccc
Q 031772 3 VWDHGST-LQACRCPLCRRR 21 (153)
Q Consensus 3 yW~~~~~-~~~~~CP~CR~~ 21 (153)
+|....+ ..|-.||-||+.
T Consensus 23 fy~eKgf~n~p~RC~~CR~~ 42 (49)
T PF13451_consen 23 FYAEKGFDNEPKRCPSCRQA 42 (49)
T ss_pred HHHhcCCcCCCccCHHHHHH
Confidence 4555444 479999999975
No 39
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=35.68 E-value=11 Score=24.28 Aligned_cols=12 Identities=25% Similarity=1.088 Sum_probs=6.7
Q ss_pred CCCCcccccccc
Q 031772 13 CRCPLCRRRITL 24 (153)
Q Consensus 13 ~~CP~CR~~i~~ 24 (153)
.+||.|++++..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 579999988876
No 40
>KOG1583 consensus UDP-N-acetylglucosamine transporter [Carbohydrate transport and metabolism]
Probab=35.62 E-value=56 Score=27.89 Aligned_cols=26 Identities=23% Similarity=0.416 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCC
Q 031772 128 LLIALLCFLHVAALYRAVLYNRHGGA 153 (153)
Q Consensus 128 ~~v~~~~l~~v~~~yr~~~~~r~~~~ 153 (153)
+.+++..+...-++|++.+++|||.+
T Consensus 168 lL~~al~~sa~mgiyqE~~Y~kyGKh 193 (330)
T KOG1583|consen 168 LLVFALLLSAYMGIYQETTYQKYGKH 193 (330)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 55677788888999999999999975
No 41
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=35.13 E-value=16 Score=26.11 Aligned_cols=13 Identities=23% Similarity=0.731 Sum_probs=10.1
Q ss_pred CCCCCcccccccc
Q 031772 12 ACRCPLCRRRITL 24 (153)
Q Consensus 12 ~~~CP~CR~~i~~ 24 (153)
-..||+|+.++|-
T Consensus 80 ~~~Cp~C~spFNp 92 (105)
T COG4357 80 CGSCPYCQSPFNP 92 (105)
T ss_pred cCCCCCcCCCCCc
Confidence 3569999988874
No 42
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=35.02 E-value=22 Score=20.09 Aligned_cols=14 Identities=43% Similarity=0.871 Sum_probs=10.4
Q ss_pred CCCCCCCCcccccc
Q 031772 9 TLQACRCPLCRRRI 22 (153)
Q Consensus 9 ~~~~~~CP~CR~~i 22 (153)
..++++||.|--+|
T Consensus 14 ~~~~irC~~CG~RI 27 (32)
T PF03604_consen 14 PGDPIRCPECGHRI 27 (32)
T ss_dssp TSSTSSBSSSS-SE
T ss_pred CCCcEECCcCCCeE
Confidence 35789999998665
No 43
>COG0343 Tgt Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]
Probab=34.98 E-value=15 Score=32.03 Aligned_cols=19 Identities=32% Similarity=0.861 Sum_probs=14.2
Q ss_pred CCCCCCcccc----cccccccCC
Q 031772 11 QACRCPLCRR----RITLLIPND 29 (153)
Q Consensus 11 ~~~~CP~CR~----~i~~L~p~~ 29 (153)
.+|.||.|+. .+.-|...+
T Consensus 297 ~~C~C~~C~~ysRayl~hL~~~~ 319 (372)
T COG0343 297 EPCSCPTCRNYSRAYLRHLRRAN 319 (372)
T ss_pred CCCCCcccCCcccccHHHHHhcc
Confidence 5899999997 566666553
No 44
>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=34.68 E-value=25 Score=21.24 Aligned_cols=24 Identities=25% Similarity=0.466 Sum_probs=14.8
Q ss_pred ccccCCCCCCCCCCcccc-cccccc
Q 031772 3 VWDHGSTLQACRCPLCRR-RITLLI 26 (153)
Q Consensus 3 yW~~~~~~~~~~CP~CR~-~i~~L~ 26 (153)
.|+..+.-....||.|.+ ++..++
T Consensus 17 ~~~~~~~~~~~~CP~Cg~~~~~r~~ 41 (52)
T TIGR02605 17 VLQKMSDDPLATCPECGGEKLRRLL 41 (52)
T ss_pred EEEecCCCCCCCCCCCCCCceeEEe
Confidence 354333345778999997 565444
No 45
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=34.47 E-value=12 Score=30.02 Aligned_cols=10 Identities=20% Similarity=0.697 Sum_probs=7.9
Q ss_pred CCCCCccccc
Q 031772 12 ACRCPLCRRR 21 (153)
Q Consensus 12 ~~~CP~CR~~ 21 (153)
-.+||+||+-
T Consensus 116 Dp~CpyCkkl 125 (232)
T PRK10877 116 DITCGYCHKL 125 (232)
T ss_pred CCCChHHHHH
Confidence 4589999974
No 46
>PRK02975 putative common antigen polymerase; Provisional
Probab=34.16 E-value=3.4e+02 Score=24.16 Aligned_cols=88 Identities=16% Similarity=0.233 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHhCCCCCCchhHHHHhhHHHHHHHHHHHHcCCCCChhHHHHHHHHHHHHHHHHHhhccCCcCCccchhhh
Q 031772 43 ILQKVESYNRIFGGPTTANGLFQRIQDLPFLLRRLVRELVDPHRSLPLVIRARVYIAMIFSAVYIFSPIDIIPEALLGIV 122 (153)
Q Consensus 43 v~~~i~~YNr~fs~~~~~~~~~~~l~~~p~l~~~l~~~~~~~~~~~~~~~~~r~~~~i~~al~Y~isP~D~IPd~i~g~l 122 (153)
++-|+++||+.||.+. .+..-|-- .-+.+..|.--++-..+. .+-.+.++++...-+.- +-++
T Consensus 138 LLFkL~sYSqIFSs~V--sGvaLKRF-FYFfIPAmLv~yFL~~tk------~~Wl~fL~~tv~FG~lt--------YviV 200 (450)
T PRK02975 138 LLFKLHSYSQIFSSEV--SGVALKRF-FYFFIPAMLVVYFLRQDS------KAWLFFLVSTVAFGLLT--------YMIV 200 (450)
T ss_pred HhhhHHHHHHHHhhhc--ccHHHHHH-HHHHHHHHHHHHhhcccH------HHHHHHHHHHHHHhcEE--------EEEE
Confidence 5668899999999876 44433322 223333333233322221 11122333333322211 2234
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHH
Q 031772 123 GLLDDLLIALLCFLHVAALYRAVLY 147 (153)
Q Consensus 123 G~lDD~~v~~~~l~~v~~~yr~~~~ 147 (153)
|=.---+++++++--..+++|.++.
