Query psy15037
Match_columns 149
No_of_seqs 138 out of 323
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 18:49:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15037.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15037hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0006|consensus 99.9 2.8E-23 6E-28 180.9 4.6 92 4-135 329-421 (446)
2 KOG1814|consensus 99.8 1.4E-22 3.1E-27 179.5 0.6 104 3-134 286-391 (445)
3 KOG1815|consensus 99.4 1.4E-13 3.1E-18 121.8 2.9 83 6-143 175-262 (444)
4 KOG1812|consensus 99.4 2.2E-13 4.7E-18 119.7 3.1 77 6-136 254-331 (384)
5 smart00647 IBR In Between Ring 98.1 2.3E-06 4.9E-11 55.7 2.2 29 5-33 35-64 (64)
6 PF01485 IBR: IBR domain; Int 97.9 5.7E-06 1.2E-10 53.6 1.5 22 10-31 40-61 (64)
7 smart00647 IBR In Between Ring 92.4 0.22 4.7E-06 31.9 3.6 31 103-133 8-44 (64)
8 PF01485 IBR: IBR domain; Int 87.0 0.3 6.5E-06 31.2 0.9 26 109-134 16-45 (64)
9 PF03119 DNA_ligase_ZBD: NAD-d 79.9 1.7 3.6E-05 25.3 2.0 25 113-137 1-25 (28)
10 COG3357 Predicted transcriptio 75.4 1.2 2.6E-05 33.3 0.6 21 9-29 57-87 (97)
11 PF13920 zf-C3HC4_3: Zinc fing 71.2 3.3 7.2E-05 25.9 1.9 14 110-123 36-49 (50)
12 PF10571 UPF0547: Uncharacteri 69.0 2.2 4.7E-05 24.5 0.6 11 10-20 14-24 (26)
13 PF14446 Prok-RING_1: Prokaryo 68.0 2.9 6.4E-05 28.1 1.1 20 10-29 5-32 (54)
14 PF09538 FYDLN_acid: Protein o 66.5 4.3 9.3E-05 30.5 1.9 23 9-31 8-39 (108)
15 PF13717 zinc_ribbon_4: zinc-r 65.2 3.4 7.4E-05 25.1 1.0 14 7-20 22-35 (36)
16 PF13639 zf-RING_2: Ring finge 60.9 1.2 2.7E-05 27.1 -1.6 23 6-29 12-34 (44)
17 PF13719 zinc_ribbon_5: zinc-r 60.5 4.8 0.0001 24.4 1.0 13 8-20 23-35 (37)
18 PRK09710 lar restriction allev 59.7 5.6 0.00012 27.7 1.3 16 109-124 4-19 (64)
19 PF09297 zf-NADH-PPase: NADH p 59.6 10 0.00022 22.0 2.3 23 110-132 2-24 (32)
20 PF13913 zf-C2HC_2: zinc-finge 59.2 4.7 0.0001 22.6 0.8 11 10-20 2-12 (25)
21 PF07975 C1_4: TFIIH C1-like d 57.8 3.1 6.7E-05 27.6 -0.2 23 8-30 19-41 (51)
22 PF13465 zf-H2C2_2: Zinc-finge 56.4 5.7 0.00012 22.1 0.8 14 7-20 11-24 (26)
23 PF13248 zf-ribbon_3: zinc-rib 55.6 6.2 0.00013 22.2 0.9 14 111-124 2-15 (26)
24 KOG1812|consensus 52.8 5.7 0.00012 35.5 0.6 25 5-30 319-343 (384)
25 TIGR02098 MJ0042_CXXC MJ0042 f 51.9 8.8 0.00019 22.7 1.2 11 10-20 25-35 (38)
26 PF15227 zf-C3HC4_4: zinc fing 51.7 3.1 6.7E-05 25.8 -0.9 15 15-29 15-29 (42)
27 PF06827 zf-FPG_IleRS: Zinc fi 51.5 8.5 0.00019 21.9 1.0 13 112-124 2-14 (30)
28 smart00834 CxxC_CXXC_SSSS Puta 50.9 10 0.00022 22.4 1.3 15 110-124 25-39 (41)
29 cd00162 RING RING-finger (Real 47.7 17 0.00036 20.6 1.9 17 105-121 29-45 (45)
30 PF13923 zf-C3HC4_2: Zinc fing 47.7 4.2 9.1E-05 24.2 -0.7 20 10-29 11-30 (39)
31 PF14835 zf-RING_6: zf-RING of 46.4 10 0.00022 26.5 0.9 26 110-135 6-34 (65)
32 PF13240 zinc_ribbon_2: zinc-r 45.8 5.7 0.00012 22.0 -0.3 13 109-121 11-23 (23)
33 cd00065 FYVE FYVE domain; Zinc 45.1 9.3 0.0002 24.1 0.6 19 8-26 16-34 (57)
34 PF01096 TFIIS_C: Transcriptio 44.2 9.3 0.0002 23.4 0.4 6 12-17 2-7 (39)
35 PRK01103 formamidopyrimidine/5 44.1 13 0.00027 31.4 1.3 14 111-124 245-258 (274)
36 PRK14810 formamidopyrimidine-D 42.6 14 0.0003 31.3 1.3 14 111-124 244-257 (272)
37 PRK14811 formamidopyrimidine-D 42.6 13 0.00029 31.3 1.3 14 111-124 235-248 (269)
38 PF13894 zf-C2H2_4: C2H2-type 42.3 11 0.00024 19.0 0.5 10 12-21 2-11 (24)
39 PF09986 DUF2225: Uncharacteri 41.1 11 0.00025 30.7 0.6 13 10-22 48-60 (214)
40 smart00064 FYVE Protein presen 40.8 12 0.00025 24.6 0.5 18 9-26 25-42 (68)
41 TIGR00577 fpg formamidopyrimid 40.5 15 0.00033 30.9 1.3 14 111-124 245-258 (272)
42 PRK10445 endonuclease VIII; Pr 40.0 16 0.00035 30.7 1.3 14 111-124 235-248 (263)
43 PF00096 zf-C2H2: Zinc finger, 39.9 11 0.00024 19.5 0.3 9 12-20 2-10 (23)
44 PRK13945 formamidopyrimidine-D 39.8 16 0.00034 31.0 1.3 14 111-124 254-267 (282)
45 PF01363 FYVE: FYVE zinc finge 39.3 13 0.00027 24.5 0.5 17 9-25 24-40 (69)
46 PF11023 DUF2614: Protein of u 38.2 15 0.00033 28.2 0.9 22 8-29 67-96 (114)
47 TIGR03655 anti_R_Lar restricti 38.2 28 0.00061 22.3 2.0 12 111-122 1-12 (53)
48 smart00184 RING Ring finger. E 37.0 6 0.00013 21.6 -1.2 16 14-29 14-29 (39)
49 PF07191 zinc-ribbons_6: zinc- 35.0 33 0.00072 24.2 2.1 19 113-133 3-21 (70)
50 PF01428 zf-AN1: AN1-like Zinc 34.2 17 0.00036 22.5 0.4 17 9-25 12-28 (43)
51 TIGR02300 FYDLN_acid conserved 34.0 22 0.00048 27.8 1.2 23 9-31 8-39 (129)
52 PF10276 zf-CHCC: Zinc-finger 33.6 22 0.00047 22.4 0.9 11 10-20 29-39 (40)
53 COG5540 RING-finger-containing 33.5 26 0.00056 31.6 1.6 18 104-121 354-371 (374)
54 PRK14559 putative protein seri 33.0 27 0.00059 33.5 1.8 8 11-18 2-9 (645)
55 PF14803 Nudix_N_2: Nudix N-te 32.7 22 0.00047 21.6 0.8 15 6-20 18-32 (34)
56 TIGR00622 ssl1 transcription f 32.6 21 0.00046 27.2 0.9 23 9-31 80-102 (112)
57 PF13453 zf-TFIIB: Transcripti 32.6 23 0.0005 21.5 0.9 12 113-124 1-12 (41)
58 PF00097 zf-C3HC4: Zinc finger 32.2 9.2 0.0002 22.5 -0.9 17 13-29 14-30 (41)
59 smart00154 ZnF_AN1 AN1-like Zi 32.1 22 0.00048 21.9 0.7 14 10-23 12-25 (39)
60 PF14354 Lar_restr_allev: Rest 30.2 29 0.00063 22.3 1.1 12 110-121 2-13 (61)
61 PF06677 Auto_anti-p27: Sjogre 30.1 45 0.00099 21.0 1.9 14 110-123 16-29 (41)
62 COG3024 Uncharacterized protei 29.8 26 0.00057 24.5 0.9 15 109-123 5-19 (65)
63 PF09723 Zn-ribbon_8: Zinc rib 29.4 38 0.00082 20.9 1.5 15 110-124 25-40 (42)
64 COG0266 Nei Formamidopyrimidin 29.0 29 0.00064 30.1 1.2 15 110-124 244-258 (273)
65 KOG1815|consensus 28.8 30 0.00064 31.2 1.3 25 6-30 240-266 (444)
66 PF14205 Cys_rich_KTR: Cystein 28.7 29 0.00063 23.6 0.9 19 11-29 5-39 (55)
67 PHA02707 hypothetical protein; 28.7 17 0.00036 22.5 -0.2 12 128-139 3-14 (37)
68 PRK00464 nrdR transcriptional 28.1 30 0.00065 27.4 1.1 14 9-22 27-40 (154)
69 PF14787 zf-CCHC_5: GAG-polypr 27.7 34 0.00073 21.4 1.0 18 20-37 4-22 (36)
70 PF07282 OrfB_Zn_ribbon: Putat 27.2 48 0.001 21.7 1.8 14 110-123 27-40 (69)
71 PHA02929 N1R/p28-like protein; 27.0 19 0.00042 30.4 -0.2 25 13-37 197-223 (238)
72 TIGR00155 pqiA_fam integral me 26.9 41 0.00088 30.3 1.8 20 1-20 4-23 (403)
73 PRK00420 hypothetical protein; 26.7 42 0.00091 25.5 1.6 17 110-126 22-39 (112)
74 smart00661 RPOL9 RNA polymeras 26.5 42 0.00091 20.7 1.3 10 10-19 20-29 (52)
75 PF02318 FYVE_2: FYVE-type zin 26.3 31 0.00067 25.5 0.8 20 8-27 69-88 (118)
76 smart00355 ZnF_C2H2 zinc finge 26.2 30 0.00065 17.3 0.5 11 12-22 2-12 (26)
77 KOG0320|consensus 25.5 19 0.00041 29.9 -0.5 11 14-24 149-159 (187)
78 PHA02325 hypothetical protein 25.4 34 0.00073 24.2 0.8 11 110-120 2-12 (72)
79 COG3809 Uncharacterized protei 25.3 34 0.00074 25.1 0.8 20 11-30 2-33 (88)
