Query 016443
Match_columns 389
No_of_seqs 216 out of 479
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:54:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016443.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016443hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2785 C2H2-type Zn-finger pr 100.0 1.7E-92 3.7E-97 696.0 20.8 358 2-388 23-389 (390)
2 PF12756 zf-C2H2_2: C2H2 type 99.8 1.9E-20 4.1E-25 152.4 2.4 99 163-266 1-100 (100)
3 KOG2482 Predicted C2H2-type Zn 99.7 1.3E-17 2.7E-22 163.6 3.5 160 46-245 196-364 (423)
4 KOG2482 Predicted C2H2-type Zn 99.5 3.5E-14 7.5E-19 139.7 6.2 95 159-263 142-237 (423)
5 PF12171 zf-C2H2_jaz: Zinc-fin 98.5 5.2E-08 1.1E-12 62.7 1.6 26 46-71 2-27 (27)
6 PF12874 zf-met: Zinc-finger o 98.3 2.7E-07 5.9E-12 57.9 2.0 25 46-70 1-25 (25)
7 smart00451 ZnF_U1 U1-like zinc 98.2 1.3E-06 2.9E-11 58.8 3.1 32 45-76 3-34 (35)
8 KOG2505 Ankyrin repeat protein 98.0 2.8E-06 6.1E-11 88.1 1.9 30 2-31 86-115 (591)
9 KOG0717 Molecular chaperone (D 97.7 1.3E-05 2.9E-10 82.6 2.2 30 46-75 293-322 (508)
10 KOG2785 C2H2-type Zn-finger pr 97.2 0.00038 8.2E-09 70.6 4.2 33 45-77 3-35 (390)
11 PF00096 zf-C2H2: Zinc finger, 96.9 0.00058 1.3E-08 41.7 1.6 22 46-67 1-22 (23)
12 PF13894 zf-C2H2_4: C2H2-type 96.4 0.0022 4.9E-08 38.6 1.8 22 46-67 1-22 (24)
13 PF13912 zf-C2H2_6: C2H2-type 96.2 0.0028 6.2E-08 40.1 1.6 24 45-68 1-24 (27)
14 KOG2462 C2H2-type Zn-finger pr 96.1 0.008 1.7E-07 58.9 4.9 58 161-245 187-244 (279)
15 KOG3408 U1-like Zn-finger-cont 95.7 0.0049 1.1E-07 53.6 1.6 76 2-77 11-89 (129)
16 PF12756 zf-C2H2_2: C2H2 type 95.7 0.0046 1E-07 49.8 1.4 30 45-74 50-79 (100)
17 PF06220 zf-U1: U1 zinc finger 95.6 0.0097 2.1E-07 41.7 2.4 31 46-76 4-36 (38)
18 smart00355 ZnF_C2H2 zinc finge 95.2 0.015 3.3E-07 35.2 2.2 21 46-66 1-21 (26)
19 PLN02748 tRNA dimethylallyltra 94.9 0.017 3.7E-07 61.0 2.7 34 44-77 417-451 (468)
20 PTZ00448 hypothetical protein; 94.8 0.019 4.2E-07 58.4 2.7 33 45-77 314-346 (373)
21 PF12171 zf-C2H2_jaz: Zinc-fin 94.2 0.0051 1.1E-07 39.3 -1.9 25 213-240 2-26 (27)
22 PF13912 zf-C2H2_6: C2H2-type 93.8 0.035 7.6E-07 35.0 1.4 25 213-242 2-26 (27)
23 PF12874 zf-met: Zinc-finger o 93.4 0.017 3.7E-07 35.8 -0.5 24 214-240 2-25 (25)
24 PHA02768 hypothetical protein; 92.6 0.071 1.5E-06 40.4 1.7 23 45-67 5-27 (55)
25 PF00096 zf-C2H2: Zinc finger, 92.5 0.053 1.1E-06 32.9 0.8 22 213-237 1-22 (23)
26 PHA00616 hypothetical protein 91.9 0.07 1.5E-06 38.6 0.9 27 45-72 1-27 (44)
27 PF13821 DUF4187: Domain of un 91.9 0.19 4.1E-06 38.0 3.3 31 197-233 15-45 (55)
28 PF13894 zf-C2H2_4: C2H2-type 91.2 0.13 2.7E-06 30.7 1.4 22 213-237 1-22 (24)
29 PF07535 zf-DBF: DBF zinc fing 89.9 0.27 5.9E-06 36.4 2.4 27 47-76 7-33 (49)
30 KOG3608 Zn finger proteins [Ge 89.5 0.44 9.5E-06 48.6 4.3 64 160-247 318-384 (467)
31 smart00451 ZnF_U1 U1-like zinc 89.4 0.18 3.9E-06 33.5 1.1 28 212-242 3-30 (35)
32 PHA00733 hypothetical protein 88.8 0.64 1.4E-05 40.8 4.4 29 161-189 99-127 (128)
33 smart00586 ZnF_DBF Zinc finger 88.8 0.3 6.5E-06 36.2 2.0 28 46-76 6-33 (49)
34 KOG3608 Zn finger proteins [Ge 88.2 0.73 1.6E-05 47.1 4.9 70 163-238 265-344 (467)
35 COG5112 UFD2 U1-like Zn-finger 87.2 0.24 5.1E-06 42.4 0.7 31 46-76 56-86 (126)
36 KOG4727 U1-like Zn-finger prot 86.1 0.79 1.7E-05 42.3 3.5 62 14-75 33-105 (193)
37 KOG2231 Predicted E3 ubiquitin 85.7 0.89 1.9E-05 50.0 4.3 80 160-243 114-211 (669)
38 PHA02768 hypothetical protein; 85.2 0.55 1.2E-05 35.6 1.7 26 211-241 4-29 (55)
39 KOG3032 Uncharacterized conser 84.4 0.63 1.4E-05 44.9 2.1 30 46-76 36-65 (264)
40 PHA00616 hypothetical protein 83.8 0.54 1.2E-05 34.1 1.1 33 162-194 2-34 (44)
41 KOG3576 Ovo and related transc 83.2 0.89 1.9E-05 43.4 2.6 63 159-236 171-233 (267)
42 PHA00732 hypothetical protein 82.4 0.95 2.1E-05 36.6 2.1 22 46-67 2-23 (79)
43 PF05605 zf-Di19: Drought indu 82.4 2.1 4.5E-05 31.7 3.8 49 162-237 3-51 (54)
44 smart00355 ZnF_C2H2 zinc finge 82.1 1 2.2E-05 26.8 1.7 20 214-236 2-21 (26)
45 KOG2837 Protein containing a U 81.8 0.23 4.9E-06 48.9 -2.0 31 45-75 25-55 (309)
46 PF13909 zf-H2C2_5: C2H2-type 81.3 0.85 1.9E-05 27.9 1.2 23 163-186 2-24 (24)
47 PHA00732 hypothetical protein 80.7 1.5 3.3E-05 35.4 2.7 45 163-238 3-47 (79)
48 PF13913 zf-C2HC_2: zinc-finge 80.7 1.3 2.8E-05 28.1 1.8 21 46-67 3-23 (25)
49 PF13465 zf-H2C2_2: Zinc-finge 78.8 0.97 2.1E-05 28.6 0.9 15 43-57 12-26 (26)
50 COG5188 PRP9 Splicing factor 3 78.6 1 2.2E-05 46.0 1.3 32 46-77 239-270 (470)
51 PHA00733 hypothetical protein 78.5 3.4 7.3E-05 36.2 4.4 50 161-238 73-122 (128)
52 KOG0227 Splicing factor 3a, su 76.4 1.1 2.3E-05 42.2 0.8 34 44-77 52-85 (222)
53 PF05605 zf-Di19: Drought indu 75.5 2.4 5.2E-05 31.4 2.3 22 45-67 2-23 (54)
54 COG5246 PRP11 Splicing factor 75.2 1.5 3.3E-05 41.0 1.4 34 44-77 52-85 (222)
55 KOG1994 Predicted RNA binding 71.9 3.5 7.6E-05 39.9 3.0 33 196-234 226-258 (268)
56 PF12013 DUF3505: Protein of u 69.1 3.6 7.7E-05 34.6 2.2 74 159-238 9-107 (109)
57 KOG2505 Ankyrin repeat protein 68.6 3.6 7.9E-05 43.9 2.5 33 45-77 66-98 (591)
58 KOG2462 C2H2-type Zn-finger pr 68.0 3.5 7.5E-05 40.8 2.1 31 42-72 212-242 (279)
59 KOG1074 Transcriptional repres 67.0 3.3 7.1E-05 46.6 1.9 53 158-236 602-654 (958)
60 KOG3623 Homeobox transcription 63.2 2.3 4.9E-05 47.2 -0.2 31 42-72 306-336 (1007)
61 smart00734 ZnF_Rad18 Rad18-lik 57.6 8.4 0.00018 24.6 1.8 20 47-67 3-22 (26)
62 PF02892 zf-BED: BED zinc fing 57.5 5.5 0.00012 27.9 1.1 22 45-66 16-41 (45)
63 PF08790 zf-LYAR: LYAR-type C2 57.0 1.2 2.7E-05 29.3 -2.1 20 46-66 1-20 (28)
64 KOG1994 Predicted RNA binding 56.2 6.1 0.00013 38.2 1.4 21 161-181 239-259 (268)
65 KOG3623 Homeobox transcription 54.2 6.8 0.00015 43.7 1.6 24 43-66 208-231 (1007)
66 PF12013 DUF3505: Protein of u 52.2 23 0.00049 29.7 4.1 27 160-186 79-109 (109)
67 smart00614 ZnF_BED BED zinc fi 49.5 8.5 0.00018 27.9 1.0 24 46-70 19-47 (50)
68 PF04988 AKAP95: A-kinase anch 47.1 13 0.00029 34.1 2.0 27 46-72 1-27 (165)
69 COG5188 PRP9 Splicing factor 3 46.0 13 0.00027 38.3 1.9 65 177-244 159-267 (470)
70 KOG3288 OTU-like cysteine prot 45.4 20 0.00043 35.5 3.0 32 41-72 272-303 (307)
71 PF04780 DUF629: Protein of un 45.2 13 0.00028 39.6 1.9 29 45-74 57-85 (466)
72 PF04959 ARS2: Arsenite-resist 45.1 14 0.0003 35.5 1.9 32 42-74 74-105 (214)
73 COG5236 Uncharacterized conser 44.8 7.4 0.00016 39.9 0.0 65 169-238 161-243 (493)
74 KOG1074 Transcriptional repres 44.4 10 0.00022 42.9 1.0 23 160-182 632-654 (958)
75 COG4049 Uncharacterized protei 44.3 9.5 0.00021 29.3 0.6 28 44-72 16-43 (65)
76 KOG0717 Molecular chaperone (D 43.9 12 0.00025 39.8 1.3 28 213-243 293-320 (508)
77 KOG3576 Ovo and related transc 41.2 8.4 0.00018 36.9 -0.1 27 162-188 213-239 (267)
78 PF14420 Clr5: Clr5 domain 39.3 15 0.00033 27.3 1.0 25 170-194 19-43 (54)
79 KOG3408 U1-like Zn-finger-cont 38.8 11 0.00025 33.0 0.3 28 212-242 57-84 (129)
80 PF12907 zf-met2: Zinc-binding 38.5 16 0.00035 26.0 1.0 24 46-69 2-28 (40)
81 KOG3993 Transcription factor ( 33.8 25 0.00054 37.1 1.8 33 42-74 353-385 (500)
82 KOG2384 Major histocompatibili 33.7 20 0.00044 34.1 1.1 63 15-78 41-116 (223)
83 PF05443 ROS_MUCR: ROS/MUCR tr 33.6 27 0.00059 31.0 1.9 39 213-267 73-111 (132)
84 KOG1146 Homeobox protein [Gene 33.6 35 0.00076 40.6 3.1 31 43-73 516-546 (1406)
85 COG5236 Uncharacterized conser 33.4 56 0.0012 33.8 4.2 74 162-238 221-304 (493)
86 PF09237 GAGA: GAGA factor; I 32.6 36 0.00077 25.7 2.0 24 44-67 23-46 (54)
87 PF09237 GAGA: GAGA factor; I 32.1 24 0.00052 26.6 1.0 28 160-187 23-50 (54)
88 KOG3454 U1 snRNP-specific prot 27.9 40 0.00086 31.1 1.9 31 45-75 3-35 (165)
89 KOG3993 Transcription factor ( 27.4 31 0.00067 36.4 1.3 29 45-75 295-323 (500)
90 PF09630 DUF2024: Domain of un 26.6 16 0.00036 29.8 -0.7 31 158-190 49-79 (81)
91 KOG4364 Chromatin assembly fac 26.5 67 0.0015 35.8 3.6 15 110-124 520-534 (811)
92 TIGR02026 BchE magnesium-proto 25.6 1.5E+02 0.0033 31.4 6.2 89 161-249 204-309 (497)
93 PF04780 DUF629: Protein of un 23.8 46 0.001 35.5 1.8 60 172-239 21-81 (466)
94 COG5067 DBF4 Protein kinase es 23.6 25 0.00054 36.7 -0.2 27 47-76 424-450 (468)
95 COG4822 CbiK Cobalamin biosynt 22.3 55 0.0012 31.9 1.8 45 163-207 143-190 (265)
96 PF14475 Mso1_Sec1_bdg: Sec1-b 21.7 24 0.00052 25.3 -0.5 20 305-324 19-38 (41)
97 KOG2636 Splicing factor 3a, su 21.2 54 0.0012 34.8 1.7 28 46-73 402-430 (497)
98 PF02148 zf-UBP: Zn-finger in 20.6 27 0.00059 26.5 -0.5 44 212-264 11-55 (63)
99 PF09538 FYDLN_acid: Protein o 20.6 33 0.00072 29.4 0.0 16 44-59 8-23 (108)
100 COG5112 UFD2 U1-like Zn-finger 20.6 31 0.00067 29.8 -0.2 29 212-243 55-83 (126)
No 1
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.7e-92 Score=695.97 Aligned_cols=358 Identities=36% Similarity=0.557 Sum_probs=274.8
Q ss_pred cccchhhhhhhhhhcCCCCCCHHHHHHHHHHHHHhhhc--cCCCCccccccccCccCCHHHHHHHhhcHhHHHhhhcCCC
Q 016443 2 WKIFLFLLLPIKQVAGVPGVTEALFLARQAALAQEKNK--NATPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRASQGTS 79 (389)
Q Consensus 2 ~k~~~hr~NlKRKVA~LPPVTaE~F~~k~~~~a~~~~~--~~~~~~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~~~~ 79 (389)
|||||||||||||||+|||||+|+|+.|+++.+.+... .++.+.++|.+|+|+|.|++|+.+||+||+|+.++.+...