T Consensus 201 GGTRANiiiAf~lFlfiGi~rgwis 225 (450)
T PRK02975 201 GGTRANIIIAFALFLFIGIIRGWIS 225 (450)
T ss_pred cCcHHHHHHHHHHHHHHHHHHhHHH
Confidence 5555555666666667777777664
No 47
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=33.83 E-value=7.2 Score=27.96 Aligned_cols=13 Identities=23% Similarity=0.664 Sum_probs=10.5
Q ss_pred CCCCCcccccccc
Q 031772 12 ACRCPLCRRRITL 24 (153)
Q Consensus 12 ~~~CP~CR~~i~~ 24 (153)
+.|||.||+-..-
T Consensus 37 aaKC~~~~k~~~S 49 (102)
T PF15176_consen 37 AAKCPVWYKYLAS 49 (102)
T ss_pred HHHhHHHHHHHhc
Confidence 6899999976654
No 48
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=33.75 E-value=14 Score=30.12 Aligned_cols=9 Identities=33% Similarity=1.065 Sum_probs=7.5
Q ss_pred CCCCccccc
Q 031772 13 CRCPLCRRR 21 (153)
Q Consensus 13 ~~CP~CR~~ 21 (153)
.+||+||+-
T Consensus 127 p~CpyC~kl 135 (251)
T PRK11657 127 PNCPYCKQF 135 (251)
T ss_pred CCChhHHHH
Confidence 489999974
No 49
>PF10041 DUF2277: Uncharacterized conserved protein (DUF2277); InterPro: IPR018735 Members of this family of hypothetical bacterial proteins have no known function.
Probab=33.55 E-value=54 Score=22.39 Aligned_cols=35 Identities=26% Similarity=0.361 Sum_probs=22.8
Q ss_pred cccccccccccCCCcccccCChHHHHHHHHHHHHHHHhCCCC
Q 031772 17 LCRRRITLLIPNDDSLRQRHDPAVGDILQKVESYNRIFGGPT 58 (153)
Q Consensus 17 ~CR~~i~~L~p~~~~~~~~~d~~~~~v~~~i~~YNr~fs~~~ 58 (153)
||| +|+.|..-+.+ .++ +++..---+|-|.-||-.
T Consensus 1 MCR-nI~~L~~fePp---aT~---~EI~aAAlQyVRKvSG~~ 35 (78)
T PF10041_consen 1 MCR-NIKTLRNFEPP---ATD---EEIRAAALQYVRKVSGFR 35 (78)
T ss_pred CCc-chhhhcCCCCC---CCH---HHHHHHHHHHHHHHccCC
Confidence 798 88888864322 222 246666778888888753
No 50
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.53 E-value=16 Score=22.00 Aligned_cols=15 Identities=33% Similarity=0.645 Sum_probs=12.0
Q ss_pred CCCCCCCCccccccc
Q 031772 9 TLQACRCPLCRRRIT 23 (153)
Q Consensus 9 ~~~~~~CP~CR~~i~ 23 (153)
..++++||.|-.+|-
T Consensus 16 ~~~~irC~~CG~rIl 30 (44)
T smart00659 16 SKDVVRCRECGYRIL 30 (44)
T ss_pred CCCceECCCCCceEE
Confidence 357999999987764
No 51
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=32.17 E-value=22 Score=20.92 Aligned_cols=16 Identities=31% Similarity=0.789 Sum_probs=8.4
Q ss_pred cccccCCCCCCCCCCcc
Q 031772 2 LVWDHGSTLQACRCPLC 18 (153)
Q Consensus 2 ~yW~~~~~~~~~~CP~C 18 (153)
++|+.....+ ..||.|
T Consensus 27 ~~~~~~~~~~-~~CP~C 42 (42)
T PF15227_consen 27 RLWKEPSGSG-FSCPEC 42 (42)
T ss_dssp HHHCCSSSST----SSS
T ss_pred HHHHccCCcC-CCCcCC
Confidence 4677765433 889987
No 52
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=31.95 E-value=19 Score=26.39 Aligned_cols=13 Identities=31% Similarity=0.679 Sum_probs=9.3
Q ss_pred CCCCCcccccccc
Q 031772 12 ACRCPLCRRRITL 24 (153)
Q Consensus 12 ~~~CP~CR~~i~~ 24 (153)
.-.|++|+++.|+
T Consensus 85 ~D~CM~C~~pLTL 97 (114)
T PF11023_consen 85 VDACMHCKEPLTL 97 (114)
T ss_pred hhccCcCCCcCcc
Confidence 3468888887775
No 53
>PRK10824 glutaredoxin-4; Provisional
Probab=31.12 E-value=17 Score=26.36 Aligned_cols=17 Identities=12% Similarity=0.270 Sum_probs=13.4
Q ss_pred CCCCCCccccccccccc
Q 031772 11 QACRCPLCRRRITLLIP 27 (153)
Q Consensus 11 ~~~~CP~CR~~i~~L~p 27 (153)
..-.||+|++-..+|-.