80 KOG3084|consensus 25.1 73 0.0016 28.7 3.0 42 102-144 142-193 (345)
81 PRK00398 rpoP DNA-directed RNA 24.9 74 0.0016 19.6 2.3 12 111-122 21-32 (46)
82 PRK03564 formate dehydrogenase 24.8 58 0.0013 28.7 2.3 24 7-30 184-224 (309)
83 PHA02926 zinc finger-like prot 24.5 17 0.00037 31.1 -0.9 19 11-29 192-210 (242)
84 PF04216 FdhE: Protein involve 24.0 37 0.00081 28.6 1.0 23 8-30 170-209 (290)
85 KOG0317|consensus 23.6 23 0.00049 31.2 -0.4 26 12-37 253-280 (293)
86 PRK00241 nudC NADH pyrophospha 23.3 69 0.0015 26.9 2.4 25 108-132 96-120 (256)
87 PF14353 CpXC: CpXC protein 23.2 36 0.00078 25.1 0.6 12 110-121 37-48 (128)
88 TIGR01562 FdhE formate dehydro 23.2 61 0.0013 28.4 2.2 23 8-30 182-222 (305)
89 PRK03824 hypA hydrogenase nick 23.2 39 0.00085 25.8 0.9 13 8-20 68-80 (135)
90 COG2176 PolC DNA polymerase II 23.2 40 0.00086 35.3 1.1 16 110-125 938-953 (1444)
91 PF03884 DUF329: Domain of unk 23.0 27 0.00059 23.6 -0.0 14 111-124 2-15 (57)
92 cd04476 RPA1_DBD_C RPA1_DBD_C: 22.2 62 0.0013 24.7 1.8 34 110-143 33-75 (166)
93 TIGR02605 CxxC_CxxC_SSSS putat 22.2 60 0.0013 20.2 1.4 15 110-124 25-40 (52)
94 PF09889 DUF2116: Uncharacteri 22.1 44 0.00095 22.7 0.8 14 111-124 3-16 (59)
95 PF10083 DUF2321: Uncharacteri 20.7 59 0.0013 26.3 1.5 14 111-124 39-52 (158)
96 PF15470 DUF4637: Domain of un 20.6 42 0.00091 27.3 0.6 20 8-27 129-148 (173)
97 PRK14892 putative transcriptio 20.5 60 0.0013 24.1 1.3 11 7-17 18-28 (99)
98 PRK08665 ribonucleotide-diphos 20.5 57 0.0012 31.8 1.6 16 113-128 726-741 (752)
99 PF14569 zf-UDP: Zinc-binding 20.5 60 0.0013 23.6 1.3 22 107-128 47-68 (80)
No 1
>KOG0006|consensus
Probab=99.88 E-value=2.8e-23 Score=180.90 Aligned_cols=92 Identities=43% Similarity=0.803 Sum_probs=80.5
Q ss_pred CCCCCCcccCCc-cCccccccccccccCCCCCCccccCcCCCCCCCcccCCcccccccccccCCCCCCCccccccccCCC
Q psy15037 4 GEDGCKRIGCTE-CGFVFCKDCLQGAHIGPCDPGRTSMDQGGASTSDYAVDPTRASQDCLQGAHIGPCDPERTSMDQGGA 82 (149)
Q Consensus 4 ~e~~~~~v~Cp~-C~~aFC~~Cke~WH~g~C~~~~~~~~~~~~~~~~y~~~~~~~~~~~l~~~~~~~~~~~r~~m~~~~~ 82 (149)
.||+.++++|++ |+|+||+.|++.||.+.|..--+ ++ +.
T Consensus 329 ~EPD~rkvtC~~gCgf~FCR~C~e~yh~geC~~~~~------as----------------------------------~t 368 (446)
T KOG0006|consen 329 PEPDQRKVTCEGGCGFAFCRECKEAYHEGECSAVFE------AS----------------------------------GT 368 (446)
T ss_pred cCCCCCcccCCCCchhHhHHHHHhhhccccceeeec------cc----------------------------------cc
Confidence 589999999995 99999999999999999984332 11 12
Q ss_pred CCCcccCChhHHhhhhhHHhhHHHHHhcCcCCCCCCcceeecCCcceeEeCCC
Q psy15037 83 STSDYAVDPTRASQARWDDASQVTIKVSTKPCPSCRTATERAGKGVYAYDLYP 135 (149)
Q Consensus 83 ~e~~Yg~d~~~~~~~~~e~~s~~~I~~ntK~CP~C~~~IEK~~GCNhM~~~~~ 135 (149)
-+..|.+|++++.+++||++|..+|+++|||||+|++|+||||||+||.|--|
T Consensus 369 ~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~ 421 (446)
T KOG0006|consen 369 TTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQP 421 (446)
T ss_pred cceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCC
Confidence 24568899999999999999999999999999999999999999999999765
No 2
>KOG1814|consensus
Probab=99.84 E-value=1.4e-22 Score=179.46 Aligned_cols=104 Identities=23% Similarity=0.373 Sum_probs=81.0
Q ss_pred CCCCCCCcccCCccCccccccccccccCC-CCCCccccCcCCCCCCCcccCCcccccccccccCCCCCCCccccccccCC
Q psy15037 3 EGEDGCKRIGCTECGFVFCKDCLQGAHIG-PCDPGRTSMDQGGASTSDYAVDPTRASQDCLQGAHIGPCDPERTSMDQGG 81 (149)
Q Consensus 3 ~~e~~~~~v~Cp~C~~aFC~~Cke~WH~g-~C~~~~~~~~~~~~~~~~y~~~~~~~~~~~l~~~~~~~~~~~r~~m~~~~ 81 (149)
..||+..+++|.+|+|+||+.|+.+||+. +|....++ +...| -+++++ +++|+ +
T Consensus 286 ~~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~------~~~l~--------~~~~~~------d~a~k-----~ 340 (445)
T KOG1814|consen 286 KQDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEK------LIELY--------LEYLEA------DEARK-----R 340 (445)
T ss_pred ccCchhhhhhhccCccHHHHHHHHhhcCCCcccCchHH------HHHHH--------HHHhhc------CHHHH-----H
Confidence 46889999999999999999999999985 79987541 11111 124443 23244 3
Q ss_pred CCCCcccCChhHHhhh-hhHHhhHHHHHhcCcCCCCCCcceeecCCcceeEeCC
Q psy15037 82 ASTSDYAVDPTRASQA-RWDDASQVTIKVSTKPCPSCRTATERAGKGVYAYDLY 134 (149)
Q Consensus 82 ~~e~~Yg~d~~~~~~~-~~e~~s~~~I~~ntK~CP~C~~~IEK~~GCNhM~~~~ 134 (149)
.+++||| +|+++. +.+..++.||..|+|+||+|.++|||++|||||+|..
T Consensus 341 ele~Ryg---~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~ 391 (445)
T KOG1814|consen 341 ELEKRYG---KRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTK 391 (445)
T ss_pred HHHHHhh---HHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeecc
Confidence 5678999 677764 4467889999999999999999999999999999974
No 3
>KOG1815|consensus
Probab=99.39 E-value=1.4e-13 Score=121.83 Aligned_cols=83 Identities=25% Similarity=0.450 Sum_probs=61.8
Q ss_pred CCCCcccCCccCccccccccccccCC-CCCCccccCcCCCCCCCcccCCcccccccccccCCCCCCCccccccccCCCCC
Q psy15037 6 DGCKRIGCTECGFVFCKDCLQGAHIG-PCDPGRTSMDQGGASTSDYAVDPTRASQDCLQGAHIGPCDPERTSMDQGGAST 84 (149)
Q Consensus 6 ~~~~~v~Cp~C~~aFC~~Cke~WH~g-~C~~~~~~~~~~~~~~~~y~~~~~~~~~~~l~~~~~~~~~~~r~~m~~~~~~e 84 (149)
.....|.|. |+..||+.|+..||.+ .|.....+ ++++
T Consensus 175 ~~~~~v~C~-~g~~FC~~C~~~~H~p~~C~~~~~w---------------------------l~k~-------------- 212 (444)
T KOG1815|consen 175 LESVEVDCG-CGHEFCFACGEESHSPVSCPGAKKW---------------------------LKKC-------------- 212 (444)
T ss_pred CCccceeCC-CCchhHhhccccccCCCcccchHHH---------------------------HHhh--------------
Confidence 456678886 5569999999999987 69886541 1111
Q ss_pred CcccCChhHHhhhhhHHhhHHHHHhcCcCCCCCCcceeecCCcceeEeCC----Cceeeeeec
Q psy15037 85 SDYAVDPTRASQARWDDASQVTIKVSTKPCPSCRTATERAGKGVYAYDLY----PMFIPLVLG 143 (149)
Q Consensus 85 ~~Yg~d~~~~~~~~~e~~s~~~I~~ntK~CP~C~~~IEK~~GCNhM~~~~----~~~~~~~~~ 143 (149)
..+....+||..|||+||+|..+|||++|||||+|.. -.|..+-||
T Consensus 213 -------------~~~se~~~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~ 262 (444)
T KOG1815|consen 213 -------------RDDSETINWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLA 262 (444)
T ss_pred -------------hhhhhhhhhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeec
Confidence 1122344599999999999999999999999999984 456655443
No 4
>KOG1812|consensus
Probab=99.37 E-value=2.2e-13 Score=119.72 Aligned_cols=77 Identities=21% Similarity=0.349 Sum_probs=60.8
Q ss_pred CCCCcccCCccCccccccccccccCC-CCCCccccCcCCCCCCCcccCCcccccccccccCCCCCCCccccccccCCCCC
Q psy15037 6 DGCKRIGCTECGFVFCKDCLQGAHIG-PCDPGRTSMDQGGASTSDYAVDPTRASQDCLQGAHIGPCDPERTSMDQGGAST 84 (149)
Q Consensus 6 ~~~~~v~Cp~C~~aFC~~Cke~WH~g-~C~~~~~~~~~~~~~~~~y~~~~~~~~~~~l~~~~~~~~~~~r~~m~~~~~~e 84 (149)
+......|+.|+..||..|+.+||.+ .|...++.. .