T Consensus 23 yKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 23 YKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred hhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 89999999999999999999999999999887554444 4577888999999999999999999999999999887665
Q ss_pred cccchhcccccCCCCCCCCCCCccccCCCCCCCCcccccccCCchhhhhhhcccccccCCCCCCCCCCcccCCCCCCCCC
Q 016443 80 NEEKEKVIIKPIPLRDVNKPPRKREANNEESEDSDDEWEEVGPDEVLVSEATNSLTNLNVGSPADDDLEEDDDDGAFEEF 159 (389)
Q Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~d~e~eweev~~~e~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (389)
..+++.+.++.++.+.+. + .. ...+++..|-+++.++....++ ..+ +..+|.+++ .+...+.
T Consensus 103 ~~e~d~a~~~q~~~~~p~---~-l~----~~~e~e~~~~E~~~~~d~~~e~-------~~d--d~~Edi~~d-~~~e~e~ 164 (390)
T KOG2785|consen 103 SEEGDSAKISQLPSRRPS---N-LQ----NKGESELKWYEVDSDEDSSEEE-------EED--DEEEDIEED-GDDEDEL 164 (390)
T ss_pred cccccchhhhhccccCcc---c-cc----cCCCcccchhhcccccccchhh-------ccC--cchhhhhhc-cchhccc
Confidence 444333444444322110 0 00 0112455666665542110000 000 111111111 1223344
Q ss_pred CCCccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhCC
Q 016443 160 DPACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAKR 239 (389)
Q Consensus 160 ~~~~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~dK~ 239 (389)
.|++||||++.+.+++.|+.||++.||||||+++||+|+.|||.||++||..+++|||||..|+.|+|++|||+||.+||
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~ 244 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKG 244 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhcc
Confidence 56999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccCCCCChhHHHHhhhhcccCCCCcCccccccccccCCCcceec--CC-CeeEEEecCCCCCCCcceeeeccccccc
Q 016443 240 HCKIHFGDGDDEEEAELEEFYDYSSSYMDEDGKQLISSSDMANTVEL--GG-GSELIITKRTDKGTSTKTFGSREYLRYY 316 (389)
Q Consensus 240 Hcki~~~~~~~e~~~e~~~FYDf~~sy~d~~~~~~~~~~~~~~~~~~--~~-g~eLvL~~~~~~~psG~~iGhR~~~ryy 316 (389)
||||+| ++ |+++||++||||++||+|..+.+.+...++.++..+ .+ .+||+| |||++||||+|+|||
T Consensus 245 HCkl~y-d~--ee~~El~efYDfsssY~d~~~~~~~~~~e~~~~~~l~~g~~~~el~l-------psga~vGhRsl~RYy 314 (390)
T KOG2785|consen 245 HCKLPY-DG--EERLELAEFYDFSSSYPDIAENQDPDSAEEDPTDELEGGDELYELTL-------PSGARVGHRSLMRYY 314 (390)
T ss_pred CcccCC-Ch--HHHhhhhhhhcCcccccCcccCCCCcchhcCCcccccccceeeeeec-------ccccccccHHHHHHH
Confidence 999999 54 899999999999999999766555444443333444 12 278999 999999999999999
Q ss_pred ccCCCCCCCch----HHHHHHHHHhhhhcccchhhhHHHHHHHHHHHHHHhhhhhhhhhhhccccccccCCCCCCC
Q 016443 317 RQKPRPSPANN----VAITAALASRYKSMGLATVQTREHMVRMKVIKEMNRTGVEAMRTRVGMKNNIIRNLPKNVP 388 (389)
Q Consensus 317 rQ~~~~~~~~~----~~~~~~~~~~y~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kvg~k~N~~~~~~~~~~ 388 (389)
||+|+|+++.. ..++.+....|+++||++.++..+....++++.++|.+ .+|.++||+++|..+||+-++-
T Consensus 315 kQ~l~p~~~~~~~~~r~~~~~~~~~~~a~~~t~~~~~~~k~~~~~~k~v~R~~-~r~~~~~g~k~n~~~~~~~~~~ 389 (390)
T KOG2785|consen 315 KQNLRPSSAVVRLVSRRALSRVKRFYPALGWTGTTGVRAKMQARDMKFVERGR-RRFALRVGMKNNYRDQLHQRVQ 389 (390)
T ss_pred hhcCCCcchHHHHHHHHHHHHHHHhhhcccchhhHHHHHHHHHHHHHHHHHHH-HHHHHHhcchhhHHHHHhhhhc
Confidence 99999998653 33345566778999999988765555556666666655 6799999999999999987764
No 2
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=99.79 E-value=1.9e-20 Score=152.38 Aligned_cols=99 Identities=45% Similarity=0.832 Sum_probs=28.0
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhCCCcc
Q 016443 163 CCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAKRHCK 242 (389)
Q Consensus 163 ~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~dK~Hck 242 (389)
+|+||+..++++..++.||...|+|.||+..+|+++.+|++|++.+|...+.|++|+ +.|.|..+|+.||+.++|++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~---~~f~s~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCN---KTFRSREALQEHMRSKHHKK 77 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS----EESSHHHHHHHHHHTTTTC
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccC---CCCcCHHHHHHHHcCccCCC
Confidence 599999999999999999999999999999999999999999999999889999999 78999999999999999999
Q ss_pred ccCCCCChhHHHHhhhhccc-CCCC
Q 016443 243 IHFGDGDDEEEAELEEFYDY-SSSY 266 (389)
Q Consensus 243 i~~~~~~~e~~~e~~~FYDf-~~sy 266 (389)
+.++.. ....++..|||| +.+|
T Consensus 78 ~~~~~~--~~~~~~~~~y~~~~~~~ 100 (100)
T PF12756_consen 78 RNSESE--ESWEEFEKFYDFWSNDY 100 (100)
T ss_dssp -S-----------------------
T ss_pred cccccc--cccccccccccccccCC
Confidence 987643 668899999999 5554
No 3
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=99.68 E-value=1.3e-17 Score=163.63 Aligned_cols=160 Identities=21% Similarity=0.376 Sum_probs=115.0
Q ss_pred cccccccCccCCHHHHHHHhhcHhHHH-hhhcCCCcccchhcccccCCCCCCCCCCCccccC---CCCCCCCcccccccC
Q 016443 46 YSCGLCGKGYRSSKALAQHLNSRSHIM-RASQGTSNEEKEKVIIKPIPLRDVNKPPRKREAN---NEESEDSDDEWEEVG 121 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~SKKHk~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~d~d~e~eweev~ 121 (389)
+.|.+|.|.|...|+++.||+.|.|++ |+++... + ...+|..+... ...-+..++.+ .++..+.+++|.+|.
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK~HrrinPknreY--D-kfyiINY~ev~-ks~t~~~~e~dret~~d~~E~D~~wsDw~ 271 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREY--D-KFYIINYLEVG-KSWTIVHSEDDRETNEDINETDDTWSDWN 271 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhccCcccCCCcccc--c-eEEEEeHhhcC-Cccchhhhhhhhhhhccccccccchhhhh
Confidence 679999999999999999999999999 5554321 1 13344332100 00000000100 112233456676666
Q ss_pred CchhhhhhhcccccccCCCCCCCCCCcccCCCCCCCCCCCCccccCCCCCCCHHHHHHHhhhhcCCCCCCcc--c---cc
Q 016443 122 PDEVLVSEATNSLTNLNVGSPADDDLEEDDDDGAFEEFDPACCFMCDLPHDAIENCMVHMHKCHGFFIPDVE--Y---LK 196 (389)
Q Consensus 122 ~~e~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~e--y---lv 196 (389)
+++. ++ ....||||.+...++..+++||..+|-|+|-... | .|
T Consensus 272 ed~a-------------------------------~a-~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~Y 319 (423)
T KOG2482|consen 272 EDDA-------------------------------EA-LSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFY 319 (423)
T ss_pred cCCC-------------------------------Cc-cceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchh
Confidence 5431 11 2368999999999999999999999999999884 3 38
Q ss_pred CHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhCCCccccC
Q 016443 197 DPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAKRHCKIHF 245 (389)
Q Consensus 197 d~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~dK~Hcki~~ 245 (389)
....|||||+++++. ..|..|. -+|.+..+++.||..-.|.-|..
T Consensus 320 qrvrviNyiRkq~~~-~~c~~cd---~~F~~e~~l~~hm~e~k~l~i~p 364 (423)
T KOG2482|consen 320 QRVRVINYIRKQKKK-SRCAECD---LSFWKEPGLLIHMVEDKHLSILP 364 (423)
T ss_pred hhhhHHHHHHHHhhc-ccccccc---ccccCcchhhhhccccccccccC
Confidence 999999999999885 7999998 58999999999999988887764
No 4
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=99.48 E-value=3.5e-14 Score=139.66 Aligned_cols=95 Identities=25% Similarity=0.473 Sum_probs=88.0
Q ss_pred CCCCccccCCCCC-CCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHh
Q 016443 159 FDPACCFMCDLPH-DAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEA 237 (389)
Q Consensus 159 ~~~~~CLFC~~~s-~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~d 237 (389)
+-..+||||+... .+..+.+.||+..|||.|..++.||....||..|.+++. .++||||. |.|++...|+.||+.
T Consensus 142 ~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~-r~~CLyCe---kifrdkntLkeHMrk 217 (423)
T KOG2482|consen 142 IFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLE-RLRCLYCE---KIFRDKNTLKEHMRK 217 (423)
T ss_pred eeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHh-hheeeeec---cccCCcHHHHHHHHh
Confidence 4567999999988 589999999999999999999999999999999999987 58999999 899999999999999
Q ss_pred CCCccccCCCCChhHHHHhhhhcccC
Q 016443 238 KRHCKIHFGDGDDEEEAELEEFYDYS 263 (389)
Q Consensus 238 K~Hcki~~~~~~~e~~~e~~~FYDf~ 263 (389)
|+|.+|+... .||++||-..