T Consensus 26 ~~p~Cpyc~~ak~lL~~ 42 (115)
T PRK10824 26 KLPSCGFSAQAVQALSA 42 (115)
T ss_pred CCCCCchHHHHHHHHHH
Confidence 34689999999888743
No 54
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=30.59 E-value=19 Score=22.14 Aligned_cols=9 Identities=33% Similarity=1.375 Sum_probs=3.7
Q ss_pred CCCCccccc
Q 031772 13 CRCPLCRRR 21 (153)
Q Consensus 13 ~~CP~CR~~ 21 (153)
-+||+|.++
T Consensus 42 W~CPiC~~~ 50 (50)
T PF02891_consen 42 WKCPICNKP 50 (50)
T ss_dssp -B-TTT---
T ss_pred eECcCCcCc
Confidence 589999874
No 55
>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=30.16 E-value=23 Score=21.82 Aligned_cols=12 Identities=17% Similarity=0.183 Sum_probs=9.6
Q ss_pred CCCCcccccccc
Q 031772 13 CRCPLCRRRITL 24 (153)
Q Consensus 13 ~~CP~CR~~i~~ 24 (153)
.+||+|+++++.
T Consensus 36 ~~cP~~~~~~~~ 47 (63)
T smart00504 36 GTDPVTGQPLTH 47 (63)
T ss_pred CCCCCCcCCCCh
Confidence 489999998753
No 56
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=29.36 E-value=22 Score=28.36 Aligned_cols=14 Identities=21% Similarity=0.812 Sum_probs=11.8
Q ss_pred CCCCCCcccccccc
Q 031772 11 QACRCPLCRRRITL 24 (153)
Q Consensus 11 ~~~~CP~CR~~i~~ 24 (153)
..++||+|.+.++.
T Consensus 4 k~~~CPvC~~~F~~ 17 (214)
T PF09986_consen 4 KKITCPVCGKEFKT 17 (214)
T ss_pred CceECCCCCCeeee
Confidence 46899999999884
No 57
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.89 E-value=23 Score=22.08 Aligned_cols=15 Identities=40% Similarity=0.953 Sum_probs=11.9
Q ss_pred CCCCCCCcccccccc
Q 031772 10 LQACRCPLCRRRITL 24 (153)
Q Consensus 10 ~~~~~CP~CR~~i~~ 24 (153)
...+.||+|...|-+
T Consensus 22 ~~~irCp~Cg~rIl~ 36 (49)
T COG1996 22 TRGIRCPYCGSRILV 36 (49)
T ss_pred cCceeCCCCCcEEEE
Confidence 468999999987743
No 58
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=28.55 E-value=21 Score=21.29 Aligned_cols=13 Identities=46% Similarity=1.086 Sum_probs=11.0
Q ss_pred CCCCCcccccccc
Q 031772 12 ACRCPLCRRRITL 24 (153)
Q Consensus 12 ~~~CP~CR~~i~~ 24 (153)
+.+||+|..++..
T Consensus 21 ~~~Cp~CG~~~~~ 33 (46)
T PRK00398 21 GVRCPYCGYRILF 33 (46)
T ss_pred ceECCCCCCeEEE
Confidence 7899999987764
No 59
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=27.57 E-value=16 Score=19.13 Aligned_cols=13 Identities=23% Similarity=0.989 Sum_probs=10.8
Q ss_pred CCCCCCccccccc
Q 031772 11 QACRCPLCRRRIT 23 (153)
Q Consensus 11 ~~~~CP~CR~~i~ 23 (153)
.|-+||.|.+.++
T Consensus 13 k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 13 KPYKCPYCGKSFS 25 (26)
T ss_dssp SSEEESSSSEEES
T ss_pred CCCCCCCCcCeeC
Confidence 7889999988764
No 60
>PTZ00062 glutaredoxin; Provisional
Probab=27.54 E-value=21 Score=28.46 Aligned_cols=15 Identities=13% Similarity=0.270 Sum_probs=12.5
Q ss_pred CCCCccccccccccc
Q 031772 13 CRCPLCRRRITLLIP 27 (153)
Q Consensus 13 ~~CP~CR~~i~~L~p 27 (153)
-.||+|++.+.+|--
T Consensus 126 p~C~~C~~~k~~L~~ 140 (204)
T PTZ00062 126 PFCRFSNAVVNMLNS 140 (204)
T ss_pred CCChhHHHHHHHHHH
Confidence 589999999988754
No 61
>PF04134 DUF393: Protein of unknown function, DUF393; InterPro: IPR007263 The DCC family, named after the conserved N-terminal DxxCxxC motif, encompasses COG3011 from COG. Proteins in this family are predicted to have a thioredoxin-like fold which, together with the presence of an invariant catalytic cysteine residue, suggests that they are a novel group of thiol-disulphide oxidoreductases []. As some of the bacterial proteins are encoded near penicillin-binding proteins, it has been suggested that these may be involved in redox regulation of cell wall biosynthesis [].
Probab=27.46 E-value=16 Score=25.33 Aligned_cols=16 Identities=50% Similarity=1.138 Sum_probs=12.9
Q ss_pred CCCcccccccccccCC
Q 031772 14 RCPLCRRRITLLIPND 29 (153)
Q Consensus 14 ~CP~CR~~i~~L~p~~ 29 (153)
.||+|+..++.+..-.