T Consensus 254 ~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~-------------------------------------------~ 290 (384)
T KOG1812|consen 254 VKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLN-------------------------------------------P 290 (384)
T ss_pred hhhcccccccCCCceeecCCCcCCCCCCHHHHHHhC-------------------------------------------C
Confidence 55667789999999999999999976 688766410 0
Q ss_pred CcccCChhHHhhhhhHHhhHHHHHhcCcCCCCCCcceeecCCcceeEeCCCc
Q psy15037 85 SDYAVDPTRASQARWDDASQVTIKVSTKPCPSCRTATERAGKGVYAYDLYPM 136 (149)
Q Consensus 85 ~~Yg~d~~~~~~~~~e~~s~~~I~~ntK~CP~C~~~IEK~~GCNhM~~~~~~ 136 (149)
..| .+....+|+..+++.||+|+.-||+++|||||+|....
T Consensus 291 ~~~-----------~d~~~~~~la~~wr~CpkC~~~ie~~~GCnhm~CrC~~ 331 (384)
T KOG1812|consen 291 EEY-----------VDDITLKYLAKRWRQCPKCKFMIELSEGCNHMTCRCGH 331 (384)
T ss_pred ccc-----------ccHHHHHHHHHhcCcCcccceeeeecCCcceEEeeccc
Confidence 011 13456778889999999999999999999999997654
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.07 E-value=2.3e-06 Score=55.68 Aligned_cols=29 Identities=45% Similarity=1.158 Sum_probs=25.4
Q ss_pred CCCCCcccCCccCccccccccccccCC-CC
Q psy15037 5 EDGCKRIGCTECGFVFCKDCLQGAHIG-PC 33 (149)
Q Consensus 5 e~~~~~v~Cp~C~~aFC~~Cke~WH~g-~C 33 (149)
+++...+.|+.|++.||+.|+..||.+ .|
T Consensus 35 ~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 35 EEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 347789999999999999999999976 45
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=97.88 E-value=5.7e-06 Score=53.64 Aligned_cols=22 Identities=36% Similarity=0.827 Sum_probs=20.3
Q ss_pred cccCCccCccccccccccccCC
Q psy15037 10 RIGCTECGFVFCKDCLQGAHIG 31 (149)
Q Consensus 10 ~v~Cp~C~~aFC~~Cke~WH~g 31 (149)
.++|+.|++.||+.|+..||.+
T Consensus 40 ~~~C~~C~~~fC~~C~~~~H~~ 61 (64)
T PF01485_consen 40 IVTCPSCGTEFCFKCGEPWHEG 61 (64)
T ss_dssp -CCTTSCCSEECSSSTSESCTT
T ss_pred eeECCCCCCcCccccCcccCCC
Confidence 3999999999999999999976
No 7
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=92.41 E-value=0.22 Score=31.94 Aligned_cols=31 Identities=16% Similarity=0.125 Sum_probs=25.1
Q ss_pred hHHHHHh--cCcCCC--CCCcceeecC--CcceeEeC
Q psy15037 103 SQVTIKV--STKPCP--SCRTATERAG--KGVYAYDL 133 (149)
Q Consensus 103 s~~~I~~--ntK~CP--~C~~~IEK~~--GCNhM~~~ 133 (149)
.+.+|.. +.+.|| +|...|+... |.++++|.
T Consensus 8 ~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~ 44 (64)
T smart00647 8 LESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCP 44 (64)
T ss_pred HHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECC
Confidence 4566665 688899 9999999975 89999983
No 8
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=86.96 E-value=0.3 Score=31.17 Aligned_cols=26 Identities=15% Similarity=0.188 Sum_probs=15.7
Q ss_pred hcCcCCCC--CCcceeecCCcce--eEeCC
Q psy15037 109 VSTKPCPS--CRTATERAGKGVY--AYDLY 134 (149)
Q Consensus 109 ~ntK~CP~--C~~~IEK~~GCNh--M~~~~ 134 (149)
.+.+.||+ |...|++..|.++ |+|..
T Consensus 16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~ 45 (64)
T PF01485_consen 16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCPS 45 (64)
T ss_dssp --CC--TTSST---ECS-SSTTS--CCTTS
T ss_pred CCccCCCCCCCcccEEecCCCCCCeeECCC
Confidence 34579988 9999999999999 89873
No 9
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=79.86 E-value=1.7 Score=25.28 Aligned_cols=25 Identities=24% Similarity=0.365 Sum_probs=15.8
Q ss_pred CCCCCCcceeecCCcceeEeCCCce
Q psy15037 113 PCPSCRTATERAGKGVYAYDLYPMF 137 (149)
Q Consensus 113 ~CP~C~~~IEK~~GCNhM~~~~~~~ 137 (149)
.||.|++++.+..|=-...|.+++.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~N~l~ 25 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCPNPLS 25 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE--CGC
T ss_pred CcCCCCCEeEcCCCCEeEECCCCCc
Confidence 4999999999999988888877643
No 10
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=75.38 E-value=1.2 Score=33.28 Aligned_cols=21 Identities=33% Similarity=0.910 Sum_probs=15.6
Q ss_pred CcccCCccCccc----------ccccccccc
Q psy15037 9 KRIGCTECGFVF----------CKDCLQGAH 29 (149)
Q Consensus 9 ~~v~Cp~C~~aF----------C~~Cke~WH 29 (149)
+++.|-.|||.| |+.||..|=
T Consensus 57 ~Pa~CkkCGfef~~~~ik~pSRCP~CKSE~I 87 (97)
T COG3357 57 RPARCKKCGFEFRDDKIKKPSRCPKCKSEWI 87 (97)
T ss_pred cChhhcccCccccccccCCcccCCcchhhcc
Confidence 567899999999 556665554
No 11
>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=71.17 E-value=3.3 Score=25.91 Aligned_cols=14 Identities=43% Similarity=0.930 Sum_probs=11.9
Q ss_pred cCcCCCCCCcceee
Q psy15037 110 STKPCPSCRTATER 123 (149)
Q Consensus 110 ntK~CP~C~~~IEK 123 (149)
+.+.||-|+.+|++
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 88999999999975
No 12
>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=69.04 E-value=2.2 Score=24.52 Aligned_cols=11 Identities=36% Similarity=0.951 Sum_probs=8.2
Q ss_pred cccCCccCccc
Q psy15037 10 RIGCTECGFVF 20 (149)
Q Consensus 10 ~v~Cp~C~~aF 20 (149)
...||.|||.|
T Consensus 14 ~~~Cp~CG~~F 24 (26)
T PF10571_consen 14 AKFCPHCGYDF 24 (26)
T ss_pred cCcCCCCCCCC
Confidence 34688888887
No 13
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.96 E-value=2.9 Score=28.14 Aligned_cols=20 Identities=35% Similarity=0.821 Sum_probs=17.4
Q ss_pred cccCCccCccc--------ccccccccc
Q psy15037 10 RIGCTECGFVF--------CKDCLQGAH 29 (149)
Q Consensus 10 ~v~Cp~C~~aF--------C~~Cke~WH 29 (149)
...|+.|+..| |..|+.+||
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYH 32 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCccc
Confidence 45789999877 999999999
No 14
>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=66.48 E-value=4.3 Score=30.47 Aligned_cols=23 Identities=26% Similarity=0.625 Sum_probs=19.6
Q ss_pred CcccCCccCccc---------cccccccccCC
Q psy15037 9 KRIGCTECGFVF---------CKDCLQGAHIG 31 (149)
Q Consensus 9 ~~v~Cp~C~~aF---------C~~Cke~WH~g 31 (149)
.+.+||.||..| |+.|...|...