T Consensus 218 K~HrrinPkn------reYDkfyiIN 237 (423)
T KOG2482|consen 218 KRHRRINPKN------REYDKFYIIN 237 (423)
T ss_pred ccCcccCCCc------cccceEEEEe
Confidence 9999998864 6999999874
No 5
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=98.49 E-value=5.2e-08 Score=62.75 Aligned_cols=26 Identities=35% Similarity=0.732 Sum_probs=25.0
Q ss_pred cccccccCccCCHHHHHHHhhcHhHH
Q 016443 46 YSCGLCGKGYRSSKALAQHLNSRSHI 71 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~SKKHk 71 (389)
|.|.+|+|.|.|+++|++|++|++||
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCcccCCCCcCCHHHHHHHHccCCCC
Confidence 67999999999999999999999997
No 6
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.33 E-value=2.7e-07 Score=57.92 Aligned_cols=25 Identities=40% Similarity=0.929 Sum_probs=24.1
Q ss_pred cccccccCccCCHHHHHHHhhcHhH
Q 016443 46 YSCGLCGKGYRSSKALAQHLNSRSH 70 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~SKKH 70 (389)
|.|.+|+++|+|+++|++|++|++|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 5799999999999999999999998
No 7
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.19 E-value=1.3e-06 Score=58.80 Aligned_cols=32 Identities=19% Similarity=0.525 Sum_probs=29.1
Q ss_pred ccccccccCccCCHHHHHHHhhcHhHHHhhhc
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSRSHIMRASQ 76 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~ 76 (389)
.|.|.+|++.|.+..+|++|++|++|+.++..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 46799999999999999999999999998653
No 8
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=97.97 E-value=2.8e-06 Score=88.07 Aligned_cols=30 Identities=17% Similarity=0.144 Sum_probs=27.9
Q ss_pred cccchhhhhhhhhhcCCCCCCHHHHHHHHH
Q 016443 2 WKIFLFLLLPIKQVAGVPGVTEALFLARQA 31 (389)
Q Consensus 2 ~k~~~hr~NlKRKVA~LPPVTaE~F~~k~~ 31 (389)
||+||||||+||||++||++|+|+|.....
T Consensus 86 yksD~HR~N~Krkl~~~~ils~edFe~i~s 115 (591)
T KOG2505|consen 86 YKSDWHRFNTKRKLRGKPILSEEDFEGIIS 115 (591)
T ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHhhh
Confidence 899999999999999999999999997643
No 9
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=1.3e-05 Score=82.61 Aligned_cols=30 Identities=33% Similarity=0.628 Sum_probs=28.3
Q ss_pred cccccccCccCCHHHHHHHhhcHhHHHhhh
Q 016443 46 YSCGLCGKGYRSSKALAQHLNSRSHIMRAS 75 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~SKKHk~~~~ 75 (389)
++|.+|+|+|.|++|++||.+||||+++++
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~ 322 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVA 322 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHH
Confidence 679999999999999999999999999865
No 10
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=97.15 E-value=0.00038 Score=70.56 Aligned_cols=33 Identities=15% Similarity=0.389 Sum_probs=30.7
Q ss_pred ccccccccCccCCHHHHHHHhhcHhHHHhhhcC
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSRSHIMRASQG 77 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~~ 77 (389)
.|+|..|...|.+....+.|++|-||+.|++..
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRk 35 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRK 35 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhH
Confidence 589999999999999999999999999998754
No 11
>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=96.87 E-value=0.00058 Score=41.74 Aligned_cols=22 Identities=36% Similarity=0.958 Sum_probs=20.7
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 016443 46 YSCGLCGKGYRSSKALAQHLNS 67 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~S 67 (389)
|.|..|+|.|.+...|+.|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5799999999999999999986
No 12
>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=96.35 E-value=0.0022 Score=38.64 Aligned_cols=22 Identities=41% Similarity=1.038 Sum_probs=18.4
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 016443 46 YSCGLCGKGYRSSKALAQHLNS 67 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~S 67 (389)
|.|.+|+++|.+..+|+.|+..
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 5799999999999999999975
No 13
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.18 E-value=0.0028 Score=40.14 Aligned_cols=24 Identities=38% Similarity=0.750 Sum_probs=21.5
Q ss_pred ccccccccCccCCHHHHHHHhhcH
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSR 68 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SK 68 (389)
+|.|..|++.|.+..+|..|+++.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 378999999999999999999654
No 14
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=96.08 E-value=0.008 Score=58.90 Aligned_cols=58 Identities=24% Similarity=0.433 Sum_probs=39.9
Q ss_pred CCccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhCCC
Q 016443 161 PACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAKRH 240 (389)
Q Consensus 161 ~~~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~dK~H 240 (389)
+..|.||++.|+-.=-+--|+...= |+| -+.|-.|+ |.|.+...||.||+--++
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHT--------------------GEK---PF~C~hC~---kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHT--------------------GEK---PFSCPHCG---KAFADRSNLRAHMQTHSD 240 (279)
T ss_pred CcccccccccccchHHhhccccccc--------------------CCC---CccCCccc---chhcchHHHHHHHHhhcC
Confidence 4567777777764444445665432 233 36788887 889999999999988777
Q ss_pred ccccC
Q 016443 241 CKIHF 245 (389)
Q Consensus 241 cki~~ 245 (389)
.| .|
T Consensus 241 ~K-~~ 244 (279)
T KOG2462|consen 241 VK-KH 244 (279)
T ss_pred Cc-cc
Confidence 76 44
No 15
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=95.74 E-value=0.0049 Score=53.55 Aligned_cols=76 Identities=18% Similarity=0.207 Sum_probs=48.2
Q ss_pred cccchhhhhhhhhhc--CCCCCCHHHHHHHHHHHHHhhhc-cCCCCccccccccCccCCHHHHHHHhhcHhHHHhhhcC
Q 016443 2 WKIFLFLLLPIKQVA--GVPGVTEALFLARQAALAQEKNK-NATPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRASQG 77 (389)
Q Consensus 2 ~k~~~hr~NlKRKVA--~LPPVTaE~F~~k~~~~a~~~~~-~~~~~~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~~ 77 (389)
.+++-||-|.=|.-+ +|+-|-...=..+...+.++-.. --.-..|+|..|.+-|-+..+++.|.++|.||.++++.
T Consensus 11 ~~~~~hr~~r~r~~~r~dLDqi~~dl~~~~~kll~~~~D~dlPG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l 89 (129)
T KOG3408|consen 11 HRSNRHRINRTRGRARKDLDQIDEDLETQKGKLLNQEIDPDLPGGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKEL 89 (129)
T ss_pred ccchhHHHHhhhccCcccccccccccccccchhhcCcCCCCCCCCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhc
Confidence 345666766655444 45555554433332222222111 11223478999999999999999999999999998754
No 16
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.73 E-value=0.0046 Score=49.76 Aligned_cols=30 Identities=37% Similarity=0.799 Sum_probs=26.2
Q ss_pred ccccccccCccCCHHHHHHHhhcHhHHHhh
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSRSHIMRA 74 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SKKHk~~~ 74 (389)
.+.|.+|++.|.|..+++.||+++.|+...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~ 79 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRN 79 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCcc
Confidence 478999999999999999999999999853
No 17
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=95.59 E-value=0.0097 Score=41.65 Aligned_cols=31 Identities=26% Similarity=0.379 Sum_probs=19.7
Q ss_pred cccccccCcc--CCHHHHHHHhhcHhHHHhhhc
Q 016443 46 YSCGLCGKGY--RSSKALAQHLNSRSHIMRASQ 76 (389)
Q Consensus 46 ~~C~~C~K~F--~S~nay~nHl~SKKHk~~~~~ 76 (389)
|.|.+|++.| .|...-++|.++.+|++++..
T Consensus 4 yyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 4 YYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp -B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred eecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 6799999999 555788999999999998753
No 18
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.25 E-value=0.015 Score=35.17 Aligned_cols=21 Identities=43% Similarity=0.947 Sum_probs=19.7
Q ss_pred cccccccCccCCHHHHHHHhh
Q 016443 46 YSCGLCGKGYRSSKALAQHLN 66 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~ 66 (389)
+.|..|+++|.+...+..|++
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 469999999999999999998
No 19
>PLN02748 tRNA dimethylallyltransferase
Probab=94.88 E-value=0.017 Score=60.96 Aligned_cols=34 Identities=29% Similarity=0.535 Sum_probs=30.1
Q ss_pred CccccccccC-ccCCHHHHHHHhhcHhHHHhhhcC
Q 016443 44 MTYSCGLCGK-GYRSSKALAQHLNSRSHIMRASQG 77 (389)
Q Consensus 44 ~~~~C~~C~K-~F~S~nay~nHl~SKKHk~~~~~~ 77 (389)
..|.|.+|++ ++..+..|+.|++|++||.+++..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~ 451 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRL 451 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHH
Confidence 4578999997 899999999999999999986643
No 20
>PTZ00448 hypothetical protein; Provisional
Probab=94.77 E-value=0.019 Score=58.43 Aligned_cols=33 Identities=24% Similarity=0.412 Sum_probs=30.6
Q ss_pred ccccccccCccCCHHHHHHHhhcHhHHHhhhcC
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSRSHIMRASQG 77 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~~ 77 (389)
.|+|..|+-.|.+.+.++.|++|-||+.|.+..
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRk 346 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRN 346 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHH
Confidence 578999999999999999999999999997754
No 21
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.24 E-value=0.0051 Score=39.34 Aligned_cols=25 Identities=36% Similarity=0.824 Sum_probs=22.9
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCC
Q 016443 213 FMCLYCNDRCHPFNSLEAVRKHMEAKRH 240 (389)
Q Consensus 213 ~~Cl~C~~~~k~F~s~eav~~HM~dK~H 240 (389)
+.|..|+ +.|.|..++++||..|.|
T Consensus 2 ~~C~~C~---k~f~~~~~~~~H~~sk~H 26 (27)
T PF12171_consen 2 FYCDACD---KYFSSENQLKQHMKSKKH 26 (27)
T ss_dssp CBBTTTT---BBBSSHHHHHCCTTSHHH
T ss_pred CCcccCC---CCcCCHHHHHHHHccCCC
Confidence 5799998 899999999999999877
No 22
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=93.76 E-value=0.035 Score=35.05 Aligned_cols=25 Identities=44% Similarity=0.953 Sum_probs=21.7
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCCcc
Q 016443 213 FMCLYCNDRCHPFNSLEAVRKHMEAKRHCK 242 (389)
Q Consensus 213 ~~Cl~C~~~~k~F~s~eav~~HM~dK~Hck 242 (389)
+.|..|+ +.|.+..++..|| +.||+
T Consensus 2 ~~C~~C~---~~F~~~~~l~~H~--~~h~~ 26 (27)
T PF13912_consen 2 FECDECG---KTFSSLSALREHK--RSHCS 26 (27)
T ss_dssp EEETTTT---EEESSHHHHHHHH--CTTTT
T ss_pred CCCCccC---CccCChhHHHHHh--HHhcC
Confidence 4799998 8999999999999 66664
No 23
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.42 E-value=0.017 Score=35.85 Aligned_cols=24 Identities=38% Similarity=0.866 Sum_probs=21.9
Q ss_pred eeeecCCCCCCCCCHHHHHHHHHhCCC
Q 016443 214 MCLYCNDRCHPFNSLEAVRKHMEAKRH 240 (389)
Q Consensus 214 ~Cl~C~~~~k~F~s~eav~~HM~dK~H 240 (389)
.|-.|+ +.|.|...+++||+.+.|
T Consensus 2 ~C~~C~---~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 2 YCDICN---KSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EETTTT---EEESSHHHHHHHHTTHHH
T ss_pred CCCCCC---CCcCCHHHHHHHHCcCCC
Confidence 688998 899999999999999876
No 24
>PHA02768 hypothetical protein; Provisional
Probab=92.61 E-value=0.071 Score=40.41 Aligned_cols=23 Identities=35% Similarity=0.817 Sum_probs=21.8
Q ss_pred ccccccccCccCCHHHHHHHhhc
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNS 67 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~S 67 (389)
.|.|..|+|.|+...++..|+++
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~ 27 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK 27 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh
Confidence 47899999999999999999998
No 25
>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=92.49 E-value=0.053 Score=32.87 Aligned_cols=22 Identities=27% Similarity=0.762 Sum_probs=19.9
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHh
Q 016443 213 FMCLYCNDRCHPFNSLEAVRKHMEA 237 (389)
Q Consensus 213 ~~Cl~C~~~~k~F~s~eav~~HM~d 237 (389)
+.|-.|+ +.|.+...++.||+.