T Consensus 6 ~C~lC~~~~~~l~~~d 21 (114)
T PF04134_consen 6 DCPLCRREVRFLRRRD 21 (114)
T ss_pred CCHhHHHHHHHHHhcC
Confidence 6999999999876543
No 62
>cd03020 DsbA_DsbC_DsbG DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins. DsbC and DsbG are kept in their reduced state by the cytoplasmic membrane protein DsbD, which utilizes the TRX/TRX reductase system in the cytosol as a source of reducing equivalents. DsbG differ from DsbC in that it has a more limited substrate specificity, and it may preferentially act later in the folding process to catalyze disulfide rearrangements in folded or partially folded proteins. Also included in the alignment is the predicted protein TrbB, whose gene was sequenced from the enterohemorrhagic E. coli type IV pilus gene cluster, which is required for efficient plasmid transfer.
Probab=27.27 E-value=23 Score=27.13 Aligned_cols=15 Identities=33% Similarity=0.636 Sum_probs=10.8
Q ss_pred CCCCCcccccccccc
Q 031772 12 ACRCPLCRRRITLLI 26 (153)
Q Consensus 12 ~~~CP~CR~~i~~L~ 26 (153)
-..||+||+--..+-
T Consensus 86 D~~Cp~C~~~~~~l~ 100 (197)
T cd03020 86 DPDCPYCRKLEKELK 100 (197)
T ss_pred CCCCccHHHHHHHHh
Confidence 368999998655543
No 63
>COG3305 Predicted membrane protein [Function unknown]
Probab=27.04 E-value=1.7e+02 Score=22.21 Aligned_cols=26 Identities=31% Similarity=0.586 Sum_probs=17.7
Q ss_pred ChhHHHHHHHHHHHHHHHHHhhccCCcC
Q 031772 87 SLPLVIRARVYIAMIFSAVYIFSPIDII 114 (153)
Q Consensus 87 ~~~~~~~~r~~~~i~~al~Y~isP~D~I 114 (153)
|+....++-..+.++.+.+|+ |+|+-
T Consensus 88 GLW~~k~W~e~fa~vs~aIyL--PfeVy 113 (152)
T COG3305 88 GLWLLKRWGEYFAVVSTAIYL--PFEVY 113 (152)
T ss_pred HHHHHHHHHHHHHHHHHhhhc--chHHH
Confidence 444444455667888888888 98863
No 64
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=27.00 E-value=24 Score=31.16 Aligned_cols=12 Identities=42% Similarity=1.154 Sum_probs=9.4
Q ss_pred CCCCCccccccc
Q 031772 12 ACRCPLCRRRIT 23 (153)
Q Consensus 12 ~~~CP~CR~~i~ 23 (153)
.-.||+||+++-
T Consensus 334 qQTCPICr~p~i 345 (491)
T COG5243 334 QQTCPICRRPVI 345 (491)
T ss_pred ccCCCcccCccc
Confidence 457999999943
No 65
>cd02066 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which
Probab=25.73 E-value=25 Score=21.21 Aligned_cols=16 Identities=38% Similarity=0.785 Sum_probs=11.5
Q ss_pred CCCCcccccccccccC
Q 031772 13 CRCPLCRRRITLLIPN 28 (153)
Q Consensus 13 ~~CP~CR~~i~~L~p~ 28 (153)
-.||.|++-...|-..
T Consensus 8 ~~Cp~C~~~~~~L~~~ 23 (72)
T cd02066 8 STCPYCKRAKRLLESL 23 (72)
T ss_pred CCCHHHHHHHHHHHHc
Confidence 4599999877766443
No 66
>PRK05208 hypothetical protein; Provisional
Probab=25.67 E-value=84 Score=24.44 Aligned_cols=33 Identities=21% Similarity=0.368 Sum_probs=29.2
Q ss_pred ccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 031772 116 EALLGIVGLLDDLLIALLCFLHVAALYRAVLYN 148 (153)
Q Consensus 116 d~i~g~lG~lDD~~v~~~~l~~v~~~yr~~~~~ 148 (153)
|.+.+++|.+|-..+..+++.-.-+.|..++.+
T Consensus 56 ~~il~vl~lIDl~Lia~lLlIv~~ggYElFISk 88 (168)
T PRK05208 56 DLILVVLSLIDVVLVANLLVMVIFSGYENFVSR 88 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHhhcc
Confidence 567899999999999999999999999998753
No 67
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=25.64 E-value=16 Score=21.78 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=9.1
Q ss_pred CCCCCCcccccc
Q 031772 11 QACRCPLCRRRI 22 (153)
Q Consensus 11 ~~~~CP~CR~~i 22 (153)
++..||||-.++
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 468999998653
No 68
>TIGR02189 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa.
Probab=25.43 E-value=42 Score=23.15 Aligned_cols=17 Identities=24% Similarity=0.575 Sum_probs=13.3
Q ss_pred CCCCCCCcccccccccc
Q 031772 10 LQACRCPLCRRRITLLI 26 (153)
Q Consensus 10 ~~~~~CP~CR~~i~~L~ 26 (153)
+..-.||+|++.-.+|-
T Consensus 13 ysk~~Cp~C~~ak~~L~ 29 (99)
T TIGR02189 13 FSRSSCCMCHVVKRLLL 29 (99)
T ss_pred EECCCCHHHHHHHHHHH
Confidence 35578999998888774
No 69
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.95 E-value=30 Score=26.48 Aligned_cols=10 Identities=40% Similarity=0.936 Sum_probs=5.0
Q ss_pred CCcccccccc
Q 031772 15 CPLCRRRITL 24 (153)
Q Consensus 15 CP~CR~~i~~ 24 (153)
||-|..+++.