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 466899999999 99999999854
No 15
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=65.20 E-value=3.4 Score=25.06 Aligned_cols=14 Identities=36% Similarity=1.118 Sum_probs=8.1
Q ss_pred CCCcccCCccCccc
Q psy15037 7 GCKRIGCTECGFVF 20 (149)
Q Consensus 7 ~~~~v~Cp~C~~aF 20 (149)
..+.++|+.|+.+|
T Consensus 22 ~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 22 KGRKVRCSKCGHVF 35 (36)
T ss_pred CCcEEECCCCCCEe
Confidence 34556666666554
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=60.91 E-value=1.2 Score=27.09 Aligned_cols=23 Identities=35% Similarity=0.723 Sum_probs=18.0
Q ss_pred CCCCcccCCccCcccccccccccc
Q psy15037 6 DGCKRIGCTECGFVFCKDCLQGAH 29 (149)
Q Consensus 6 ~~~~~v~Cp~C~~aFC~~Cke~WH 29 (149)
++...+..+ |+..||..|...|=
T Consensus 12 ~~~~~~~l~-C~H~fh~~Ci~~~~ 34 (44)
T PF13639_consen 12 DGEKVVKLP-CGHVFHRSCIKEWL 34 (44)
T ss_dssp TTSCEEEET-TSEEEEHHHHHHHH
T ss_pred CCCeEEEcc-CCCeeCHHHHHHHH
Confidence 345566666 99999999998884
No 17
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=60.55 E-value=4.8 Score=24.43 Aligned_cols=13 Identities=38% Similarity=1.196 Sum_probs=7.1
Q ss_pred CCcccCCccCccc
Q psy15037 8 CKRIGCTECGFVF 20 (149)
Q Consensus 8 ~~~v~Cp~C~~aF 20 (149)
.+++.|+.|+..|
T Consensus 23 ~~~vrC~~C~~~f 35 (37)
T PF13719_consen 23 GRKVRCPKCGHVF 35 (37)
T ss_pred CcEEECCCCCcEe
Confidence 4455566555554
No 18
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=59.74 E-value=5.6 Score=27.72 Aligned_cols=16 Identities=31% Similarity=0.727 Sum_probs=12.5
Q ss_pred hcCcCCCCCCcceeec
Q psy15037 109 VSTKPCPSCRTATERA 124 (149)
Q Consensus 109 ~ntK~CP~C~~~IEK~ 124 (149)
.+.||||.|...+...
T Consensus 4 d~lKPCPFCG~~~~~v 19 (64)
T PRK09710 4 DNVKPCPFCGCPSVTV 19 (64)
T ss_pred ccccCCCCCCCceeEE
Confidence 3789999998876543
No 19
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=59.58 E-value=10 Score=22.02 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=15.3
Q ss_pred cCcCCCCCCcceeecCCcceeEe
Q psy15037 110 STKPCPSCRTATERAGKGVYAYD 132 (149)
Q Consensus 110 ntK~CP~C~~~IEK~~GCNhM~~ 132 (149)
+.+-||.|..+.+.+.+=-.|.|
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C 24 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRC 24 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEE
T ss_pred CCcccCcCCccccCCCCcCEeEC
Confidence 67889999999999988777777
No 20
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=59.15 E-value=4.7 Score=22.57 Aligned_cols=11 Identities=36% Similarity=0.860 Sum_probs=9.1
Q ss_pred cccCCccCccc
Q psy15037 10 RIGCTECGFVF 20 (149)
Q Consensus 10 ~v~Cp~C~~aF 20 (149)
++.||.|+..|
T Consensus 2 l~~C~~CgR~F 12 (25)
T PF13913_consen 2 LVPCPICGRKF 12 (25)
T ss_pred CCcCCCCCCEE
Confidence 57899888888
No 21
>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=57.83 E-value=3.1 Score=27.58 Aligned_cols=23 Identities=35% Similarity=0.662 Sum_probs=13.8
Q ss_pred CCcccCCccCccccccccccccC
Q psy15037 8 CKRIGCTECGFVFCKDCLQGAHI 30 (149)
Q Consensus 8 ~~~v~Cp~C~~aFC~~Cke~WH~ 30 (149)
..+..||.|+..||..|=.-=|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTT
T ss_pred CCeEECCCCCCccccCcChhhhc
Confidence 46789999999999999666664
No 22
>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=56.44 E-value=5.7 Score=22.11 Aligned_cols=14 Identities=43% Similarity=0.804 Sum_probs=11.8
Q ss_pred CCCcccCCccCccc
Q psy15037 7 GCKRIGCTECGFVF 20 (149)
Q Consensus 7 ~~~~v~Cp~C~~aF 20 (149)
+.++..|+.|+.+|
T Consensus 11 ~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 11 GEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSEEESSSSEEE
T ss_pred CCCCCCCCCCcCee
Confidence 45778999999988
No 23
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=55.60 E-value=6.2 Score=22.16 Aligned_cols=14 Identities=21% Similarity=0.636 Sum_probs=8.6
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
++.||+|...|+.+
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 2 EMFCPNCGAEIDPD 15 (26)
T ss_pred cCCCcccCCcCCcc
Confidence 35677777766443
No 24
>KOG1812|consensus
Probab=52.83 E-value=5.7 Score=35.48 Aligned_cols=25 Identities=32% Similarity=0.901 Sum_probs=21.8
Q ss_pred CCCCCcccCCccCccccccccccccC
Q psy15037 5 EDGCKRIGCTECGFVFCKDCLQGAHI 30 (149)
Q Consensus 5 e~~~~~v~Cp~C~~aFC~~Cke~WH~ 30 (149)
..+.+.++|. |++.||..|...|+.
T Consensus 319 ~~GCnhm~Cr-C~~~fcy~C~~~~~~ 343 (384)
T KOG1812|consen 319 SEGCNHMTCR-CGHQFCYMCGGDWKT 343 (384)
T ss_pred cCCcceEEee-ccccchhhcCcchhh
Confidence 3458889999 999999999999974
No 25
>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=51.90 E-value=8.8 Score=22.73 Aligned_cols=11 Identities=36% Similarity=1.253 Sum_probs=6.2
Q ss_pred cccCCccCccc
Q psy15037 10 RIGCTECGFVF 20 (149)
Q Consensus 10 ~v~Cp~C~~aF 20 (149)
.+.||.|+..|
T Consensus 25 ~v~C~~C~~~~ 35 (38)
T TIGR02098 25 KVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEE
Confidence 45666665554
No 26
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=51.70 E-value=3.1 Score=25.80 Aligned_cols=15 Identities=40% Similarity=1.163 Sum_probs=13.4
Q ss_pred ccCcccccccccccc
Q psy15037 15 ECGFVFCKDCLQGAH 29 (149)
Q Consensus 15 ~C~~aFC~~Cke~WH 29 (149)
.||.+||..|.+.|-
T Consensus 15 ~CGH~FC~~Cl~~~~ 29 (42)
T PF15227_consen 15 PCGHSFCRSCLERLW 29 (42)
T ss_dssp SSSSEEEHHHHHHHH
T ss_pred CCcCHHHHHHHHHHH
Confidence 699999999988875
No 27
>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=51.52 E-value=8.5 Score=21.94 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=8.0
Q ss_pred cCCCCCCcceeec
Q psy15037 112 KPCPSCRTATERA 124 (149)
Q Consensus 112 K~CP~C~~~IEK~ 124 (149)
++||+|...|++.
T Consensus 2 ~~C~rC~~~~~~~ 14 (30)
T PF06827_consen 2 EKCPRCWNYIEDI 14 (30)
T ss_dssp SB-TTT--BBEEE
T ss_pred CcCccCCCcceEe
Confidence 6899999999764
No 28
>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=50.88 E-value=10 Score=22.41 Aligned_cols=15 Identities=27% Similarity=0.691 Sum_probs=12.3
Q ss_pred cCcCCCCCCcceeec
Q psy15037 110 STKPCPSCRTATERA 124 (149)
Q Consensus 110 ntK~CP~C~~~IEK~ 124 (149)
....||.|++.++|.
T Consensus 25 ~~~~CP~Cg~~~~r~ 39 (41)
T smart00834 25 PLATCPECGGDVRRL 39 (41)
T ss_pred CCCCCCCCCCcceec
Confidence 467899999988774
No 29
>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=47.72 E-value=17 Score=20.55 Aligned_cols=17 Identities=35% Similarity=0.718 Sum_probs=12.1
Q ss_pred HHHHhcCcCCCCCCcce
Q psy15037 105 VTIKVSTKPCPSCRTAT 121 (149)
Q Consensus 105 ~~I~~ntK~CP~C~~~I 121 (149)
.|++.....||.|+..+
T Consensus 29 ~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 29 KWLKSGKNTCPLCRTPI 45 (45)
T ss_pred HHHHhCcCCCCCCCCcC
Confidence 35555677899998764
No 30
>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=47.66 E-value=4.2 Score=24.23 Aligned_cols=20 Identities=35% Similarity=0.884 Sum_probs=16.9
Q ss_pred cccCCccCcccccccccccc
Q psy15037 10 RIGCTECGFVFCKDCLQGAH 29 (149)
Q Consensus 10 ~v~Cp~C~~aFC~~Cke~WH 29 (149)
.+.-..||.+||..|.+.|.
T Consensus 11 ~~~~~~CGH~fC~~C~~~~~ 30 (39)
T PF13923_consen 11 PVVVTPCGHSFCKECIEKYL 30 (39)
T ss_dssp EEEECTTSEEEEHHHHHHHH
T ss_pred cCEECCCCCchhHHHHHHHH
Confidence 45677899999999988886
No 31
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=46.39 E-value=10 Score=26.51 Aligned_cols=26 Identities=12% Similarity=0.098 Sum_probs=13.2
Q ss_pred cCcCCCCCCcceeec---CCcceeEeCCC
Q psy15037 110 STKPCPSCRTATERA---GKGVYAYDLYP 135 (149)
Q Consensus 110 ntK~CP~C~~~IEK~---~GCNhM~~~~~ 135 (149)
+.-.|++|..-.... +||-|+.|++=
T Consensus 6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~C 34 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVCLGGCEHIFCSSC 34 (65)
T ss_dssp HTTS-SSS-S--SS-B---SSS--B-TTT
T ss_pred HhcCCcHHHHHhcCCceeccCccHHHHHH
Confidence 346799999877655 89999999874
No 32
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=45.75 E-value=5.7 Score=22.01 Aligned_cols=13 Identities=38% Similarity=0.759 Sum_probs=7.0
Q ss_pred hcCcCCCCCCcce
Q psy15037 109 VSTKPCPSCRTAT 121 (149)
Q Consensus 109 ~ntK~CP~C~~~I 121 (149)
.+.+-||+|.++|
T Consensus 11 ~~~~fC~~CG~~l 23 (23)
T PF13240_consen 11 DDAKFCPNCGTPL 23 (23)
T ss_pred CcCcchhhhCCcC
Confidence 3445566665543
No 33
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=45.09 E-value=9.3 Score=24.07 Aligned_cols=19 Identities=37% Similarity=1.060 Sum_probs=15.6
Q ss_pred CCcccCCccCccccccccc
Q psy15037 8 CKRIGCTECGFVFCKDCLQ 26 (149)
Q Consensus 8 ~~~v~Cp~C~~aFC~~Cke 26 (149)
.++..|..|+.+||..|-.