T Consensus 1 y~C~~C~---~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICG---KSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTT---EEESSHHHHHHHHHH
T ss_pred CCCCCCC---CccCCHHHHHHHHhH
Confidence 3799998 899999999999985
No 26
>PHA00616 hypothetical protein
Probab=91.94 E-value=0.07 Score=38.64 Aligned_cols=27 Identities=37% Similarity=0.640 Sum_probs=22.4
Q ss_pred ccccccccCccCCHHHHHHHhhcHhHHH
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSRSHIM 72 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SKKHk~ 72 (389)
.|+|..|++.|.....+..|+++ .|.+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~-~hg~ 27 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS-VHKQ 27 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH-hcCC
Confidence 37899999999999999999954 3443
No 27
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=91.93 E-value=0.19 Score=38.00 Aligned_cols=31 Identities=23% Similarity=0.585 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHH
Q 016443 197 DPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRK 233 (389)
Q Consensus 197 d~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~ 233 (389)
-+..||.|||.+ .+-|+||+ -+|.|.+.+..
T Consensus 15 ~L~~l~~YLR~~---~~YC~~Cg---~~Y~d~~dL~~ 45 (55)
T PF13821_consen 15 RLDKLLSYLREE---HNYCFWCG---TKYDDEEDLER 45 (55)
T ss_pred HHHHHHHHHHhh---CceeeeeC---CccCCHHHHHh
Confidence 467899999998 46999998 57888877653
No 28
>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=91.22 E-value=0.13 Score=30.72 Aligned_cols=22 Identities=36% Similarity=0.822 Sum_probs=17.9
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHh
Q 016443 213 FMCLYCNDRCHPFNSLEAVRKHMEA 237 (389)
Q Consensus 213 ~~Cl~C~~~~k~F~s~eav~~HM~d 237 (389)
+.|-.|+ +.|.+..+++.||..
T Consensus 1 ~~C~~C~---~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICG---KSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS----EESSHHHHHHHHHH
T ss_pred CCCcCCC---CcCCcHHHHHHHHHh
Confidence 3799998 899999999999975
No 29
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=89.90 E-value=0.27 Score=36.40 Aligned_cols=27 Identities=30% Similarity=0.516 Sum_probs=23.8
Q ss_pred ccccccCccCCHHHHHHHhhcHhHHHhhhc
Q 016443 47 SCGLCGKGYRSSKALAQHLNSRSHIMRASQ 76 (389)
Q Consensus 47 ~C~~C~K~F~S~nay~nHl~SKKHk~~~~~ 76 (389)
+|+.|...|.+ |..|+.|++|+.-+.+
T Consensus 7 YCE~C~~ky~~---l~~Hi~s~~Hr~FA~~ 33 (49)
T PF07535_consen 7 YCENCRVKYDD---LEEHIQSEKHRKFAEN 33 (49)
T ss_pred cCccccchhhh---HHHHhCCHHHHHHHcC
Confidence 59999999986 8999999999997654
No 30
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=89.45 E-value=0.44 Score=48.62 Aligned_cols=64 Identities=19% Similarity=0.310 Sum_probs=54.9
Q ss_pred CCCcccc--CCCCCCCHHHHHHHhhhhc-CCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHH
Q 016443 160 DPACCFM--CDLPHDAIENCMVHMHKCH-GFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHME 236 (389)
Q Consensus 160 ~~~~CLF--C~~~s~s~e~nl~HM~~~H-~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~ 236 (389)
+.-.|-| |.....+......||.+.| ||.-| .+.|-+|. |.|.+=.+|-.|++
T Consensus 318 ~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~---------------------~Y~CH~Cd---r~ft~G~~L~~HL~ 373 (467)
T KOG3608|consen 318 TVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPI---------------------LYACHCCD---RFFTSGKSLSAHLM 373 (467)
T ss_pred cceecCCCCCcHHHHHHHHHHHHHHHhccCCCCC---------------------ceeeecch---hhhccchhHHHHHH
Confidence 3456888 9999999999999999999 76533 25899998 88999999999999
Q ss_pred hCCCccccCCC
Q 016443 237 AKRHCKIHFGD 247 (389)
Q Consensus 237 dK~Hcki~~~~ 247 (389)
.|.-.+||++-
T Consensus 374 kkH~f~~PsGh 384 (467)
T KOG3608|consen 374 KKHGFRLPSGH 384 (467)
T ss_pred HhhcccCCCCC
Confidence 99999999864
No 31
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=89.35 E-value=0.18 Score=33.49 Aligned_cols=28 Identities=36% Similarity=0.708 Sum_probs=25.0
Q ss_pred CceeeecCCCCCCCCCHHHHHHHHHhCCCcc
Q 016443 212 DFMCLYCNDRCHPFNSLEAVRKHMEAKRHCK 242 (389)
Q Consensus 212 ~~~Cl~C~~~~k~F~s~eav~~HM~dK~Hck 242 (389)
.+.|..|+ +.|.+..++++|+..+.|-+
T Consensus 3 ~~~C~~C~---~~~~~~~~~~~H~~gk~H~~ 30 (35)
T smart00451 3 GFYCKLCN---VTFTDEISVEAHLKGKKHKK 30 (35)
T ss_pred CeEccccC---CccCCHHHHHHHHChHHHHH
Confidence 46899999 89999999999999998854
No 32
>PHA00733 hypothetical protein
Probab=88.81 E-value=0.64 Score=40.80 Aligned_cols=29 Identities=17% Similarity=0.419 Sum_probs=25.4
Q ss_pred CCccccCCCCCCCHHHHHHHhhhhcCCCC
Q 016443 161 PACCFMCDLPHDAIENCMVHMHKCHGFFI 189 (389)
Q Consensus 161 ~~~CLFC~~~s~s~e~nl~HM~~~H~F~I 189 (389)
+..|-.|+..+........||.+.|+.-+
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~~~~ 127 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHNICV 127 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcCccc
Confidence 35799999999999999999999998643
No 33
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=88.81 E-value=0.3 Score=36.20 Aligned_cols=28 Identities=32% Similarity=0.421 Sum_probs=23.6
Q ss_pred cccccccCccCCHHHHHHHhhcHhHHHhhhc
Q 016443 46 YSCGLCGKGYRSSKALAQHLNSRSHIMRASQ 76 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~ 76 (389)
-+|+.|...|. .|..|+.|++|+.-+..
T Consensus 6 GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~~ 33 (49)
T smart00586 6 GYCENCREKYD---DLETHLLSEKHRRFAEN 33 (49)
T ss_pred cccccHhHHHh---hHHHHhccHHHHHHHcC
Confidence 45999999998 57889999999996553
No 34
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=88.15 E-value=0.73 Score=47.05 Aligned_cols=70 Identities=17% Similarity=0.294 Sum_probs=50.6
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcCCCCCCc----ccc----cCHHHHHHHHHHHhcCCceeee--cCCCCCCCCCHHHHH
Q 016443 163 CCFMCDLPHDAIENCMVHMHKCHGFFIPDV----EYL----KDPKGLLTYLGLKVKRDFMCLY--CNDRCHPFNSLEAVR 232 (389)
Q Consensus 163 ~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~----eyl----vd~~gLl~YL~~kI~~~~~Cl~--C~~~~k~F~s~eav~ 232 (389)
.|..|+...+...++-.||...|+=+=|-. +|+ .|+.+-+.|=.+-+ +.|-. |. -.|++...++
T Consensus 265 kCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~---y~C~h~~C~---~s~r~~~q~~ 338 (467)
T KOG3608|consen 265 KCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTV---YQCEHPDCH---YSVRTYTQMR 338 (467)
T ss_pred cccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccc---eecCCCCCc---HHHHHHHHHH
Confidence 378888888888888889888888766655 232 35555555444333 57877 88 4678999999
Q ss_pred HHHHhC
Q 016443 233 KHMEAK 238 (389)
Q Consensus 233 ~HM~dK 238 (389)
.||+.-
T Consensus 339 ~H~~ev 344 (467)
T KOG3608|consen 339 RHFLEV 344 (467)
T ss_pred HHHHHh
Confidence 999874
No 35
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=87.25 E-value=0.24 Score=42.40 Aligned_cols=31 Identities=29% Similarity=0.471 Sum_probs=28.9
Q ss_pred cccccccCccCCHHHHHHHhhcHhHHHhhhc
Q 016443 46 YSCGLCGKGYRSSKALAQHLNSRSHIMRASQ 76 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~ 76 (389)
++|--|.+-|-|+.|+..|.++|-|+.++..
T Consensus 56 hYCieCaryf~t~~aL~~HkkgkvHkRR~Ke 86 (126)
T COG5112 56 HYCIECARYFITEKALMEHKKGKVHKRRAKE 86 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhccchhHHHHHH
Confidence 5799999999999999999999999998764
No 36
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=86.07 E-value=0.79 Score=42.34 Aligned_cols=62 Identities=18% Similarity=0.220 Sum_probs=44.1
Q ss_pred hhcCCCCCCHHHHHHH---HHHH-HHhhhc-------cCCCCccccccccCccCCHHHHHHHhhcHhHHHhhh
Q 016443 14 QVAGVPGVTEALFLAR---QAAL-AQEKNK-------NATPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRAS 75 (389)
Q Consensus 14 KVA~LPPVTaE~F~~k---~~~~-a~~~~~-------~~~~~~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~ 75 (389)
.-|.=|||+.|...++ +..- .-++.. .+....|+|.+|+-+|...-.|-.||+-|+|..+..
T Consensus 33 ~~k~~~~vqre~L~~rdykvdl~sKLgkt~vitk~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlg 105 (193)
T KOG4727|consen 33 LKKDGPPVQREHLKHRDYKVDLESKLGKTVVITKSTPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLG 105 (193)
T ss_pred HhhcCCchhHHHHhhhhhhhHhHhhccceeEeccCCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHh
Confidence 3467799998887765 1111 111111 123456899999999999999999999999999754
No 37
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.70 E-value=0.89 Score=49.96 Aligned_cols=80 Identities=20% Similarity=0.392 Sum_probs=59.4
Q ss_pred CCCccccCCCCCCCHHHHHHHhhhhcCCCCCCc-----cc------ccCHHHHHHHHH-----HHhcCC-ceeeecCCCC
Q 016443 160 DPACCFMCDLPHDAIENCMVHMHKCHGFFIPDV-----EY------LKDPKGLLTYLG-----LKVKRD-FMCLYCNDRC 222 (389)
Q Consensus 160 ~~~~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~-----ey------lvd~~gLl~YL~-----~kI~~~-~~Cl~C~~~~ 222 (389)
.-..|++| ..+.+++.+-.||...|+++.-.. .+ +|=...|...+. .+...| -+|++|+
T Consensus 114 ~~~~~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~--- 189 (669)
T KOG2231|consen 114 NKKECLHC-TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCH--- 189 (669)
T ss_pred ccCCCccc-cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhh---
Confidence 34579999 888999999999999999987333 11 355566666664 444555 6899999
Q ss_pred CCCCCHHHHHHHHHh-CCCccc
Q 016443 223 HPFNSLEAVRKHMEA-KRHCKI 243 (389)
Q Consensus 223 k~F~s~eav~~HM~d-K~Hcki 243 (389)
..|-....++.||+- .-+|.+
T Consensus 190 ~~fld~~el~rH~~~~h~~chf 211 (669)
T KOG2231|consen 190 ERFLDDDELYRHLRFDHEFCHF 211 (669)
T ss_pred hhhccHHHHHHhhccceeheee
Confidence 678999999999983 445544
No 38
>PHA02768 hypothetical protein; Provisional
Probab=85.22 E-value=0.55 Score=35.61 Aligned_cols=26 Identities=15% Similarity=0.437 Sum_probs=23.3
Q ss_pred CCceeeecCCCCCCCCCHHHHHHHHHhCCCc
Q 016443 211 RDFMCLYCNDRCHPFNSLEAVRKHMEAKRHC 241 (389)
Q Consensus 211 ~~~~Cl~C~~~~k~F~s~eav~~HM~dK~Hc 241 (389)
.|+.|-.|+ +.|....+|+.||+. |.