T Consensus 31 c~~c~~~f~~ 40 (154)
T PRK00464 31 CLACGKRFTT 40 (154)
T ss_pred ccccCCcceE
Confidence 5555555544
No 70
>PF14348 DUF4400: Domain of unknown function (DUF4400)
Probab=24.91 E-value=2.6e+02 Score=21.57 Aligned_cols=22 Identities=23% Similarity=0.484 Sum_probs=16.7
Q ss_pred HHHHHHH-HHHhhccCCcCCccc
Q 031772 97 YIAMIFS-AVYIFSPIDIIPEAL 118 (153)
Q Consensus 97 ~~~i~~a-l~Y~isP~D~IPd~i 118 (153)
+..+++. ++|++.|+-+-|-.+
T Consensus 156 ~~~~~~~~~lyL~lP~~i~P~~~ 178 (198)
T PF14348_consen 156 IPLLILPWVLYLSLPFSIPPNLV 178 (198)
T ss_pred HHHHHHHHHHHHHcccccChHHH
Confidence 3455555 899999998878776
No 71
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=24.88 E-value=18 Score=23.06 Aligned_cols=16 Identities=19% Similarity=0.337 Sum_probs=12.4
Q ss_pred CCCCCccccccccccc
Q 031772 12 ACRCPLCRRRITLLIP 27 (153)
Q Consensus 12 ~~~CP~CR~~i~~L~p 27 (153)
.-.||.|++.-..|--
T Consensus 6 ~~~Cp~C~~ak~~L~~ 21 (72)
T TIGR02194 6 KNNCVQCKMTKKALEE 21 (72)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 4579999988887743
No 72
>PRK07668 hypothetical protein; Validated
Probab=24.85 E-value=4e+02 Score=22.03 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhhccCCcCCc-------cchhhhhhhHHHHHHHHHHHHHHHHHHHH
Q 031772 97 YIAMIFSAVYIFSPIDIIPE-------ALLGIVGLLDDLLIALLCFLHVAALYRAV 145 (153)
Q Consensus 97 ~~~i~~al~Y~isP~D~IPd-------~i~g~lG~lDD~~v~~~~l~~v~~~yr~~ 145 (153)
..++++.++|++.|..++.+ ...-++|+. .++.+...-..-..|..
T Consensus 79 ~~~ii~~l~~~~i~~~~f~~~~~~~~~s~~~iig~~---~~~~l~i~~~~~~~r~~ 131 (254)
T PRK07668 79 LFIIIGILSFWIIANILFGNPNHPLTYSLIQLIGYP---ISLILTIIGLIFLLRMA 131 (254)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCceeeeehHHhhHH---HHHHHHHHHHHHHHHHH
Confidence 35677788888877666544 233456665 33333333333444443
No 73
>KOG1752 consensus Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]
Probab=24.64 E-value=19 Score=25.65 Aligned_cols=46 Identities=15% Similarity=0.283 Sum_probs=25.1
Q ss_pred CCCCCCCcccccccccccCCCccc--ccCChHHHHHHHHHHHHHHHhCCCC
Q 031772 10 LQACRCPLCRRRITLLIPNDDSLR--QRHDPAVGDILQKVESYNRIFGGPT 58 (153)
Q Consensus 10 ~~~~~CP~CR~~i~~L~p~~~~~~--~~~d~~~~~v~~~i~~YNr~fs~~~ 58 (153)
+..-.||+|.+ +..|+....... -|-|+. +.-.+|++|..+.+|+.
T Consensus 19 fSKs~C~~c~~-~k~ll~~~~v~~~vvELD~~--~~g~eiq~~l~~~tg~~ 66 (104)
T KOG1752|consen 19 FSKSSCPYCHR-AKELLSDLGVNPKVVELDED--EDGSEIQKALKKLTGQR 66 (104)
T ss_pred EECCcCchHHH-HHHHHHhCCCCCEEEEccCC--CCcHHHHHHHHHhcCCC
Confidence 35678999998 665555432210 011111 12237777777777664
No 74
>PRK01008 queuine tRNA-ribosyltransferase; Provisional
Probab=24.33 E-value=83 Score=27.44 Aligned_cols=14 Identities=29% Similarity=0.771 Sum_probs=10.8
Q ss_pred CCCCCCCccccccc
Q 031772 10 LQACRCPLCRRRIT 23 (153)
Q Consensus 10 ~~~~~CP~CR~~i~ 23 (153)
...|+||.|+...|
T Consensus 316 d~~C~C~~C~~~yt 329 (372)
T PRK01008 316 EPGCSCLACSSGIS 329 (372)
T ss_pred CCCCCCcCcCCCCC
Confidence 45999999986444
No 75
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=24.22 E-value=34 Score=21.69 Aligned_cols=16 Identities=19% Similarity=0.252 Sum_probs=12.3
Q ss_pred CCCCCccccccccccc
Q 031772 12 ACRCPLCRRRITLLIP 27 (153)
Q Consensus 12 ~~~CP~CR~~i~~L~p 27 (153)
.-.||.|++-...|-.
T Consensus 8 ~~~C~~C~ka~~~L~~ 23 (73)
T cd03027 8 RLGCEDCTAVRLFLRE 23 (73)
T ss_pred cCCChhHHHHHHHHHH
Confidence 4579999988877743
No 76
>TIGR00365 monothiol glutaredoxin, Grx4 family. The gene for the member of this glutaredoxin family in E. coli, originally designated ydhD, is now designated grxD. Its protein, Grx4, is a monothiol glutaredoxin similar to Grx5 of yeast, which is involved in iron-sulfur cluster formation.
Probab=24.06 E-value=28 Score=24.01 Aligned_cols=17 Identities=24% Similarity=0.440 Sum_probs=13.5
Q ss_pred CCCCCCccccccccccc
Q 031772 11 QACRCPLCRRRITLLIP 27 (153)
Q Consensus 11 ~~~~CP~CR~~i~~L~p 27 (153)
+...||+|.+-..+|-.