T Consensus 16 ~rk~~Cr~Cg~~~C~~C~~ 34 (57)
T cd00065 16 RRRHHCRNCGRIFCSKCSS 34 (57)
T ss_pred ccccccCcCcCCcChHHcC
Confidence 4567899999999999844
No 34
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=44.16 E-value=9.3 Score=23.43 Aligned_cols=6 Identities=50% Similarity=1.652 Sum_probs=1.4
Q ss_pred cCCccC
Q psy15037 12 GCTECG 17 (149)
Q Consensus 12 ~Cp~C~ 17 (149)
.||.|+
T Consensus 2 ~Cp~Cg 7 (39)
T PF01096_consen 2 KCPKCG 7 (39)
T ss_dssp --SSS-
T ss_pred CCcCCC
Confidence 344444
No 35
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=44.15 E-value=13 Score=31.37 Aligned_cols=14 Identities=36% Similarity=0.864 Sum_probs=11.9
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
-+|||.|.++|+|.
T Consensus 245 g~pC~~Cg~~I~~~ 258 (274)
T PRK01103 245 GEPCRRCGTPIEKI 258 (274)
T ss_pred CCCCCCCCCeeEEE
Confidence 46899999999874
No 36
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.60 E-value=14 Score=31.27 Aligned_cols=14 Identities=36% Similarity=0.937 Sum_probs=12.2
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
.++||.|.++|++.
T Consensus 244 g~pCprCG~~I~~~ 257 (272)
T PRK14810 244 GEPCLNCKTPIRRV 257 (272)
T ss_pred CCcCCCCCCeeEEE
Confidence 57999999999864
No 37
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.59 E-value=13 Score=31.34 Aligned_cols=14 Identities=43% Similarity=1.073 Sum_probs=12.1
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
-++||.|.++|+|.
T Consensus 235 g~pC~~Cg~~I~~~ 248 (269)
T PRK14811 235 GQPCPRCGTPIEKI 248 (269)
T ss_pred cCCCCcCCCeeEEE
Confidence 57999999999874
No 38
>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=42.32 E-value=11 Score=18.96 Aligned_cols=10 Identities=40% Similarity=0.883 Sum_probs=5.2
Q ss_pred cCCccCcccc
Q psy15037 12 GCTECGFVFC 21 (149)
Q Consensus 12 ~Cp~C~~aFC 21 (149)
.|+.|++.|=
T Consensus 2 ~C~~C~~~~~ 11 (24)
T PF13894_consen 2 QCPICGKSFR 11 (24)
T ss_dssp E-SSTS-EES
T ss_pred CCcCCCCcCC
Confidence 4777777663
No 39
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=41.06 E-value=11 Score=30.74 Aligned_cols=13 Identities=23% Similarity=0.675 Sum_probs=10.3
Q ss_pred cccCCccCccccc
Q psy15037 10 RIGCTECGFVFCK 22 (149)
Q Consensus 10 ~v~Cp~C~~aFC~ 22 (149)
..+||+|||+|=-
T Consensus 48 V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 48 VWVCPHCGYAAFE 60 (214)
T ss_pred EEECCCCCCcccc
Confidence 4679999999843
No 40
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.52 E-value=15 Score=30.91 Aligned_cols=14 Identities=36% Similarity=0.864 Sum_probs=11.9
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
-++||.|.++|+|.
T Consensus 245 g~pC~~Cg~~I~~~ 258 (272)
T TIGR00577 245 GEPCRRCGTPIEKI 258 (272)
T ss_pred CCCCCCCCCeeEEE
Confidence 45999999999874
No 42
>PRK10445 endonuclease VIII; Provisional
Probab=39.99 E-value=16 Score=30.72 Aligned_cols=14 Identities=21% Similarity=0.622 Sum_probs=12.2
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
-++||.|..+|+|.
T Consensus 235 g~~Cp~Cg~~I~~~ 248 (263)
T PRK10445 235 GEACERCGGIIEKT 248 (263)
T ss_pred CCCCCCCCCEeEEE
Confidence 48999999999864
No 43
>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=39.86 E-value=11 Score=19.54 Aligned_cols=9 Identities=44% Similarity=1.058 Sum_probs=6.2
Q ss_pred cCCccCccc
Q psy15037 12 GCTECGFVF 20 (149)
Q Consensus 12 ~Cp~C~~aF 20 (149)
.|+.|+.+|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 477777766
No 44
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.83 E-value=16 Score=31.01 Aligned_cols=14 Identities=50% Similarity=0.966 Sum_probs=12.1
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
-+|||.|.++|+|.
T Consensus 254 g~pC~~Cg~~I~~~ 267 (282)
T PRK13945 254 GKPCRKCGTPIERI 267 (282)
T ss_pred cCCCCcCCCeeEEE
Confidence 47999999999874
No 45
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=39.26 E-value=13 Score=24.52 Aligned_cols=17 Identities=41% Similarity=1.095 Sum_probs=8.5
Q ss_pred CcccCCccCcccccccc
Q psy15037 9 KRIGCTECGFVFCKDCL 25 (149)
Q Consensus 9 ~~v~Cp~C~~aFC~~Ck 25 (149)
++-.|..||.+||..|.
T Consensus 24 rrhhCr~CG~~vC~~Cs 40 (69)
T PF01363_consen 24 RRHHCRNCGRVVCSSCS 40 (69)
T ss_dssp -EEE-TTT--EEECCCS
T ss_pred eeEccCCCCCEECCchh
Confidence 44557777777777763
No 46
>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=38.23 E-value=15 Score=28.21 Aligned_cols=22 Identities=23% Similarity=0.677 Sum_probs=17.0
Q ss_pred CCcccCCccCccc--------ccccccccc
Q psy15037 8 CKRIGCTECGFVF--------CKDCLQGAH 29 (149)
Q Consensus 8 ~~~v~Cp~C~~aF--------C~~Cke~WH 29 (149)
+..++||.|+... |..|+++=+
T Consensus 67 av~V~CP~C~K~TKmLGr~D~CM~C~~pLT 96 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGRVDACMHCKEPLT 96 (114)
T ss_pred ceeeECCCCCChHhhhchhhccCcCCCcCc
Confidence 4568899999877 777776665
No 47
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=38.21 E-value=28 Score=22.35 Aligned_cols=12 Identities=50% Similarity=0.991 Sum_probs=9.7
Q ss_pred CcCCCCCCccee
Q psy15037 111 TKPCPSCRTATE 122 (149)
Q Consensus 111 tK~CP~C~~~IE 122 (149)
.||||.|...-+
T Consensus 1 LkPCPfCGg~~~ 12 (53)
T TIGR03655 1 LKPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCCcce
Confidence 389999988765
No 48
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=37.04 E-value=6 Score=21.59 Aligned_cols=16 Identities=31% Similarity=0.980 Sum_probs=13.8
Q ss_pred CccCcccccccccccc
Q psy15037 14 TECGFVFCKDCLQGAH 29 (149)
Q Consensus 14 p~C~~aFC~~Cke~WH 29 (149)
..|+.+||..|...|-
T Consensus 14 ~~C~H~~c~~C~~~~~ 29 (39)
T smart00184 14 LPCGHTFCRSCIRKWL 29 (39)
T ss_pred ecCCChHHHHHHHHHH
Confidence 4699999999998885
No 49
>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=34.95 E-value=33 Score=24.19 Aligned_cols=19 Identities=26% Similarity=0.413 Sum_probs=12.5
Q ss_pred CCCCCCcceeecCCcceeEeC
Q psy15037 113 PCPSCRTATERAGKGVYAYDL 133 (149)
Q Consensus 113 ~CP~C~~~IEK~~GCNhM~~~ 133 (149)
.||.|+.+++.++ .+.+|.
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~ 21 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCE 21 (70)
T ss_dssp B-SSS-SBEEEET--TEEEET
T ss_pred cCCCCCCccEEeC--CEEECc
Confidence 5899999998888 455554
No 50
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=34.23 E-value=17 Score=22.52 Aligned_cols=17 Identities=29% Similarity=0.708 Sum_probs=11.4
Q ss_pred CcccCCccCcccccccc
Q psy15037 9 KRIGCTECGFVFCKDCL 25 (149)
Q Consensus 9 ~~v~Cp~C~~aFC~~Ck 25 (149)
..+.|+.|+..||..=+
T Consensus 12 ~~~~C~~C~~~FC~~Hr 28 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHR 28 (43)
T ss_dssp SHEE-TTTS-EE-TTTH
T ss_pred CCeECCCCCcccCcccc
Confidence 56889999999998753
No 51
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. 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=33.96 E-value=22 Score=27.83 Aligned_cols=23 Identities=13% Similarity=0.042 Sum_probs=18.0
Q ss_pred CcccCCccCccc---------cccccccccCC
Q psy15037 9 KRIGCTECGFVF---------CKDCLQGAHIG 31 (149)
Q Consensus 9 ~~v~Cp~C~~aF---------C~~Cke~WH~g 31 (149)
.+.+||.|+..| |..|...|...