T Consensus 4 ~~y~C~~CG---K~Fs~~~~L~~H~r~--H~ 29 (55)
T PHA02768 4 LGYECPICG---EIYIKRKSMITHLRK--HN 29 (55)
T ss_pred cccCcchhC---CeeccHHHHHHHHHh--cC
Confidence 468999998 899999999999998 55
No 39
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=84.42 E-value=0.63 Score=44.88 Aligned_cols=30 Identities=20% Similarity=0.403 Sum_probs=27.1
Q ss_pred cccccccCccCCHHHHHHHhhcHhHHHhhhc
Q 016443 46 YSCGLCGKGYRSSKALAQHLNSRSHIMRASQ 76 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~ 76 (389)
..|.+|+--.. ++-|+.|++||+|++++.+
T Consensus 36 l~C~vCn~piK-p~lW~vHvnsKkHre~id~ 65 (264)
T KOG3032|consen 36 LVCRVCNVPIK-PSLWDVHVNSKKHREAIDS 65 (264)
T ss_pred eeEEEecCccc-HHHHHHHhccHHHHHHHHH
Confidence 57999999999 9999999999999997543
No 40
>PHA00616 hypothetical protein
Probab=83.84 E-value=0.54 Score=34.07 Aligned_cols=33 Identities=18% Similarity=0.270 Sum_probs=27.2
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCCCCCCccc
Q 016443 162 ACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEY 194 (389)
Q Consensus 162 ~~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~ey 194 (389)
-+|+.|+..+........||.+.||=.--..+|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 479999999999999999999999964333343
No 41
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=83.22 E-value=0.89 Score=43.36 Aligned_cols=63 Identities=21% Similarity=0.386 Sum_probs=40.1
Q ss_pred CCCCccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHH
Q 016443 159 FDPACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHME 236 (389)
Q Consensus 159 ~~~~~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~ 236 (389)
+.|-.|-.|++.+...-..-.|..+.||- ..-..|-.++-. .++|--|+ -.-...+..-.|..
T Consensus 171 vrpykc~~c~kaftqrcsleshl~kvhgv-----------~~~yaykerr~k-l~vcedcg---~t~~~~e~~~~h~~ 233 (267)
T KOG3576|consen 171 VRPYKCSLCEKAFTQRCSLESHLKKVHGV-----------QHQYAYKERRAK-LYVCEDCG---YTSERPEVYYLHLK 233 (267)
T ss_pred ccccchhhhhHHHHhhccHHHHHHHHcCc-----------hHHHHHHHhhhh-eeeecccC---CCCCChhHHHHHHH
Confidence 35667888888887777777788888884 222345555544 46788886 34445555555554
No 42
>PHA00732 hypothetical protein
Probab=82.44 E-value=0.95 Score=36.59 Aligned_cols=22 Identities=32% Similarity=0.567 Sum_probs=20.2
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 016443 46 YSCGLCGKGYRSSKALAQHLNS 67 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~S 67 (389)
|.|..|++.|.+..+++.|++.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhc
Confidence 6799999999999999999873
No 43
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=82.38 E-value=2.1 Score=31.67 Aligned_cols=49 Identities=14% Similarity=0.317 Sum_probs=37.3
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHh
Q 016443 162 ACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEA 237 (389)
Q Consensus 162 ~~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~d 237 (389)
-.|.||+. .-++..++.|....|... . ....|..|.. . ....+..||.-
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~---~------------------~~v~CPiC~~---~--~~~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSE---S------------------KNVVCPICSS---R--VTDNLIRHLNS 51 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCC---C------------------CCccCCCchh---h--hhhHHHHHHHH
Confidence 36999999 778999999999999863 1 1248999973 2 33488899874
No 44
>smart00355 ZnF_C2H2 zinc finger.
Probab=82.10 E-value=1 Score=26.81 Aligned_cols=20 Identities=35% Similarity=0.707 Sum_probs=18.5
Q ss_pred eeeecCCCCCCCCCHHHHHHHHH
Q 016443 214 MCLYCNDRCHPFNSLEAVRKHME 236 (389)
Q Consensus 214 ~Cl~C~~~~k~F~s~eav~~HM~ 236 (389)
.|..|+ +.|.+...++.||+
T Consensus 2 ~C~~C~---~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECG---KVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCc---chhCCHHHHHHHHH
Confidence 688998 89999999999998
No 45
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=81.80 E-value=0.23 Score=48.86 Aligned_cols=31 Identities=26% Similarity=0.445 Sum_probs=28.2
Q ss_pred ccccccccCccCCHHHHHHHhhcHhHHHhhh
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSRSHIMRAS 75 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~ 75 (389)
-|+|.+|+|.|+++|.|+-|..|-.|.....
T Consensus 25 RwyCqmCQkQcrDeNGFkCH~~SeSHqRql~ 55 (309)
T KOG2837|consen 25 RWYCQMCQKQCRDENGFKCHTMSESHQRQLL 55 (309)
T ss_pred HHHHHHHHHHhccccccccccCCHHHHHHHH
Confidence 4789999999999999999999999998544
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=81.33 E-value=0.85 Score=27.92 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=18.3
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcC
Q 016443 163 CCFMCDLPHDAIENCMVHMHKCHG 186 (389)
Q Consensus 163 ~CLFC~~~s~s~e~nl~HM~~~H~ 186 (389)
.|-+|+..+. ......||...|+
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCcCC-HHHHHHHHHhhCc
Confidence 4899999997 7788899999986
No 47
>PHA00732 hypothetical protein
Probab=80.68 E-value=1.5 Score=35.43 Aligned_cols=45 Identities=18% Similarity=0.424 Sum_probs=36.3
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhC
Q 016443 163 CCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAK 238 (389)
Q Consensus 163 ~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~dK 238 (389)
.|-.|+..+.+......||...|. +..|-.|+ +.|. .+..|+..|
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~r~~H~-------------------------~~~C~~Cg---KsF~---~l~~H~~~~ 47 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHARRNHT-------------------------LTKCPVCN---KSYR---RLNQHFYSQ 47 (79)
T ss_pred cCCCCCCccCCHHHHHHHhhcccC-------------------------CCccCCCC---CEeC---Chhhhhccc
Confidence 599999999999999999986664 12699998 7777 588888666
No 48
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=80.66 E-value=1.3 Score=28.06 Aligned_cols=21 Identities=24% Similarity=0.725 Sum_probs=17.9
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 016443 46 YSCGLCGKGYRSSKALAQHLNS 67 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~S 67 (389)
..|..|+.+| ...++..|++.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4699999999 88899999763
No 49
>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=78.85 E-value=0.97 Score=28.63 Aligned_cols=15 Identities=33% Similarity=0.966 Sum_probs=12.5
Q ss_pred CCccccccccCccCC
Q 016443 43 PMTYSCGLCGKGYRS 57 (389)
Q Consensus 43 ~~~~~C~~C~K~F~S 57 (389)
...|.|..|+|+|.+
T Consensus 12 ~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 12 EKPYKCPYCGKSFSN 26 (26)
T ss_dssp SSSEEESSSSEEESS
T ss_pred CCCCCCCCCcCeeCc
Confidence 346899999999974
No 50
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=78.59 E-value=1 Score=45.99 Aligned_cols=32 Identities=25% Similarity=0.520 Sum_probs=28.4
Q ss_pred cccccccCccCCHHHHHHHhhcHhHHHhhhcC
Q 016443 46 YSCGLCGKGYRSSKALAQHLNSRSHIMRASQG 77 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~~ 77 (389)
++|..|++-|.....|+.|+.+|.|..++...
T Consensus 239 ~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~ 270 (470)
T COG5188 239 VYCVKCGREFSRSKVFEYHLEGKRHCKEGQGK 270 (470)
T ss_pred eeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhh
Confidence 45999999999999999999999999875543
No 51
>PHA00733 hypothetical protein
Probab=78.48 E-value=3.4 Score=36.25 Aligned_cols=50 Identities=20% Similarity=0.467 Sum_probs=41.6
Q ss_pred CCccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhC
Q 016443 161 PACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAK 238 (389)
Q Consensus 161 ~~~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~dK 238 (389)
+..|-.|+..+.+......||.. |. . .+.|-.|+ +.|....++..||..|
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r~-h~-----------------------~-~~~C~~Cg---K~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIRY-TE-----------------------H-SKVCPVCG---KEFRNTDSTLDHVCKK 122 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHhc-CC-----------------------c-CccCCCCC---CccCCHHHHHHHHHHh
Confidence 45799999999999999999974 21 0 15899998 8999999999999876
No 52
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=76.43 E-value=1.1 Score=42.21 Aligned_cols=34 Identities=18% Similarity=0.319 Sum_probs=30.8
Q ss_pred CccccccccCccCCHHHHHHHhhcHhHHHhhhcC
Q 016443 44 MTYSCGLCGKGYRSSKALAQHLNSRSHIMRASQG 77 (389)
Q Consensus 44 ~~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~~ 77 (389)
-.|.|.+|.-.-.++++|-.|..-|||+.|++.+
T Consensus 52 G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarr 85 (222)
T KOG0227|consen 52 GKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARR 85 (222)
T ss_pred cceeehhhhhhhcchhhhhhhhccchhhHHHHHH
Confidence 3589999999999999999999999999987654
No 53
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=75.54 E-value=2.4 Score=31.35 Aligned_cols=22 Identities=32% Similarity=0.718 Sum_probs=19.0
Q ss_pred ccccccccCccCCHHHHHHHhhc
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNS 67 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~S 67 (389)
.|.|.+|+| ..|..+|..|+..
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~ 23 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED 23 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh
Confidence 478999999 7889999999864
No 54
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=75.21 E-value=1.5 Score=40.96 Aligned_cols=34 Identities=21% Similarity=0.358 Sum_probs=30.5
Q ss_pred CccccccccCccCCHHHHHHHhhcHhHHHhhhcC
Q 016443 44 MTYSCGLCGKGYRSSKALAQHLNSRSHIMRASQG 77 (389)
Q Consensus 44 ~~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~~ 77 (389)
-.|.|.+|.-+--|+++|..|..-|||+.|.+.+
T Consensus 52 Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rr 85 (222)
T COG5246 52 GKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRR 85 (222)
T ss_pred CcEEeeeeccccccHHHHHHhhccchhhhhHHHH
Confidence 3578999999999999999999999999986644
No 55
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=71.94 E-value=3.5 Score=39.85 Aligned_cols=33 Identities=15% Similarity=0.517 Sum_probs=27.4
Q ss_pred cCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHH
Q 016443 196 KDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKH 234 (389)
Q Consensus 196 vd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~H 234 (389)
-++..|..||+.- .+-||||| -.|.+.++|-.|
T Consensus 226 e~lt~in~~LR~e---h~YC~fCG---~~y~~~edl~eh 258 (268)
T KOG1994|consen 226 ERLTKINIFLRSE---HYYCFFCG---IKYKDEEDLYEH 258 (268)
T ss_pred HHHHHHHHHHhcc---ceEEEEec---cccCCHHHHHHh
Confidence 3677899999976 46899998 578999999876
No 56
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=69.06 E-value=3.6 Score=34.60 Aligned_cols=74 Identities=24% Similarity=0.416 Sum_probs=48.7
Q ss_pred CCCCccccCCCCCCCHHHHHHHhhhhcCCCC------------------CCcccc---cCHHHHHHHHHHHhcCCcee--
Q 016443 159 FDPACCFMCDLPHDAIENCMVHMHKCHGFFI------------------PDVEYL---KDPKGLLTYLGLKVKRDFMC-- 215 (389)
Q Consensus 159 ~~~~~CLFC~~~s~s~e~nl~HM~~~H~F~I------------------P~~eyl---vd~~gLl~YL~~kI~~~~~C-- 215 (389)
.....|.-|.+.-.. .+...|+...|.-.- ++.+-+ -+...-|..| .|+.|+.|
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gL--p~~~G~~C~~ 85 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGL--PVYDGYRCQC 85 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCC--CCCCCeeeec
Confidence 466789999876644 788899997775431 111111 1111122222 56789999
Q ss_pred --eecCCCCCCCCCHHHHHHHHHhC
Q 016443 216 --LYCNDRCHPFNSLEAVRKHMEAK 238 (389)
Q Consensus 216 --l~C~~~~k~F~s~eav~~HM~dK 238 (389)
..|+. .+.+...++.|++.+
T Consensus 86 ~~~~C~y---~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 86 DPPHCGY---ITRSKKTMRKHWRKE 107 (109)
T ss_pred CCCCCCc---EeccHHHHHHHHHHh
Confidence 99985 457999999999875
No 57
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=68.59 E-value=3.6 Score=43.86 Aligned_cols=33 Identities=18% Similarity=0.359 Sum_probs=30.1
Q ss_pred ccccccccCccCCHHHHHHHhhcHhHHHhhhcC
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSRSHIMRASQG 77 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~~ 77 (389)
.+.|..|+-.|.|.+..+.|.+|-+|+.|..+.