T Consensus 23 ~~~~Cp~C~~ak~lL~~ 39 (97)
T TIGR00365 23 QFPQCGFSARAVQILKA 39 (97)
T ss_pred CCCCCchHHHHHHHHHH
Confidence 56789999988888743
No 77
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=23.75 E-value=32 Score=23.84 Aligned_cols=13 Identities=38% Similarity=0.608 Sum_probs=10.3
Q ss_pred CCCCCcccccccc
Q 031772 12 ACRCPLCRRRITL 24 (153)
Q Consensus 12 ~~~CP~CR~~i~~ 24 (153)
.-.||+|||+..+
T Consensus 70 k~~CPld~q~w~~ 82 (88)
T COG5194 70 KGVCPLDRQTWVL 82 (88)
T ss_pred CCCCCCCCceeEE
Confidence 4579999998754
No 78
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=23.69 E-value=64 Score=30.44 Aligned_cols=59 Identities=10% Similarity=0.082 Sum_probs=42.6
Q ss_pred CCCCCCCcccccccccccCCCcccccCChHHHHHHHHHHHHHHHhCCCCCCchhHHHHhh
Q 031772 10 LQACRCPLCRRRITLLIPNDDSLRQRHDPAVGDILQKVESYNRIFGGPTTANGLFQRIQD 69 (153)
Q Consensus 10 ~~~~~CP~CR~~i~~L~p~~~~~~~~~d~~~~~v~~~i~~YNr~fs~~~~~~~~~~~l~~ 69 (153)
-.|-.-||-|.+-|-+-|.+.-++++..++++++.++|++||+.|=.... ..+-+..-|
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~~i~~~~~~YY~~~~-p~IsD~eYD 64 (689)
T PRK14351 6 EEPDDNPYLRDPPTDFEPVEELSEDEAEEQAEQLREAIREHDHRYYVEAD-PVIADRAYD 64 (689)
T ss_pred cCCCCCCcccCCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCCChHHHH
Confidence 45778899999999888887555555557799999999999998743211 344555554
No 79
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=23.68 E-value=28 Score=24.17 Aligned_cols=13 Identities=23% Similarity=0.810 Sum_probs=6.3
Q ss_pred CCCCCCccccccc
Q 031772 11 QACRCPLCRRRIT 23 (153)
Q Consensus 11 ~~~~CP~CR~~i~ 23 (153)
.+-.||.|.+++.
T Consensus 32 ~rS~C~~C~~~L~ 44 (92)
T PF06750_consen 32 PRSHCPHCGHPLS 44 (92)
T ss_pred CCCcCcCCCCcCc
Confidence 3445555555444
No 80
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.51 E-value=37 Score=29.47 Aligned_cols=21 Identities=29% Similarity=0.564 Sum_probs=13.6
Q ss_pred CCCCCC-C-CCcccccccccccC
Q 031772 8 STLQAC-R-CPLCRRRITLLIPN 28 (153)
Q Consensus 8 ~~~~~~-~-CP~CR~~i~~L~p~ 28 (153)
+|+... + ||+|+|.+-.=..+
T Consensus 261 pWL~~~r~~CPvCK~di~~~~~~ 283 (348)
T KOG4628|consen 261 PWLTQTRTFCPVCKRDIRTDSGS 283 (348)
T ss_pred hhHhhcCccCCCCCCcCCCCCCC
Confidence 454433 4 99999987654433
No 81
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=23.41 E-value=33 Score=31.37 Aligned_cols=10 Identities=40% Similarity=1.381 Sum_probs=8.7
Q ss_pred CCCCCCcccc
Q 031772 11 QACRCPLCRR 20 (153)
Q Consensus 11 ~~~~CP~CR~ 20 (153)
.+|+||.|+.
T Consensus 171 ~~C~C~~C~~ 180 (540)
T TIGR00432 171 FPCSCPVCSN 180 (540)
T ss_pred CCCCCccccc
Confidence 5999999983
No 82
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=23.31 E-value=35 Score=21.57 Aligned_cols=11 Identities=45% Similarity=1.020 Sum_probs=9.4
Q ss_pred CCCcccccccc
Q 031772 14 RCPLCRRRITL 24 (153)
Q Consensus 14 ~CP~CR~~i~~ 24 (153)
+||.|-+.|++
T Consensus 4 ~CP~CG~~iev 14 (54)
T TIGR01206 4 ECPDCGAEIEL 14 (54)
T ss_pred CCCCCCCEEec
Confidence 79999998876
No 83
>PRK10638 glutaredoxin 3; Provisional
Probab=23.20 E-value=34 Score=22.38 Aligned_cols=17 Identities=35% Similarity=0.809 Sum_probs=12.8
Q ss_pred CCCCCCccccccccccc
Q 031772 11 QACRCPLCRRRITLLIP 27 (153)
Q Consensus 11 ~~~~CP~CR~~i~~L~p 27 (153)
..-.||+|++-...|--
T Consensus 8 ~~~~Cp~C~~a~~~L~~ 24 (83)
T PRK10638 8 TKATCPFCHRAKALLNS 24 (83)
T ss_pred ECCCChhHHHHHHHHHH
Confidence 34579999988887643
No 84
>PRK13533 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=22.66 E-value=35 Score=30.82 Aligned_cols=10 Identities=40% Similarity=1.494 Sum_probs=8.6
Q ss_pred CCCCCCcccc
Q 031772 11 QACRCPLCRR 20 (153)
Q Consensus 11 ~~~~CP~CR~ 20 (153)
.+|+||.|+.
T Consensus 273 ~~C~C~~C~~ 282 (487)
T PRK13533 273 LPCSCPVCSK 282 (487)
T ss_pred CCCCChhcCc
Confidence 5899999983
No 85
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=22.66 E-value=25 Score=20.08 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=8.9
Q ss_pred CCCCCCccccccc
Q 031772 11 QACRCPLCRRRIT 23 (153)
Q Consensus 11 ~~~~CP~CR~~i~ 23 (153)
.-+.||.|-++|.
T Consensus 3 ~~~~C~nC~R~v~ 15 (33)
T PF08209_consen 3 PYVECPNCGRPVA 15 (33)
T ss_dssp -EEE-TTTSSEEE
T ss_pred CeEECCCCcCCcc
Confidence 3468999998875
No 86
>TIGR02183 GRXA Glutaredoxin, GrxA family. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase.