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCcc
Confidence 466899999888 77888777743
No 52
>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=33.61 E-value=22 Score=22.40 Aligned_cols=11 Identities=27% Similarity=0.812 Sum_probs=9.7
Q ss_pred cccCCccCccc
Q psy15037 10 RIGCTECGFVF 20 (149)
Q Consensus 10 ~v~Cp~C~~aF 20 (149)
.+.||+|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 68999999877
No 53
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.54 E-value=26 Score=31.59 Aligned_cols=18 Identities=33% Similarity=0.584 Sum_probs=16.9
Q ss_pred HHHHHhcCcCCCCCCcce
Q psy15037 104 QVTIKVSTKPCPSCRTAT 121 (149)
Q Consensus 104 ~~~I~~ntK~CP~C~~~I 121 (149)
.+||......||-|+++|
T Consensus 354 ~kW~~~y~~~CPvCrt~i 371 (374)
T COG5540 354 DKWLLGYSNKCPVCRTAI 371 (374)
T ss_pred HHHHhhhcccCCccCCCC
Confidence 689999999999999987
No 54
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=32.96 E-value=27 Score=33.51 Aligned_cols=8 Identities=38% Similarity=1.211 Sum_probs=3.7
Q ss_pred ccCCccCc
Q psy15037 11 IGCTECGF 18 (149)
Q Consensus 11 v~Cp~C~~ 18 (149)
+.||.|++
T Consensus 2 ~~Cp~Cg~ 9 (645)
T PRK14559 2 LICPQCQF 9 (645)
T ss_pred CcCCCCCC
Confidence 34555543
No 55
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=32.73 E-value=22 Score=21.57 Aligned_cols=15 Identities=40% Similarity=1.059 Sum_probs=10.1
Q ss_pred CCCCcccCCccCccc
Q psy15037 6 DGCKRIGCTECGFVF 20 (149)
Q Consensus 6 ~~~~~v~Cp~C~~aF 20 (149)
++..+..|+.|++++
T Consensus 18 d~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 18 DDRERLVCPACGFIH 32 (34)
T ss_dssp -SS-EEEETTTTEEE
T ss_pred CCccceECCCCCCEE
Confidence 345667899999864
No 56
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.59 E-value=21 Score=27.18 Aligned_cols=23 Identities=39% Similarity=0.700 Sum_probs=19.8
Q ss_pred CcccCCccCccccccccccccCC
Q psy15037 9 KRIGCTECGFVFCKDCLQGAHIG 31 (149)
Q Consensus 9 ~~v~Cp~C~~aFC~~Cke~WH~g 31 (149)
.+-+|+.|+..||..|-.-+|..
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred cceeCCCCCCccccccchhhhhh
Confidence 45679999999999999999954
No 57
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.56 E-value=23 Score=21.53 Aligned_cols=12 Identities=42% Similarity=0.911 Sum_probs=9.3
Q ss_pred CCCCCCcceeec
Q psy15037 113 PCPSCRTATERA 124 (149)
Q Consensus 113 ~CP~C~~~IEK~ 124 (149)
.||+|++.++..
T Consensus 1 ~CP~C~~~l~~~ 12 (41)
T PF13453_consen 1 KCPRCGTELEPV 12 (41)
T ss_pred CcCCCCcccceE
Confidence 599999987643
No 58
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=32.24 E-value=9.2 Score=22.52 Aligned_cols=17 Identities=41% Similarity=0.979 Sum_probs=14.1
Q ss_pred CCccCcccccccccccc
Q psy15037 13 CTECGFVFCKDCLQGAH 29 (149)
Q Consensus 13 Cp~C~~aFC~~Cke~WH 29 (149)
=..|+..||..|...|-
T Consensus 14 ~~~C~H~fC~~C~~~~~ 30 (41)
T PF00097_consen 14 LLPCGHSFCRDCLRKWL 30 (41)
T ss_dssp ETTTSEEEEHHHHHHHH
T ss_pred EecCCCcchHHHHHHHH
Confidence 45799999999988775
No 59
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=32.06 E-value=22 Score=21.86 Aligned_cols=14 Identities=36% Similarity=1.130 Sum_probs=12.3
Q ss_pred cccCCccCcccccc
Q psy15037 10 RIGCTECGFVFCKD 23 (149)
Q Consensus 10 ~v~Cp~C~~aFC~~ 23 (149)
...|..|+..||..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 67899999999975
No 60
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=30.25 E-value=29 Score=22.30 Aligned_cols=12 Identities=50% Similarity=1.121 Sum_probs=9.1
Q ss_pred cCcCCCCCCcce
Q psy15037 110 STKPCPSCRTAT 121 (149)
Q Consensus 110 ntK~CP~C~~~I 121 (149)
..||||-|..+.
T Consensus 2 ~LkPCPFCG~~~ 13 (61)
T PF14354_consen 2 ELKPCPFCGSAD 13 (61)
T ss_pred CCcCCCCCCCcc
Confidence 469999997543
No 61
>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=30.09 E-value=45 Score=20.97 Aligned_cols=14 Identities=36% Similarity=0.769 Sum_probs=11.9
Q ss_pred cCcCCCCCCcceee
Q psy15037 110 STKPCPSCRTATER 123 (149)
Q Consensus 110 ntK~CP~C~~~IEK 123 (149)
....||.|.+|+-+
T Consensus 16 L~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 16 LDEHCPDCGTPLMR 29 (41)
T ss_pred hcCccCCCCCeeEE
Confidence 45789999999977
No 62
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.79 E-value=26 Score=24.50 Aligned_cols=15 Identities=33% Similarity=0.725 Sum_probs=12.6
Q ss_pred hcCcCCCCCCcceee
Q psy15037 109 VSTKPCPSCRTATER 123 (149)
Q Consensus 109 ~ntK~CP~C~~~IEK 123 (149)
..|.+||.|..+++.
T Consensus 5 ~~~v~CP~Cgkpv~w 19 (65)
T COG3024 5 RITVPCPTCGKPVVW 19 (65)
T ss_pred cccccCCCCCCcccc
Confidence 357899999999876
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=29.36 E-value=38 Score=20.88 Aligned_cols=15 Identities=33% Similarity=0.955 Sum_probs=11.9
Q ss_pred cCcCCCCCCc-ceeec
Q psy15037 110 STKPCPSCRT-ATERA 124 (149)
Q Consensus 110 ntK~CP~C~~-~IEK~ 124 (149)
.+..||.|+. .++|.
T Consensus 25 ~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 25 DPVPCPECGSTEVRRV 40 (42)
T ss_pred CCCcCCCCCCCceEEe
Confidence 5678999999 77663
No 64
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=29.03 E-value=29 Score=30.06 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=13.1
Q ss_pred cCcCCCCCCcceeec
Q psy15037 110 STKPCPSCRTATERA 124 (149)
Q Consensus 110 ntK~CP~C~~~IEK~ 124 (149)
.-+||+.|.++|+|.
T Consensus 244 ~GepC~~CGt~I~k~ 258 (273)
T COG0266 244 AGEPCRRCGTPIEKI 258 (273)
T ss_pred CCCCCCccCCEeEEE
Confidence 467999999999985
No 65
>KOG1815|consensus
Probab=28.80 E-value=30 Score=31.16 Aligned_cols=25 Identities=32% Similarity=0.850 Sum_probs=19.3
Q ss_pred CCCCcccCCc--cCccccccccccccC
Q psy15037 6 DGCKRIGCTE--CGFVFCKDCLQGAHI 30 (149)
Q Consensus 6 ~~~~~v~Cp~--C~~aFC~~Cke~WH~ 30 (149)
.++....|.. |++.||..|.+.|-.
T Consensus 240 ~gc~~~~~~~~~c~~~FCw~Cl~~~~~ 266 (444)
T KOG1815|consen 240 GGCNHMTCKSASCKHEFCWVCLASLSD 266 (444)
T ss_pred CCccccccccCCcCCeeceeeeccccc
Confidence 3455556765 999999999999973
No 66
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=28.73 E-value=29 Score=23.55 Aligned_cols=19 Identities=37% Similarity=0.896 Sum_probs=13.7
Q ss_pred ccCCccC----------------cccccccccccc
Q psy15037 11 IGCTECG----------------FVFCKDCLQGAH 29 (149)
Q Consensus 11 v~Cp~C~----------------~aFC~~Cke~WH 29 (149)
+.||.|+ -.||+.||+.--
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~Etl 39 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETL 39 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEE
Confidence 5688888 358988876543
No 67
>PHA02707 hypothetical protein; Provisional
Probab=28.67 E-value=17 Score=22.54 Aligned_cols=12 Identities=33% Similarity=0.617 Sum_probs=9.5
Q ss_pred ceeEeCCCceee
Q psy15037 128 VYAYDLYPMFIP 139 (149)
Q Consensus 128 NhM~~~~~~~~~ 139 (149)
|--.|+||+||-
T Consensus 3 nfslcl~pvfil 14 (37)
T PHA02707 3 NFSLCLCPVFIL 14 (37)
T ss_pred ceeeehhhHHHH
Confidence 456799999984
No 68
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=28.07 E-value=30 Score=27.42 Aligned_cols=14 Identities=36% Similarity=0.804 Sum_probs=10.4
Q ss_pred CcccCCccCccccc
Q psy15037 9 KRIGCTECGFVFCK 22 (149)
Q Consensus 9 ~~v~Cp~C~~aFC~ 22 (149)
+..+|+.|++.|=.
T Consensus 27 ~~~~c~~c~~~f~~ 40 (154)
T PRK00464 27 RRRECLACGKRFTT 40 (154)
T ss_pred eeeeccccCCcceE
Confidence 34789988888853
No 69
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=27.65 E-value=34 Score=21.39 Aligned_cols=18 Identities=28% Similarity=0.739 Sum_probs=10.4
Q ss_pred ccccccccccC-CCCCCcc
Q psy15037 20 FCKDCLQGAHI-GPCDPGR 37 (149)
Q Consensus 20 FC~~Cke~WH~-g~C~~~~ 37 (149)
-|+.|++.+|- ..|....