T Consensus 66 ~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krk 98 (591)
T KOG2505|consen 66 SDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRK 98 (591)
T ss_pred cccccccCCccccHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999999999987654
No 58
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=68.01 E-value=3.5 Score=40.84 Aligned_cols=31 Identities=26% Similarity=0.623 Sum_probs=25.8
Q ss_pred CCCccccccccCccCCHHHHHHHhhcHhHHH
Q 016443 42 TPMTYSCGLCGKGYRSSKALAQHLNSRSHIM 72 (389)
Q Consensus 42 ~~~~~~C~~C~K~F~S~nay~nHl~SKKHk~ 72 (389)
....|.|..|+|.|.+..-|+.||+--.+..
T Consensus 212 GEKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 212 GEKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred CCCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 4457899999999999999999998655444
No 59
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=66.95 E-value=3.3 Score=46.57 Aligned_cols=53 Identities=23% Similarity=0.472 Sum_probs=39.3
Q ss_pred CCCCCccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHH
Q 016443 158 EFDPACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHME 236 (389)
Q Consensus 158 ~~~~~~CLFC~~~s~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~kI~~~~~Cl~C~~~~k~F~s~eav~~HM~ 236 (389)
.-++++|+||-+.-+-...+-.|-. +|+= ++ -+.|-.|+ |.|.+.-.|+.||-
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyr-tHtG---ER-------------------PFkCKiCg---RAFtTkGNLkaH~~ 654 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYR-THTG---ER-------------------PFKCKICG---RAFTTKGNLKAHMS 654 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhh-cccC---cC-------------------cccccccc---chhccccchhhccc
Confidence 3478999999998877777777766 4541 22 36788887 88888888888884
No 60
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=63.24 E-value=2.3 Score=47.23 Aligned_cols=31 Identities=23% Similarity=0.496 Sum_probs=27.5
Q ss_pred CCCccccccccCccCCHHHHHHHhhcHhHHH
Q 016443 42 TPMTYSCGLCGKGYRSSKALAQHLNSRSHIM 72 (389)
Q Consensus 42 ~~~~~~C~~C~K~F~S~nay~nHl~SKKHk~ 72 (389)
....|.|.-|+|.|+-.+.|-.||-|||=.-
T Consensus 306 GEKPfeCpnCkKRFSHSGSySSHmSSKKCIs 336 (1007)
T KOG3623|consen 306 GEKPFECPNCKKRFSHSGSYSSHMSSKKCIS 336 (1007)
T ss_pred CCCCcCCcccccccccCCcccccccccchhh
Confidence 3456889999999999999999999999884
No 61
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=57.55 E-value=8.4 Score=24.65 Aligned_cols=20 Identities=25% Similarity=0.605 Sum_probs=17.4
Q ss_pred ccccccCccCCHHHHHHHhhc
Q 016443 47 SCGLCGKGYRSSKALAQHLNS 67 (389)
Q Consensus 47 ~C~~C~K~F~S~nay~nHl~S 67 (389)
.|.+|++.+ +......|+.+
T Consensus 3 ~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 3 QCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHHH
Confidence 599999999 88899999863
No 62
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=57.52 E-value=5.5 Score=27.91 Aligned_cols=22 Identities=36% Similarity=0.673 Sum_probs=14.9
Q ss_pred ccccccccCccCCH----HHHHHHhh
Q 016443 45 TYSCGLCGKGYRSS----KALAQHLN 66 (389)
Q Consensus 45 ~~~C~~C~K~F~S~----nay~nHl~ 66 (389)
...|.+|++.|... ..+..||+
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 35799999999874 88999994
No 63
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=57.02 E-value=1.2 Score=29.26 Aligned_cols=20 Identities=25% Similarity=0.642 Sum_probs=14.9
Q ss_pred cccccccCccCCHHHHHHHhh
Q 016443 46 YSCGLCGKGYRSSKALAQHLN 66 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~ 66 (389)
|+|.-|+|.| +...|++|.+
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 5799999999 7788888853
No 64
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=56.18 E-value=6.1 Score=38.24 Aligned_cols=21 Identities=24% Similarity=0.520 Sum_probs=18.7
Q ss_pred CCccccCCCCCCCHHHHHHHh
Q 016443 161 PACCFMCDLPHDAIENCMVHM 181 (389)
Q Consensus 161 ~~~CLFC~~~s~s~e~nl~HM 181 (389)
.--||||+..+.+-++.+.|-
T Consensus 239 h~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 239 HYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ceEEEEeccccCCHHHHHHhC
Confidence 457999999999999999983
No 65
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=54.19 E-value=6.8 Score=43.65 Aligned_cols=24 Identities=25% Similarity=0.760 Sum_probs=20.0
Q ss_pred CCccccccccCccCCHHHHHHHhh
Q 016443 43 PMTYSCGLCGKGYRSSKALAQHLN 66 (389)
Q Consensus 43 ~~~~~C~~C~K~F~S~nay~nHl~ 66 (389)
...++|.+|...|.--..++.|++
T Consensus 208 sqlltcpycdrgykrltslkeHik 231 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIK 231 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHH
Confidence 345799999999988888888874
No 66
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=52.20 E-value=23 Score=29.72 Aligned_cols=27 Identities=26% Similarity=0.351 Sum_probs=24.4
Q ss_pred CCCcc----ccCCCCCCCHHHHHHHhhhhcC
Q 016443 160 DPACC----FMCDLPHDAIENCMVHMHKCHG 186 (389)
Q Consensus 160 ~~~~C----LFC~~~s~s~e~nl~HM~~~H~ 186 (389)
+--.| ..|++...+....-.|+...||
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 44679 9999999999999999999997
No 67
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=49.47 E-value=8.5 Score=27.94 Aligned_cols=24 Identities=38% Similarity=0.711 Sum_probs=19.4
Q ss_pred cccccccCccCCH-----HHHHHHhhcHhH
Q 016443 46 YSCGLCGKGYRSS-----KALAQHLNSRSH 70 (389)
Q Consensus 46 ~~C~~C~K~F~S~-----nay~nHl~SKKH 70 (389)
-.|.+|+|.+.-. ..|..||++ +|
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~-~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRR-KH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHh-HC
Confidence 3699999999554 699999987 44
No 68
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=47.10 E-value=13 Score=34.15 Aligned_cols=27 Identities=26% Similarity=0.548 Sum_probs=24.1
Q ss_pred cccccccCccCCHHHHHHHhhcHhHHH
Q 016443 46 YSCGLCGKGYRSSKALAQHLNSRSHIM 72 (389)
Q Consensus 46 ~~C~~C~K~F~S~nay~nHl~SKKHk~ 72 (389)
|.|.+|+=.=..+...++||.|+-|++
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E 27 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKE 27 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHH
Confidence 579999877777888999999999998
No 69
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=45.96 E-value=13 Score=38.33 Aligned_cols=65 Identities=29% Similarity=0.517 Sum_probs=46.4
Q ss_pred HHHHhhhhcCCC-CCCcc----cccCHHHHHHHHHHHhc---------------------------------------CC
Q 016443 177 CMVHMHKCHGFF-IPDVE----YLKDPKGLLTYLGLKVK---------------------------------------RD 212 (389)
Q Consensus 177 nl~HM~~~H~F~-IP~~e----ylvd~~gLl~YL~~kI~---------------------------------------~~ 212 (389)
.++.+.+-|-|. ||.+. |+-.+-.|-.||+.=|. .+
T Consensus 159 ylefLk~le~fd~~~~p~Kn~rY~~yl~~L~eYl~~F~~~~ypL~~~~kv~a~~~~~f~~a~~rG~~~~~~~~g~~~~~~ 238 (470)
T COG5188 159 YLEFLKKLERFDLTTEPSKNFRYLEYLSELNEYLGRFIKVKYPLKMFRKVVASAPKIFSRAEARGFGKKNGMEGAEWFPK 238 (470)
T ss_pred HHHHHHHHHHhhccCCcccchhHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhchhHhHHHHHccCCcccccchhhhccc
Confidence 466777778888 66663 56566666666654221 12
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCCcccc
Q 016443 213 FMCLYCNDRCHPFNSLEAVRKHMEAKRHCKIH 244 (389)
Q Consensus 213 ~~Cl~C~~~~k~F~s~eav~~HM~dK~Hcki~ 244 (389)
.-|..|+ |-|+...-...|...|.|||-.
T Consensus 239 ~YC~~C~---r~f~~~~VFe~Hl~gK~H~k~~ 267 (470)
T COG5188 239 VYCVKCG---REFSRSKVFEYHLEGKRHCKEG 267 (470)
T ss_pred eeeHhhh---hHhhhhHHHHHHHhhhhhhhhh
Confidence 3578886 8899989999999999999864
No 70
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=45.44 E-value=20 Score=35.46 Aligned_cols=32 Identities=25% Similarity=0.506 Sum_probs=29.1
Q ss_pred CCCCccccccccCccCCHHHHHHHhhcHhHHH
Q 016443 41 ATPMTYSCGLCGKGYRSSKALAQHLNSRSHIM 72 (389)
Q Consensus 41 ~~~~~~~C~~C~K~F~S~nay~nHl~SKKHk~ 72 (389)
.++++..|.+|++.|--+..-..|.++..|+.
T Consensus 272 t~~ftlRC~~Cq~glvGq~ea~eHA~~TGH~n 303 (307)
T KOG3288|consen 272 TAKFTLRCMVCQMGLVGQKEAAEHAKATGHVN 303 (307)
T ss_pred ccceEEEeeecccceeeHHHHHHHHHhcCCCc
Confidence 46788899999999999999999999999974
No 71
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=45.23 E-value=13 Score=39.57 Aligned_cols=29 Identities=17% Similarity=0.446 Sum_probs=24.8
Q ss_pred ccccccccCccCCHHHHHHHhhcHhHHHhh
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSRSHIMRA 74 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SKKHk~~~ 74 (389)
-+.|..|.+.|.+..++.+||-+ +|....
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~-eH~~~l 85 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQ-EHPAGL 85 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHH-hhhhhc
Confidence 36899999999999999999986 477653
No 72
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=45.14 E-value=14 Score=35.46 Aligned_cols=32 Identities=22% Similarity=0.540 Sum_probs=24.6
Q ss_pred CCCccccccccCccCCHHHHHHHhhcHhHHHhh
Q 016443 42 TPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRA 74 (389)
Q Consensus 42 ~~~~~~C~~C~K~F~S~nay~nHl~SKKHk~~~ 74 (389)
+...|-|.+|+|.|....=.+.||. +||-+.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~v 105 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKV 105 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHh-hcCHHHH
Confidence 4556899999999999999999998 4688854
No 73
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=44.75 E-value=7.4 Score=39.91 Aligned_cols=65 Identities=20% Similarity=0.418 Sum_probs=45.8
Q ss_pred CCCCCHHHHHHHhhhhcCCCCCCc------cc-----ccCHHHHHHHH-------HHHhcCCceeeecCCCCCCCCCHHH
Q 016443 169 LPHDAIENCMVHMHKCHGFFIPDV------EY-----LKDPKGLLTYL-------GLKVKRDFMCLYCNDRCHPFNSLEA 230 (389)
Q Consensus 169 ~~s~s~e~nl~HM~~~H~F~IP~~------ey-----lvd~~gLl~YL-------~~kI~~~~~Cl~C~~~~k~F~s~ea 230 (389)
.....+-+.-.|....|+|+|-+. .| |.-..+|-+.= |-| ...+|++|+ ..|.+-..