Probab=21.99 E-value=27 Score=23.30 Aligned_cols=16 Identities=31% Similarity=0.530 Sum_probs=12.4
Q ss_pred CCCCCccccccccccc
Q 031772 12 ACRCPLCRRRITLLIP 27 (153)
Q Consensus 12 ~~~CP~CR~~i~~L~p 27 (153)
.-.||+|++--.+|-.
T Consensus 7 ~~~Cp~C~~ak~~L~~ 22 (86)
T TIGR02183 7 RPGCPYCVRAKQLAEK 22 (86)
T ss_pred CCCCccHHHHHHHHHH
Confidence 3489999988887654
No 87
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=21.95 E-value=36 Score=22.15 Aligned_cols=14 Identities=29% Similarity=0.923 Sum_probs=10.2
Q ss_pred CCCCCCCccccccc
Q 031772 10 LQACRCPLCRRRIT 23 (153)
Q Consensus 10 ~~~~~CP~CR~~i~ 23 (153)
+.-.-||.|+.+..
T Consensus 6 LeiLaCP~~kg~L~ 19 (60)
T COG2835 6 LEILACPVCKGPLV 19 (60)
T ss_pred heeeeccCcCCcce
Confidence 34567999999833
No 88
>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=21.64 E-value=62 Score=18.18 Aligned_cols=13 Identities=23% Similarity=0.700 Sum_probs=6.6
Q ss_pred CCCCCCccccccc
Q 031772 11 QACRCPLCRRRIT 23 (153)
Q Consensus 11 ~~~~CP~CR~~i~ 23 (153)
....||.|..++.
T Consensus 25 ~~~~CP~Cg~~~~ 37 (41)
T smart00834 25 PLATCPECGGDVR 37 (41)
T ss_pred CCCCCCCCCCcce
Confidence 3455666655433
No 89
>PF04186 FxsA: FxsA cytoplasmic membrane protein ; InterPro: IPR007313 This is a bacterial family of cytoplasmic membrane proteins. It includes two transmembrane regions. The molecular function of FxsA is unknown, but in Escherichia coli its overexpression has been shown to alleviate the exclusion of phage T7 in those cells with an F plasmid.; GO: 0016020 membrane
Probab=21.44 E-value=3.2e+02 Score=19.67 Aligned_cols=27 Identities=41% Similarity=0.555 Sum_probs=21.7
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 031772 123 GLLDDLLIALLCFLHVAALYRAVLYNR 149 (153)
Q Consensus 123 G~lDD~~v~~~~l~~v~~~yr~~~~~r 149 (153)
|++-|++=+++++--+-..+++.+.+|
T Consensus 84 GflTD~lGllLllP~~R~~~~~~l~~~ 110 (119)
T PF04186_consen 84 GFLTDILGLLLLLPPVRRLLRRLLMKR 110 (119)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 889999888888887778777776655
No 90
>TIGR00645 HI0507 conserved hypothetical transmembrane protein. This conserved hypothetical protein with four predicted transmembrane regions is found in E. coli, Haemophilus influenzae, and Helicobacter pylori, among completed genomes. A similar protein from Aquifex aeolicus appears to share a central region of homology and a similar overall arrangement of hydrophobic stretches, and forms a bidirectional best hit with several members of the seed alignment. However, it is uncertain whether the observed similarity represents full-length homology and/or equivalent function, and so it is excluded from the seed and scores below the trusted cutoff.
Probab=21.38 E-value=89 Score=24.30 Aligned_cols=33 Identities=24% Similarity=0.401 Sum_probs=29.0
Q ss_pred CccchhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 031772 115 PEALLGIVGLLDDLLIALLCFLHVAALYRAVLY 147 (153)
Q Consensus 115 Pd~i~g~lG~lDD~~v~~~~l~~v~~~yr~~~~ 147 (153)
-|.+.+++|.+|-..+..+++.-.-+.|..++.
T Consensus 51 ~~~il~vl~lID~~Lia~lLlIv~~ggYElFIS 83 (167)
T TIGR00645 51 NDLMLGVLNLVDVVMIAGLLVMVTIGGYEIFVS 83 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccHhHhhc
Confidence 356789999999999999999999999998875
No 91
>PHA03050 glutaredoxin; Provisional
Probab=21.34 E-value=25 Score=24.91 Aligned_cols=15 Identities=33% Similarity=0.970 Sum_probs=11.9
Q ss_pred CCCCCCccccccccc
Q 031772 11 QACRCPLCRRRITLL 25 (153)
Q Consensus 11 ~~~~CP~CR~~i~~L 25 (153)
..-.||+|++--.+|
T Consensus 19 s~~~CPyC~~ak~~L 33 (108)
T PHA03050 19 VKFTCPFCRNALDIL 33 (108)
T ss_pred ECCCChHHHHHHHHH
Confidence 456799999887776
No 92
>cd01283 cytidine_deaminase Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.
Probab=20.82 E-value=28 Score=24.36 Aligned_cols=17 Identities=24% Similarity=0.729 Sum_probs=13.6
Q ss_pred CCCCcccccccccccCC
Q 031772 13 CRCPLCRRRITLLIPND 29 (153)
Q Consensus 13 ~~CP~CR~~i~~L~p~~ 29 (153)
-=|++||+.+..+.+.+
T Consensus 78 sPC~~C~~~l~~~~~~~ 94 (112)
T cd01283 78 SPCGACRQVLAEFLPSR 94 (112)
T ss_pred CCCHHHHHHHHHhCCCC
Confidence 45999999999887643
No 93
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.80 E-value=31 Score=21.62 Aligned_cols=13 Identities=31% Similarity=0.884 Sum_probs=10.1
Q ss_pred CCCCCCccccccc
Q 031772 11 QACRCPLCRRRIT 23 (153)
Q Consensus 11 ~~~~CP~CR~~i~ 23 (153)
-.--||.|-++++
T Consensus 11 p~KICpvCqRPFs 23 (54)
T COG4338 11 PDKICPVCQRPFS 23 (54)
T ss_pred chhhhhhhcCchH
Confidence 3445999999887
No 94
>PRK06386 replication factor A; Reviewed
Probab=20.75 E-value=39 Score=29.39 Aligned_cols=17 Identities=18% Similarity=0.600 Sum_probs=12.9
Q ss_pred CCCCcccccccc-cccCC
Q 031772 13 CRCPLCRRRITL-LIPND 29 (153)
Q Consensus 13 ~~CP~CR~~i~~-L~p~~ 29 (153)
-+||-|++.+.. -||..