T Consensus 4 ~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 4 LCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp C-TTTSSSCS-TTT---TC
T ss_pred cCcccCCCcchhhhhhhhh
Confidence 48899999995 5798754
No 70
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.24 E-value=48 Score=21.74 Aligned_cols=14 Identities=21% Similarity=0.892 Sum_probs=12.9
Q ss_pred cCcCCCCCCcceee
Q psy15037 110 STKPCPSCRTATER 123 (149)
Q Consensus 110 ntK~CP~C~~~IEK 123 (149)
+|+.||.|....++
T Consensus 27 TSq~C~~CG~~~~~ 40 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK 40 (69)
T ss_pred CccCccCccccccc
Confidence 79999999999987
No 71
>PHA02929 N1R/p28-like protein; Provisional
Probab=27.04 E-value=19 Score=30.45 Aligned_cols=25 Identities=28% Similarity=0.691 Sum_probs=19.4
Q ss_pred CCccCccccccccccccCC--CCCCcc
Q psy15037 13 CTECGFVFCKDCLQGAHIG--PCDPGR 37 (149)
Q Consensus 13 Cp~C~~aFC~~Cke~WH~g--~C~~~~ 37 (149)
=+.|+.+||..|-..|... .|..=+
T Consensus 197 l~~C~H~FC~~CI~~Wl~~~~tCPlCR 223 (238)
T PHA02929 197 LSNCNHVFCIECIDIWKKEKNTCPVCR 223 (238)
T ss_pred cCCCCCcccHHHHHHHHhcCCCCCCCC
Confidence 3579999999999999853 476533
No 72
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=26.92 E-value=41 Score=30.25 Aligned_cols=20 Identities=30% Similarity=0.644 Sum_probs=12.4
Q ss_pred CCCCCCCCCcccCCccCccc
Q psy15037 1 MNEGEDGCKRIGCTECGFVF 20 (149)
Q Consensus 1 ~~~~e~~~~~v~Cp~C~~aF 20 (149)
|++.+++...+.||.|+...
T Consensus 4 ~~~~~~~~~~~~C~~Cd~l~ 23 (403)
T TIGR00155 4 MCEHHPAAKHILCSQCDMLV 23 (403)
T ss_pred ccccCCCCCeeeCCCCCCcc
Confidence 44555555566677777555
No 73
>PRK00420 hypothetical protein; Validated
Probab=26.69 E-value=42 Score=25.48 Aligned_cols=17 Identities=24% Similarity=0.450 Sum_probs=13.7
Q ss_pred cCcCCCCCCcceee-cCC
Q psy15037 110 STKPCPSCRTATER-AGK 126 (149)
Q Consensus 110 ntK~CP~C~~~IEK-~~G 126 (149)
-+..||.|.+|.-+ ..|
T Consensus 22 l~~~CP~Cg~pLf~lk~g 39 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDG 39 (112)
T ss_pred ccCCCCCCCCcceecCCC
Confidence 45899999999987 444
No 74
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=26.52 E-value=42 Score=20.70 Aligned_cols=10 Identities=40% Similarity=1.205 Sum_probs=7.2
Q ss_pred cccCCccCcc
Q psy15037 10 RIGCTECGFV 19 (149)
Q Consensus 10 ~v~Cp~C~~a 19 (149)
...||.|+|.
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 6678888754
No 75
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=26.35 E-value=31 Score=25.50 Aligned_cols=20 Identities=25% Similarity=0.561 Sum_probs=16.8
Q ss_pred CCcccCCccCcccccccccc
Q psy15037 8 CKRIGCTECGFVFCKDCLQG 27 (149)
Q Consensus 8 ~~~v~Cp~C~~aFC~~Cke~ 27 (149)
.+...|..|+..+|..|...
T Consensus 69 ~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 69 NRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp TTCEEETTTTEEEETTSEEE
T ss_pred CCCCcCCcCCccccCccCCc
Confidence 34588999999999999765
No 76
>smart00355 ZnF_C2H2 zinc finger.
Probab=26.18 E-value=30 Score=17.29 Aligned_cols=11 Identities=55% Similarity=1.111 Sum_probs=6.6
Q ss_pred cCCccCccccc
Q psy15037 12 GCTECGFVFCK 22 (149)
Q Consensus 12 ~Cp~C~~aFC~ 22 (149)
.|+.|++.|-.
T Consensus 2 ~C~~C~~~f~~ 12 (26)
T smart00355 2 RCPECGKVFKS 12 (26)
T ss_pred CCCCCcchhCC
Confidence 46666666643
No 77
>KOG0320|consensus
Probab=25.54 E-value=19 Score=29.85 Aligned_cols=11 Identities=64% Similarity=1.697 Sum_probs=10.1
Q ss_pred CccCccccccc
Q psy15037 14 TECGFVFCKDC 24 (149)
Q Consensus 14 p~C~~aFC~~C 24 (149)
.+||.+||..|
T Consensus 149 TkCGHvFC~~C 159 (187)
T KOG0320|consen 149 TKCGHVFCSQC 159 (187)
T ss_pred cccchhHHHHH
Confidence 48999999999
No 78
>PHA02325 hypothetical protein
Probab=25.43 E-value=34 Score=24.24 Aligned_cols=11 Identities=45% Similarity=1.008 Sum_probs=9.5
Q ss_pred cCcCCCCCCcc
Q psy15037 110 STKPCPSCRTA 120 (149)
Q Consensus 110 ntK~CP~C~~~ 120 (149)
++|-||+|.+.
T Consensus 2 ~~k~CPkC~A~ 12 (72)
T PHA02325 2 DTKICPKCGAR 12 (72)
T ss_pred CccccCccCCE
Confidence 68999999875
No 79
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.25 E-value=34 Score=25.09 Aligned_cols=20 Identities=25% Similarity=0.582 Sum_probs=15.7
Q ss_pred ccCCccC------------ccccccccccccC
Q psy15037 11 IGCTECG------------FVFCKDCLQGAHI 30 (149)
Q Consensus 11 v~Cp~C~------------~aFC~~Cke~WH~ 30 (149)
..||.|+ +-.|+.|+..|=.
T Consensus 2 llCP~C~v~l~~~~rs~vEiD~CPrCrGVWLD 33 (88)
T COG3809 2 LLCPICGVELVMSVRSGVEIDYCPRCRGVWLD 33 (88)
T ss_pred cccCcCCceeeeeeecCceeeeCCccccEeec
Confidence 4578777 4579999999985
No 80
>KOG3084|consensus
Probab=25.11 E-value=73 Score=28.70 Aligned_cols=42 Identities=21% Similarity=0.254 Sum_probs=27.7
Q ss_pred hhHHHHHhcCcCCCCCCcceeecCC-----cceeEeC-----CCceeeeeecc
Q psy15037 102 ASQVTIKVSTKPCPSCRTATERAGK-----GVYAYDL-----YPMFIPLVLGV 144 (149)
Q Consensus 102 ~s~~~I~~ntK~CP~C~~~IEK~~G-----CNhM~~~-----~~~~~~~~~~~ 144 (149)
...+|+.. .|-||+|..+.--..| |-.-+|- ||-+=|.|+++
T Consensus 142 s~l~W~sk-ykFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr~dPvVIm~ 193 (345)
T KOG3084|consen 142 SLLDWVSK-YKFCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYPRTDPVVIML 193 (345)
T ss_pred HHHHHHHH-hccCcccCCCcccccCCccceeecccCCcCCeeccCCCCeEEEE
Confidence 34677654 6999999998744333 4444444 77777777664
No 81
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=24.85 E-value=74 Score=19.62 Aligned_cols=12 Identities=25% Similarity=0.504 Sum_probs=7.5
Q ss_pred CcCCCCCCccee
Q psy15037 111 TKPCPSCRTATE 122 (149)
Q Consensus 111 tK~CP~C~~~IE 122 (149)
...||.|++++.
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 456777766654
No 82
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.80 E-value=58 Score=28.67 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=19.9
Q ss_pred CCCcccCCccC-----------------ccccccccccccC
Q psy15037 7 GCKRIGCTECG-----------------FVFCKDCLQGAHI 30 (149)
Q Consensus 7 ~~~~v~Cp~C~-----------------~aFC~~Cke~WH~ 30 (149)
...+..||.|| |.+|..|.-.||-
T Consensus 184 ~~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~ 224 (309)
T PRK03564 184 GEQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHV 224 (309)
T ss_pred ccCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccc
Confidence 34567899887 7799999999994
No 83
>PHA02926 zinc finger-like protein; Provisional
Probab=24.53 E-value=17 Score=31.15 Aligned_cols=19 Identities=26% Similarity=0.597 Sum_probs=15.9
Q ss_pred ccCCccCcccccccccccc
Q psy15037 11 IGCTECGFVFCKDCLQGAH 29 (149)
Q Consensus 11 v~Cp~C~~aFC~~Cke~WH 29 (149)
..=+.|+.+||..|-..|.
T Consensus 192 GIL~~CnHsFCl~CIr~Wr 210 (242)
T PHA02926 192 GLLDSCNHIFCITCINIWH 210 (242)
T ss_pred cccCCCCchHHHHHHHHHH
Confidence 3345899999999999996
No 84
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=23.99 E-value=37 Score=28.60 Aligned_cols=23 Identities=26% Similarity=0.626 Sum_probs=14.3
Q ss_pred CCcccCCccC-----------------ccccccccccccC
Q psy15037 8 CKRIGCTECG-----------------FVFCKDCLQGAHI 30 (149)
Q Consensus 8 ~~~v~Cp~C~-----------------~aFC~~Cke~WH~ 30 (149)
.....||.|| |.+|..|.-.||.