T Consensus 161 ~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFK--GHP~C~FC~---~~FYdDDE 235 (493)
T COG5236 161 RRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFK--GHPLCIFCK---IYFYDDDE 235 (493)
T ss_pred hhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcC--CCchhhhcc---ceecChHH
Confidence 344679999999999999998765 11 22233333221 112 235899999 78999999
Q ss_pred HHHHHHhC
Q 016443 231 VRKHMEAK 238 (389)
Q Consensus 231 v~~HM~dK 238 (389)
|..||+.+
T Consensus 236 L~~HcR~~ 243 (493)
T COG5236 236 LRRHCRLR 243 (493)
T ss_pred HHHHHHhh
Confidence 99999987
No 74
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=44.43 E-value=10 Score=42.91 Aligned_cols=23 Identities=26% Similarity=0.454 Sum_probs=19.2
Q ss_pred CCCccccCCCCCCCHHHHHHHhh
Q 016443 160 DPACCFMCDLPHDAIENCMVHMH 182 (389)
Q Consensus 160 ~~~~CLFC~~~s~s~e~nl~HM~ 182 (389)
.|-.|-.|++.|.+--.+-.||.
T Consensus 632 RPFkCKiCgRAFtTkGNLkaH~~ 654 (958)
T KOG1074|consen 632 RPFKCKICGRAFTTKGNLKAHMS 654 (958)
T ss_pred Cccccccccchhccccchhhccc
Confidence 46679999999988888888987
No 75
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=44.34 E-value=9.5 Score=29.26 Aligned_cols=28 Identities=29% Similarity=0.543 Sum_probs=23.0
Q ss_pred CccccccccCccCCHHHHHHHhhcHhHHH
Q 016443 44 MTYSCGLCGKGYRSSKALAQHLNSRSHIM 72 (389)
Q Consensus 44 ~~~~C~~C~K~F~S~nay~nHl~SKKHk~ 72 (389)
..+.|.-|++.|..+..|--|++ |.|-.
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVN-KaH~~ 43 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVN-KAHGW 43 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhh-HHhhh
Confidence 44689999999999999999987 34444
No 76
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=43.91 E-value=12 Score=39.83 Aligned_cols=28 Identities=29% Similarity=0.682 Sum_probs=25.8
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCCccc
Q 016443 213 FMCLYCNDRCHPFNSLEAVRKHMEAKRHCKI 243 (389)
Q Consensus 213 ~~Cl~C~~~~k~F~s~eav~~HM~dK~Hcki 243 (389)
..|+.|+ |.|+|..++..|-.+|.|-+.
T Consensus 293 lyC~vCn---KsFKseKq~kNHEnSKKHken 320 (508)
T KOG0717|consen 293 LYCVVCN---KSFKSEKQLKNHENSKKHKEN 320 (508)
T ss_pred eEEeecc---ccccchHHHHhhHHHHHHHHH
Confidence 5899999 899999999999999999864
No 77
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=41.22 E-value=8.4 Score=36.91 Aligned_cols=27 Identities=22% Similarity=0.378 Sum_probs=23.7
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCCC
Q 016443 162 ACCFMCDLPHDAIENCMVHMHKCHGFF 188 (389)
Q Consensus 162 ~~CLFC~~~s~s~e~nl~HM~~~H~F~ 188 (389)
-+|-=|++++...+..+.|....|-|.
T Consensus 213 ~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 213 YVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred eeecccCCCCCChhHHHHHHHhcCCCC
Confidence 468889999999999999999988763
No 78
>PF14420 Clr5: Clr5 domain
Probab=39.33 E-value=15 Score=27.31 Aligned_cols=25 Identities=28% Similarity=0.481 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhhhhcCCCCCCccc
Q 016443 170 PHDAIENCMVHMHKCHGFFIPDVEY 194 (389)
Q Consensus 170 ~s~s~e~nl~HM~~~H~F~IP~~ey 194 (389)
..-++++.+.||...|||..-...|
T Consensus 19 e~~tl~~v~~~M~~~~~F~at~rqy 43 (54)
T PF14420_consen 19 ENKTLEEVMEIMKEEHGFKATKRQY 43 (54)
T ss_pred CCCcHHHHHHHHHHHhCCCcCHHHH
Confidence 4568999999999999999876655
No 79
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=38.75 E-value=11 Score=33.04 Aligned_cols=28 Identities=29% Similarity=0.669 Sum_probs=26.2
Q ss_pred CceeeecCCCCCCCCCHHHHHHHHHhCCCcc
Q 016443 212 DFMCLYCNDRCHPFNSLEAVRKHMEAKRHCK 242 (389)
Q Consensus 212 ~~~Cl~C~~~~k~F~s~eav~~HM~dK~Hck 242 (389)
.+-||-|. |-|.+..+++.|-+.|-|-+
T Consensus 57 qfyCi~Ca---RyFi~~~~l~~H~ktK~HKr 84 (129)
T KOG3408|consen 57 QFYCIECA---RYFIDAKALKTHFKTKVHKR 84 (129)
T ss_pred eeehhhhh---hhhcchHHHHHHHhccHHHH
Confidence 57999998 89999999999999999986
No 80
>PF12907 zf-met2: Zinc-binding
Probab=38.49 E-value=16 Score=25.98 Aligned_cols=24 Identities=17% Similarity=0.573 Sum_probs=19.1
Q ss_pred cccccccCcc---CCHHHHHHHhhcHh
Q 016443 46 YSCGLCGKGY---RSSKALAQHLNSRS 69 (389)
Q Consensus 46 ~~C~~C~K~F---~S~nay~nHl~SKK 69 (389)
+.|.+|.-+| .+..+|++|..||-
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKH 28 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKH 28 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccC
Confidence 4799999655 67789999998763
No 81
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=33.82 E-value=25 Score=37.08 Aligned_cols=33 Identities=27% Similarity=0.481 Sum_probs=25.3
Q ss_pred CCCccccccccCccCCHHHHHHHhhcHhHHHhh
Q 016443 42 TPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRA 74 (389)
Q Consensus 42 ~~~~~~C~~C~K~F~S~nay~nHl~SKKHk~~~ 74 (389)
+...|.|.+|+|+|....-++-|+-+-.-..++
T Consensus 353 s~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~ 385 (500)
T KOG3993|consen 353 SSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLA 385 (500)
T ss_pred cCceeecHHhhhhhHHHHHHHHhHHhhhccccc
Confidence 334789999999999999999997764433333
No 82
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=33.72 E-value=20 Score=34.14 Aligned_cols=63 Identities=13% Similarity=0.252 Sum_probs=39.9
Q ss_pred hcCCCCCCHHHHHHHH---------HHHHHhhhc----cCCCCccccccccCccCCHHHHHHHhhcHhHHHhhhcCC
Q 016443 15 VAGVPGVTEALFLARQ---------AALAQEKNK----NATPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRASQGT 78 (389)
Q Consensus 15 VA~LPPVTaE~F~~k~---------~~~a~~~~~----~~~~~~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~~~~ 78 (389)
|-++-..++..|.+|- ...-.+... ......++|++|..-| -.+++-||..|--|.-+..+.+
T Consensus 41 v~d~ssldaaqlaek~g~~~fvh~lfe~~~ets~p~nss~~e~lfyCE~Cd~~i-p~~~~snH~tSttHllsl~~~p 116 (223)
T KOG2384|consen 41 VTDESSLDAAQLAEKGGAQAFVHSLFENDRETSHPMNSSRDEALFYCEVCDIYI-PNSKKSNHFTSTTHLLSLQHIP 116 (223)
T ss_pred ccccccchHHHHHHhcChHHHHHHHHHHhccCCCcccCCCCCccchhhhhhhhc-cCCCCccchhhHHHHhhhccCC
Confidence 4456667777777651 111111111 2244568899997554 5577889999999999866553
No 83
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=33.62 E-value=27 Score=31.01 Aligned_cols=39 Identities=21% Similarity=0.583 Sum_probs=24.9
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCCccccCCCCChhHHHHhhhhcccCCCCc
Q 016443 213 FMCLYCNDRCHPFNSLEAVRKHMEAKRHCKIHFGDGDDEEEAELEEFYDYSSSYM 267 (389)
Q Consensus 213 ~~Cl~C~~~~k~F~s~eav~~HM~dK~Hcki~~~~~~~e~~~e~~~FYDf~~sy~ 267 (389)
-+||-|| |.|+++ ..|.+.. ..|. ..||..=|.+...||
T Consensus 73 i~clecG---k~~k~L---krHL~~~--~glt--------p~eYR~kwGlp~dyp 111 (132)
T PF05443_consen 73 IICLECG---KKFKTL---KRHLRTH--HGLT--------PEEYRAKWGLPKDYP 111 (132)
T ss_dssp EE-TBT-----EESBH---HHHHHHT--T-S---------HHHHHHHTT-GGG--
T ss_pred eEEccCC---cccchH---HHHHHHc--cCCC--------HHHHHHHhCcCCCCc
Confidence 4899997 889987 8888875 2232 469999999998886
No 84
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=33.58 E-value=35 Score=40.59 Aligned_cols=31 Identities=26% Similarity=0.423 Sum_probs=28.7
Q ss_pred CCccccccccCccCCHHHHHHHhhcHhHHHh
Q 016443 43 PMTYSCGLCGKGYRSSKALAQHLNSRSHIMR 73 (389)
Q Consensus 43 ~~~~~C~~C~K~F~S~nay~nHl~SKKHk~~ 73 (389)
...|.|..|.-+|.+...+-+||+|-+|+.+
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS~~h~~~ 546 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQSDLHRNE 546 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHHHhhHHH
Confidence 3457899999999999999999999999997
No 85
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.41 E-value=56 Score=33.75 Aligned_cols=74 Identities=18% Similarity=0.322 Sum_probs=52.9
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCC-CC------CCcccccCHHHHHHHHHHHhcCCceee--ec-CCCCCCCCCHHHH
Q 016443 162 ACCFMCDLPHDAIENCMVHMHKCHGF-FI------PDVEYLKDPKGLLTYLGLKVKRDFMCL--YC-NDRCHPFNSLEAV 231 (389)
Q Consensus 162 ~~CLFC~~~s~s~e~nl~HM~~~H~F-~I------P~~eylvd~~gLl~YL~~kI~~~~~Cl--~C-~~~~k~F~s~eav 231 (389)
-.|.||...+-+=+++..||...|-- +| |..+|..+-+.|-.....- ...|. .| ..+.-.|..--.|
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~---hy~ct~qtc~~~k~~vf~~~~el 297 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNA---HYCCTFQTCRVGKCYVFPYHTEL 297 (493)
T ss_pred chhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcC---ceEEEEEEEecCcEEEeccHHHH
Confidence 46999999999999999999999952 33 3346777878887776543 23443 24 2233468888889
Q ss_pred HHHHHhC
Q 016443 232 RKHMEAK 238 (389)
Q Consensus 232 ~~HM~dK 238 (389)
+.|+..-
T Consensus 298 ~~h~~~~ 304 (493)
T COG5236 298 LEHLTRF 304 (493)
T ss_pred HHHHHHH
Confidence 9998764
No 86
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=32.62 E-value=36 Score=25.73 Aligned_cols=24 Identities=33% Similarity=0.671 Sum_probs=17.3
Q ss_pred CccccccccCccCCHHHHHHHhhc
Q 016443 44 MTYSCGLCGKGYRSSKALAQHLNS 67 (389)
Q Consensus 44 ~~~~C~~C~K~F~S~nay~nHl~S 67 (389)
..-+|.+|+-++.+...++-||..
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHHHH
Confidence 445799999999999999999965
No 87
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=32.10 E-value=24 Score=26.63 Aligned_cols=28 Identities=25% Similarity=0.312 Sum_probs=20.8
Q ss_pred CCCccccCCCCCCCHHHHHHHhhhhcCC
Q 016443 160 DPACCFMCDLPHDAIENCMVHMHKCHGF 187 (389)
Q Consensus 160 ~~~~CLFC~~~s~s~e~nl~HM~~~H~F 187 (389)
.|..|.-|+.....-...-.||...|+.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 5678999999999999999999999974
No 88
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=27.91 E-value=40 Score=31.10 Aligned_cols=31 Identities=23% Similarity=0.373 Sum_probs=25.7
Q ss_pred ccccccccC--ccCCHHHHHHHhhcHhHHHhhh
Q 016443 45 TYSCGLCGK--GYRSSKALAQHLNSRSHIMRAS 75 (389)
Q Consensus 45 ~~~C~~C~K--~F~S~nay~nHl~SKKHk~~~~ 75 (389)
-|.|.+|++ +=.|...=+.|+.=+||+.+++
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk 35 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVK 35 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHH
Confidence 367999993 5567888899999999999864
No 89
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=27.36 E-value=31 Score=36.37 Aligned_cols=29 Identities=34% Similarity=0.567 Sum_probs=24.0
Q ss_pred ccccccccCccCCHHHHHHHhhcHhHHHhhh
Q 016443 45 TYSCGLCGKGYRSSKALAQHLNSRSHIMRAS 75 (389)
Q Consensus 45 ~~~C~~C~K~F~S~nay~nHl~SKKHk~~~~ 75 (389)
.|.|.-|+|.|+-..-+..|- +|||-+.+
T Consensus 295 EYrCPEC~KVFsCPANLASHR--RWHKPR~e 323 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHR--RWHKPRPE 323 (500)
T ss_pred eecCCcccccccCchhhhhhh--cccCCchh
Confidence 488999999999999999986 58887643
No 90
>PF09630 DUF2024: Domain of unknown function (DUF2024); InterPro: IPR018592 This protein of 86 residues is expressed in bacteria. It consists of two alpha helices and four beta strands. Its function is unknown.; PDB: 2HFQ_A.