T Consensus 237 ~rCP~C~R~l~~g~C~~H 254 (358)
T PRK06386 237 TKCSVCNKIIEDGVCKDH 254 (358)
T ss_pred ecCcCCCeEccCCcCCCC
Confidence 479999999975 46654
No 95
>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=20.71 E-value=54 Score=19.23 Aligned_cols=16 Identities=19% Similarity=0.538 Sum_probs=11.9
Q ss_pred CCCCCCCcccc-ccccc
Q 031772 10 LQACRCPLCRR-RITLL 25 (153)
Q Consensus 10 ~~~~~CP~CR~-~i~~L 25 (153)
-.+..||-|.+ .+..+
T Consensus 24 ~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 24 DDPVPCPECGSTEVRRV 40 (42)
T ss_pred CCCCcCCCCCCCceEEe
Confidence 46899999998 55443
No 96
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=20.70 E-value=53 Score=28.51 Aligned_cols=19 Identities=16% Similarity=0.340 Sum_probs=13.3
Q ss_pred CcccccCC-----CCCCCCCCccc
Q 031772 1 MLVWDHGS-----TLQACRCPLCR 19 (153)
Q Consensus 1 ~~yW~~~~-----~~~~~~CP~CR 19 (153)
+.||.+.= .-.|-|||+|-
T Consensus 42 ~~~~~~pm~p~~~~~~pg~~p~~~ 65 (409)
T PRK09783 42 VLFWYDPMYPNTRFDKPGKSPFMD 65 (409)
T ss_pred eEEEeCCCCCCcCCCCCCCCCCCC
Confidence 35888771 13588999994
No 97
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=20.52 E-value=1.2e+02 Score=22.50 Aligned_cols=30 Identities=27% Similarity=0.587 Sum_probs=17.3
Q ss_pred CCCCCCcccccccccccCCCcccccCChHHHHHHHHHHH
Q 031772 11 QACRCPLCRRRITLLIPNDDSLRQRHDPAVGDILQKVES 49 (153)
Q Consensus 11 ~~~~CP~CR~~i~~L~p~~~~~~~~~d~~~~~v~~~i~~ 49 (153)
.-.+||.|- +++..+-+.+..++++.+|.+
T Consensus 39 ~~LRC~vCq---------nqsiadSna~iA~dmR~~Vr~ 68 (126)
T PRK10144 39 SQLRCPQCQ---------NQNLLESNAPVAVSMRHQVYS 68 (126)
T ss_pred HcCCCCCCC---------CCChhhcCCHHHHHHHHHHHH
Confidence 457899997 333333345555556655543
No 98
>PRK00112 tgt queuine tRNA-ribosyltransferase; Provisional
Probab=20.46 E-value=57 Score=28.23 Aligned_cols=11 Identities=36% Similarity=0.927 Sum_probs=9.2
Q ss_pred CCCCCCCcccc
Q 031772 10 LQACRCPLCRR 20 (153)
Q Consensus 10 ~~~~~CP~CR~ 20 (153)
..+|+||.|+.
T Consensus 301 ~~~C~C~~C~~ 311 (366)
T PRK00112 301 DPECDCYTCRN 311 (366)
T ss_pred CCCCCCcccCc
Confidence 45999999983
No 99
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=20.41 E-value=25 Score=23.85 Aligned_cols=14 Identities=29% Similarity=0.653 Sum_probs=8.0
Q ss_pred CCCCCccccccccc
Q 031772 12 ACRCPLCRRRITLL 25 (153)
Q Consensus 12 ~~~CP~CR~~i~~L 25 (153)
.-.||+|++--..+
T Consensus 14 ~~~C~~C~~~~~~~ 27 (112)
T PF13098_consen 14 DPWCPYCKKLEKEL 27 (112)
T ss_dssp -TT-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHHH
Confidence 45799999554433
No 100
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.17 E-value=44 Score=19.37 Aligned_cols=10 Identities=30% Similarity=1.099 Sum_probs=7.6
Q ss_pred CCCccccccc
Q 031772 14 RCPLCRRRIT 23 (153)
Q Consensus 14 ~CP~CR~~i~ 23 (153)
+||-|+....
T Consensus 1 ~CP~C~~~l~ 10 (41)
T PF13453_consen 1 KCPRCGTELE 10 (41)
T ss_pred CcCCCCcccc
Confidence 6999987544
No 101
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=20.03 E-value=1e+02 Score=19.97 Aligned_cols=19 Identities=26% Similarity=0.539 Sum_probs=15.0
Q ss_pred CCCCcccccccccccCCCc
Q 031772 13 CRCPLCRRRITLLIPNDDS 31 (153)
Q Consensus 13 ~~CP~CR~~i~~L~p~~~~ 31 (153)
-+||.|-.....-.|...+
T Consensus 18 e~Cp~CG~~t~~~~PprFS 36 (59)
T COG2260 18 EKCPVCGGDTKVPHPPRFS 36 (59)
T ss_pred ccCCCCCCccccCCCCCCC
Confidence 6899999888777887644
Done!