T Consensus 170 w~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~ 209 (290)
T PF04216_consen 170 WQRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF 209 (290)
T ss_dssp TT-SS-TTT---EEEEEEE------EEEEEETTT--EEE-
T ss_pred ccCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee
Confidence 3457888886 7799999999995
No 85
>KOG0317|consensus
Probab=23.61 E-value=23 Score=31.25 Aligned_cols=26 Identities=31% Similarity=0.700 Sum_probs=18.9
Q ss_pred cCCccCccccccccccccCC--CCCCcc
Q psy15037 12 GCTECGFVFCKDCLQGAHIG--PCDPGR 37 (149)
Q Consensus 12 ~Cp~C~~aFC~~Cke~WH~g--~C~~~~ 37 (149)
.|.-||..||..|-..|=.. .|..=+
T Consensus 253 SaTpCGHiFCWsCI~~w~~ek~eCPlCR 280 (293)
T KOG0317|consen 253 SATPCGHIFCWSCILEWCSEKAECPLCR 280 (293)
T ss_pred CcCcCcchHHHHHHHHHHccccCCCccc
Confidence 45679999999999999632 354433
No 86
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=23.33 E-value=69 Score=26.87 Aligned_cols=25 Identities=12% Similarity=0.065 Sum_probs=19.1
Q ss_pred HhcCcCCCCCCcceeecCCcceeEe
Q psy15037 108 KVSTKPCPSCRTATERAGKGVYAYD 132 (149)
Q Consensus 108 ~~ntK~CP~C~~~IEK~~GCNhM~~ 132 (149)
..+.+-||+|..+++...+=..+.|
T Consensus 96 ~~~~~fC~~CG~~~~~~~~~~~~~C 120 (256)
T PRK00241 96 YRSHRFCGYCGHPMHPSKTEWAMLC 120 (256)
T ss_pred hhcCccccccCCCCeecCCceeEEC
Confidence 4568999999999987655455665
No 87
>PF14353 CpXC: CpXC protein
Probab=23.25 E-value=36 Score=25.08 Aligned_cols=12 Identities=33% Similarity=0.678 Sum_probs=5.9
Q ss_pred cCcCCCCCCcce
Q psy15037 110 STKPCPSCRTAT 121 (149)
Q Consensus 110 ntK~CP~C~~~I 121 (149)
++-.||+|+..+
T Consensus 37 ~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 37 FSFTCPSCGHKF 48 (128)
T ss_pred CEEECCCCCCce
Confidence 344455555444
No 88
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=23.24 E-value=61 Score=28.41 Aligned_cols=23 Identities=30% Similarity=0.716 Sum_probs=19.4
Q ss_pred CCcccCCccC------------------ccccccccccccC
Q psy15037 8 CKRIGCTECG------------------FVFCKDCLQGAHI 30 (149)
Q Consensus 8 ~~~v~Cp~C~------------------~aFC~~Cke~WH~ 30 (149)
..+..||.|| |.+|..|.-.||.
T Consensus 182 ~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~ 222 (305)
T TIGR01562 182 ESRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHY 222 (305)
T ss_pred CCCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccc
Confidence 4566899887 7899999999995
No 89
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.21 E-value=39 Score=25.84 Aligned_cols=13 Identities=23% Similarity=0.647 Sum_probs=9.4
Q ss_pred CCcccCCccCccc
Q psy15037 8 CKRIGCTECGFVF 20 (149)
Q Consensus 8 ~~~v~Cp~C~~aF 20 (149)
+....|+.|++.|
T Consensus 68 p~~~~C~~CG~~~ 80 (135)
T PRK03824 68 EAVLKCRNCGNEW 80 (135)
T ss_pred ceEEECCCCCCEE
Confidence 4567788888766
No 90
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=23.17 E-value=40 Score=35.32 Aligned_cols=16 Identities=38% Similarity=0.922 Sum_probs=13.8
Q ss_pred cCcCCCCCCcceeecC
Q psy15037 110 STKPCPSCRTATERAG 125 (149)
Q Consensus 110 ntK~CP~C~~~IEK~~ 125 (149)
--|.||+|++|..|+|
T Consensus 938 pdK~CPkCg~pl~kDG 953 (1444)
T COG2176 938 PDKDCPKCGTPLKKDG 953 (1444)
T ss_pred CCCCCCcCCCccccCC
Confidence 4589999999998776
No 91
>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=22.96 E-value=27 Score=23.58 Aligned_cols=14 Identities=36% Similarity=0.750 Sum_probs=8.1
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
|.+||.|..+++-.
T Consensus 2 ~v~CP~C~k~~~~~ 15 (57)
T PF03884_consen 2 TVKCPICGKPVEWS 15 (57)
T ss_dssp EEE-TTT--EEE-S
T ss_pred cccCCCCCCeeccc
Confidence 57899999998763
No 92
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=22.20 E-value=62 Score=24.72 Aligned_cols=34 Identities=21% Similarity=0.381 Sum_probs=23.6
Q ss_pred cCcCCCCCCcceeecC-------Cccee--EeCCCceeeeeec
Q psy15037 110 STKPCPSCRTATERAG-------KGVYA--YDLYPMFIPLVLG 143 (149)
Q Consensus 110 ntK~CP~C~~~IEK~~-------GCNhM--~~~~~~~~~~~~~ 143 (149)
-...||.|+..+..++ .|+.. ++.|.+-+.+.+.
T Consensus 33 ~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~ 75 (166)
T cd04476 33 WYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVA 75 (166)
T ss_pred EEccccccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEEE
Confidence 3567999999998775 37776 4555566665554
No 93
>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=22.16 E-value=60 Score=20.22 Aligned_cols=15 Identities=27% Similarity=0.660 Sum_probs=11.3
Q ss_pred cCcCCCCCCc-ceeec
Q psy15037 110 STKPCPSCRT-ATERA 124 (149)
Q Consensus 110 ntK~CP~C~~-~IEK~ 124 (149)
....||.|.+ .++|.
T Consensus 25 ~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 25 PLATCPECGGEKLRRL 40 (52)
T ss_pred CCCCCCCCCCCceeEE
Confidence 4567999998 67664
No 94
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=22.14 E-value=44 Score=22.70 Aligned_cols=14 Identities=29% Similarity=0.679 Sum_probs=11.6
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
-|.||.|..||.-+
T Consensus 3 HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD 16 (59)
T ss_pred CCcCCcCCCcCCcc
Confidence 47899999999754
No 95
>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=20.73 E-value=59 Score=26.30 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=11.0
Q ss_pred CcCCCCCCcceeec
Q psy15037 111 TKPCPSCRTATERA 124 (149)
Q Consensus 111 tK~CP~C~~~IEK~ 124 (149)
-..||+|.++|.-.
T Consensus 39 I~~Cp~C~~~IrG~ 52 (158)
T PF10083_consen 39 ITSCPNCSTPIRGD 52 (158)
T ss_pred HHHCcCCCCCCCCc
Confidence 35699999999644
No 96
>PF15470 DUF4637: Domain of unknown function (DUF4637)
Probab=20.61 E-value=42 Score=27.27 Aligned_cols=20 Identities=40% Similarity=0.991 Sum_probs=16.7
Q ss_pred CCcccCCccCcccccccccc
Q psy15037 8 CKRIGCTECGFVFCKDCLQG 27 (149)
Q Consensus 8 ~~~v~Cp~C~~aFC~~Cke~ 27 (149)
++..-|+.|-..||..|+-.
T Consensus 129 p~~g~C~rCEILfCkKC~tL 148 (173)
T PF15470_consen 129 PRRGGCARCEILFCKKCRTL 148 (173)
T ss_pred CCCCCccceeeeeehhhccc
Confidence 46678999999999999644
No 97
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.48 E-value=60 Score=24.08 Aligned_cols=11 Identities=36% Similarity=0.715 Sum_probs=9.1
Q ss_pred CCCcccCCccC
Q psy15037 7 GCKRIGCTECG 17 (149)
Q Consensus 7 ~~~~v~Cp~C~ 17 (149)
-++.+.||.|+
T Consensus 18 lpt~f~CP~Cg 28 (99)
T PRK14892 18 LPKIFECPRCG 28 (99)
T ss_pred CCcEeECCCCC
Confidence 35788999999
No 98
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=20.46 E-value=57 Score=31.78 Aligned_cols=16 Identities=31% Similarity=0.692 Sum_probs=15.2
Q ss_pred CCCCCCcceeecCCcc
Q psy15037 113 PCPSCRTATERAGKGV 128 (149)
Q Consensus 113 ~CP~C~~~IEK~~GCN 128 (149)
.||.|...+...+||+
T Consensus 726 ~Cp~Cg~~l~~~~GC~ 741 (752)
T PRK08665 726 ACPECGSILEHEEGCV 741 (752)
T ss_pred CCCCCCcccEECCCCC
Confidence 5999999999999998
No 99
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=20.46 E-value=60 Score=23.60 Aligned_cols=22 Identities=27% Similarity=0.523 Sum_probs=9.8
Q ss_pred HHhcCcCCCCCCcceeecCCcc
Q psy15037 107 IKVSTKPCPSCRTATERAGKGV 128 (149)
Q Consensus 107 I~~ntK~CP~C~~~IEK~~GCN 128 (149)
++.-++-||+|+++-.+..|+-
T Consensus 47 rkeg~q~CpqCkt~ykr~kgsp 68 (80)
T PF14569_consen 47 RKEGNQVCPQCKTRYKRHKGSP 68 (80)
T ss_dssp HHTS-SB-TTT--B----TT--
T ss_pred hhcCcccccccCCCcccccCCC
Confidence 4667899999999988877763
Done!