Probab=26.58 E-value=16 Score=29.84 Aligned_cols=31 Identities=19% Similarity=0.369 Sum_probs=17.4
Q ss_pred CCCCCccccCCCCCCCHHHHHHHhhhhcCCCCC
Q 016443 158 EFDPACCFMCDLPHDAIENCMVHMHKCHGFFIP 190 (389)
Q Consensus 158 ~~~~~~CLFC~~~s~s~e~nl~HM~~~H~F~IP 190 (389)
.+....|-||.-... ...+.==-+.|||||-
T Consensus 49 ~vt~~eC~FCHse~A--~~ev~~~I~~~Gy~I~ 79 (81)
T PF09630_consen 49 DVTQKECRFCHSEEA--PPEVEQAIKQQGYFII 79 (81)
T ss_dssp ---TTTEEEEEEEE----HHHHHHHHHHSEEEE
T ss_pred ccccccCcccccccC--CHHHHHHHHHCCeEEE
Confidence 467788999975543 3333333457899874
No 91
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=26.50 E-value=67 Score=35.76 Aligned_cols=15 Identities=60% Similarity=1.026 Sum_probs=10.2
Q ss_pred CCCCcccccccCCch
Q 016443 110 SEDSDDEWEEVGPDE 124 (389)
Q Consensus 110 d~d~e~eweev~~~e 124 (389)
+.|+++|||+-.+++
T Consensus 520 EVdSDeEWEEEepGE 534 (811)
T KOG4364|consen 520 EVDSDEEWEEEEPGE 534 (811)
T ss_pred cccCcccccccCCCc
Confidence 446788888766654
No 92
>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase. This model respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This model identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologs of this gene are not found in plants which rely solely on the aerobic cyclase.
Probab=25.58 E-value=1.5e+02 Score=31.41 Aligned_cols=89 Identities=13% Similarity=0.172 Sum_probs=49.1
Q ss_pred CCccccCCCCC-------CCHHHH---HHHhhhhcC---CCCCCcccccCHHHHHHHHHHHhcCC--ceeeecCCCCCCC
Q 016443 161 PACCFMCDLPH-------DAIENC---MVHMHKCHG---FFIPDVEYLKDPKGLLTYLGLKVKRD--FMCLYCNDRCHPF 225 (389)
Q Consensus 161 ~~~CLFC~~~s-------~s~e~n---l~HM~~~H~---F~IP~~eylvd~~gLl~YL~~kI~~~--~~Cl~C~~~~k~F 225 (389)
+-.|-||.... .+++.. |+++...|| |+|-+-.+.++...++.++..-+..+ .+=..|..+.-..
T Consensus 204 p~~C~FC~~~~~~~~~R~rs~e~Vv~Ei~~l~~~~gv~~~~~~Dd~f~~~~~~~~~l~~~l~~~~~l~i~w~~~~r~~~i 283 (497)
T TIGR02026 204 PFTCNFCSQWKFWRRYRHRDPKKFVDEIEWLVRTHGVGFFILADEEPTINRKKFQEFCEEIIARNPISVTWGINTRVTDI 283 (497)
T ss_pred CCCCCCCCCCCCCceeecCCHHHHHHHHHHHHHHcCCCEEEEEecccccCHHHHHHHHHHHHhcCCCCeEEEEecccccc
Confidence 46799997543 355544 445545565 45556666677776666666544332 2334555322111
Q ss_pred CCHHHHHHHHHhCCCcc--ccCCCCC
Q 016443 226 NSLEAVRKHMEAKRHCK--IHFGDGD 249 (389)
Q Consensus 226 ~s~eav~~HM~dK~Hck--i~~~~~~ 249 (389)
..-+.+-+.|++-|-.+ |..++.+
T Consensus 284 ~~d~ell~~l~~aG~~~v~iGiES~~ 309 (497)
T TIGR02026 284 VRDADILHLYRRAGLVHISLGTEAAA 309 (497)
T ss_pred cCCHHHHHHHHHhCCcEEEEccccCC
Confidence 11246777888877544 4445543
No 93
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=23.80 E-value=46 Score=35.52 Aligned_cols=60 Identities=18% Similarity=0.218 Sum_probs=38.3
Q ss_pred CCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHH-HhcCCceeeecCCCCCCCCCHHHHHHHHHhCC
Q 016443 172 DAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGL-KVKRDFMCLYCNDRCHPFNSLEAVRKHMEAKR 239 (389)
Q Consensus 172 ~s~e~nl~HM~~~H~F~IP~~eylvd~~gLl~YL~~-kI~~~~~Cl~C~~~~k~F~s~eav~~HM~dK~ 239 (389)
-++.+...|-...|+-- ----+...|.|+.+ +--...+|..|. +.|.+.++++.||.++.
T Consensus 21 Vsi~eL~sy~~~~~~~~-----a~~~Lseal~fak~n~sWrFWiCp~Cs---kkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 21 VSIDELKSYYESVYDRE-----AADALSEALSFAKENKSWRFWICPRCS---KKFSDAESCLSHMEQEH 81 (466)
T ss_pred eEHHHHHHHHHhccchH-----HHHHHHHHHHHHHhcCceeEeeCCccc---ceeCCHHHHHHHHHHhh
Confidence 35667777766665411 01123455666643 222345788887 78999999999999873
No 94
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=23.61 E-value=25 Score=36.69 Aligned_cols=27 Identities=37% Similarity=0.554 Sum_probs=23.0
Q ss_pred ccccccCccCCHHHHHHHhhcHhHHHhhhc
Q 016443 47 SCGLCGKGYRSSKALAQHLNSRSHIMRASQ 76 (389)
Q Consensus 47 ~C~~C~K~F~S~nay~nHl~SKKHk~~~~~ 76 (389)
+|+-|.-.|.| +++|+.|++|+.-+.+
T Consensus 424 YCENCreky~~---lE~Hi~s~~HrrFAEn 450 (468)
T COG5067 424 YCENCREKYES---LEQHIVSEKHRRFAEN 450 (468)
T ss_pred hhHHHHHHHHH---HHHHhhhhhhhhhhhc
Confidence 49999999965 7999999999996554
No 95
>COG4822 CbiK Cobalamin biosynthesis protein CbiK, Co2+ chelatase [Coenzyme metabolism]
Probab=22.35 E-value=55 Score=31.85 Aligned_cols=45 Identities=24% Similarity=0.302 Sum_probs=28.4
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcCC---CCCCcccccCHHHHHHHHHH
Q 016443 163 CCFMCDLPHDAIENCMVHMHKCHGF---FIPDVEYLKDPKGLLTYLGL 207 (389)
Q Consensus 163 ~CLFC~~~s~s~e~nl~HM~~~H~F---~IP~~eylvd~~gLl~YL~~ 207 (389)
+|-=-.|.+.+--.+|.||.+.||| |+--.+-.-+++.||.||+.
T Consensus 143 mgHGt~h~s~~~YacLd~~~~~~~f~~v~v~~ve~yP~~d~vi~~l~~ 190 (265)
T COG4822 143 MGHGTDHHSNAAYACLDHVLDEYGFDNVFVAAVEGYPLVDTVIEYLRK 190 (265)
T ss_pred EecCCCccHHHHHHHHHHHHHhcCCCceEEEEecCCCcHHHHHHHHHH
Confidence 3333345556778899999999999 33333333455666666654
No 96
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=21.75 E-value=24 Score=25.30 Aligned_cols=20 Identities=40% Similarity=0.642 Sum_probs=15.8
Q ss_pred ceeeecccccccccCCCCCC
Q 016443 305 KTFGSREYLRYYRQKPRPSP 324 (389)
Q Consensus 305 ~~iGhR~~~ryyrQ~~~~~~ 324 (389)
-++=||.|+.||....+|-+
T Consensus 19 dT~v~r~l~~yY~~k~~~~P 38 (41)
T PF14475_consen 19 DTHVHRVLRKYYTEKGRPFP 38 (41)
T ss_pred hhHHHHHHHHHHHHcCCCCC
Confidence 45669999999999876654
No 97
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=21.21 E-value=54 Score=34.80 Aligned_cols=28 Identities=36% Similarity=0.803 Sum_probs=26.4
Q ss_pred ccccccc-CccCCHHHHHHHhhcHhHHHh
Q 016443 46 YSCGLCG-KGYRSSKALAQHLNSRSHIMR 73 (389)
Q Consensus 46 ~~C~~C~-K~F~S~nay~nHl~SKKHk~~ 73 (389)
|.|.+|+ ++|.-..||+-|-+--.|..-
T Consensus 402 y~CEICGNy~Y~GrkaF~RHF~EwRH~hG 430 (497)
T KOG2636|consen 402 YNCEICGNYVYKGRKAFDRHFNEWRHAHG 430 (497)
T ss_pred cceeeccCccccCcHHHHHHhHHHHHhhc
Confidence 7999998 999999999999999999883
No 98
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=20.64 E-value=27 Score=26.49 Aligned_cols=44 Identities=20% Similarity=0.321 Sum_probs=26.2
Q ss_pred CceeeecCCCCCCCCCHHHHHHHHHhCCCcc-ccCCCCChhHHHHhhhhcccCC
Q 016443 212 DFMCLYCNDRCHPFNSLEAVRKHMEAKRHCK-IHFGDGDDEEEAELEEFYDYSS 264 (389)
Q Consensus 212 ~~~Cl~C~~~~k~F~s~eav~~HM~dK~Hck-i~~~~~~~e~~~e~~~FYDf~~ 264 (389)
..+||.|+..|=.-.+..-.+.|+++.+|.- |...+. .+|.|.-
T Consensus 11 lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~H~l~v~~~~~---------~i~C~~C 55 (63)
T PF02148_consen 11 LWLCLTCGYVGCGRYSNGHALKHYKETGHPLAVSLSTG---------SIWCYAC 55 (63)
T ss_dssp EEEETTTS-EEETTTSTSHHHHHHHHHT--EEEETTTT---------CEEETTT
T ss_pred eEEeCCCCcccccCCcCcHHHHhhcccCCeEEEECCCC---------eEEEcCC
Confidence 3589999854422223467899999999986 444432 3677753
No 99
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.59 E-value=33 Score=29.38 Aligned_cols=16 Identities=19% Similarity=0.544 Sum_probs=13.2
Q ss_pred CccccccccCccCCHH
Q 016443 44 MTYSCGLCGKGYRSSK 59 (389)
Q Consensus 44 ~~~~C~~C~K~F~S~n 59 (389)
....|.-|++.|+.-|
T Consensus 8 tKR~Cp~CG~kFYDLn 23 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLN 23 (108)
T ss_pred CcccCCCCcchhccCC
Confidence 3467999999999865
No 100
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=20.56 E-value=31 Score=29.79 Aligned_cols=29 Identities=24% Similarity=0.457 Sum_probs=26.1
Q ss_pred CceeeecCCCCCCCCCHHHHHHHHHhCCCccc
Q 016443 212 DFMCLYCNDRCHPFNSLEAVRKHMEAKRHCKI 243 (389)
Q Consensus 212 ~~~Cl~C~~~~k~F~s~eav~~HM~dK~Hcki 243 (389)
.+-||-|. |-|-+..+|..|.+.|-|-+-
T Consensus 55 qhYCieCa---ryf~t~~aL~~HkkgkvHkRR 83 (126)
T COG5112 55 QHYCIECA---RYFITEKALMEHKKGKVHKRR 83 (126)
T ss_pred eeeeehhH---HHHHHHHHHHHHhccchhHHH
Confidence 47899998 899999999999999999863
Done!