Query 042126
Match_columns 369
No_of_seqs 204 out of 446
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 03:08:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042126.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042126hhsearch_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 1.9E-81 4.1E-86 613.4 21.3 336 1-365 36-380 (390)
2 PF12756 zf-C2H2_2: C2H2 type 99.8 8.6E-21 1.9E-25 153.2 2.3 99 149-252 1-100 (100)
3 KOG2482 Predicted C2H2-type Zn 99.7 2.6E-18 5.7E-23 167.2 2.2 159 32-231 196-364 (423)
4 KOG2482 Predicted C2H2-type Zn 99.5 2.7E-14 5.8E-19 139.4 5.8 95 145-249 142-237 (423)
5 PF12171 zf-C2H2_jaz: Zinc-fin 98.5 4.7E-08 1E-12 62.4 1.6 26 32-57 2-27 (27)
6 PF12874 zf-met: Zinc-finger o 98.3 2.5E-07 5.3E-12 57.7 2.0 25 32-56 1-25 (25)
7 smart00451 ZnF_U1 U1-like zinc 98.2 1.4E-06 3E-11 58.3 3.4 32 31-62 3-34 (35)
8 KOG0717 Molecular chaperone (D 97.7 1.6E-05 3.5E-10 81.4 2.3 31 32-62 293-323 (508)
9 KOG2785 C2H2-type Zn-finger pr 97.3 0.00026 5.7E-09 71.2 4.2 33 31-63 3-35 (390)
10 PF00096 zf-C2H2: Zinc finger, 96.9 0.00051 1.1E-08 41.6 1.6 22 32-53 1-22 (23)
11 KOG2462 C2H2-type Zn-finger pr 96.5 0.0035 7.6E-08 60.9 4.9 29 199-231 216-244 (279)
12 PF13894 zf-C2H2_4: C2H2-type 96.4 0.002 4.4E-08 38.5 1.8 22 32-53 1-22 (24)
13 PF13912 zf-C2H2_6: C2H2-type 96.3 0.0022 4.9E-08 40.3 1.6 24 31-54 1-24 (27)
14 PF12756 zf-C2H2_2: C2H2 type 95.8 0.0041 8.9E-08 49.7 1.4 30 31-60 50-79 (100)
15 PF06220 zf-U1: U1 zinc finger 95.6 0.01 2.2E-07 41.2 2.6 30 32-61 4-35 (38)
16 PTZ00448 hypothetical protein; 95.6 0.0084 1.8E-07 60.5 2.8 33 31-63 314-346 (373)
17 smart00355 ZnF_C2H2 zinc finge 95.5 0.012 2.6E-07 35.4 2.2 21 32-52 1-21 (26)
18 KOG3408 U1-like Zn-finger-cont 95.3 0.0095 2.1E-07 51.4 1.8 34 30-63 56-89 (129)
19 PLN02748 tRNA dimethylallyltra 95.1 0.014 3E-07 61.1 2.6 34 30-63 417-451 (468)
20 PF12171 zf-C2H2_jaz: Zinc-fin 94.5 0.004 8.6E-08 39.5 -2.0 25 199-226 2-26 (27)
21 PF13912 zf-C2H2_6: C2H2-type 93.9 0.03 6.4E-07 35.1 1.3 25 199-228 2-26 (27)
22 PF12874 zf-met: Zinc-finger o 93.9 0.011 2.5E-07 36.3 -0.7 24 200-226 2-25 (25)
23 PHA00733 hypothetical protein 93.9 0.088 1.9E-06 45.8 4.5 49 148-224 74-122 (128)
24 PF13821 DUF4187: Domain of un 93.1 0.11 2.3E-06 39.0 3.3 31 183-219 15-45 (55)
25 PHA02768 hypothetical protein; 93.0 0.059 1.3E-06 40.5 1.7 24 31-54 5-28 (55)
26 PF00096 zf-C2H2: Zinc finger, 92.9 0.041 8.9E-07 33.1 0.7 22 199-223 1-22 (23)
27 PF07535 zf-DBF: DBF zinc fing 92.1 0.15 3.3E-06 37.4 2.9 28 33-63 7-34 (49)
28 PHA00616 hypothetical protein 91.7 0.078 1.7E-06 38.1 0.9 22 32-53 2-23 (44)
29 PF13894 zf-C2H2_4: C2H2-type 91.6 0.1 2.2E-06 30.8 1.3 22 199-223 1-22 (24)
30 KOG3608 Zn finger proteins [Ge 91.2 0.24 5.2E-06 50.1 4.1 64 146-233 318-384 (467)
31 KOG3608 Zn finger proteins [Ge 90.6 0.29 6.3E-06 49.5 4.0 71 148-224 264-344 (467)
32 smart00451 ZnF_U1 U1-like zinc 90.3 0.14 3E-06 33.8 1.1 28 198-228 3-30 (35)
33 PHA00733 hypothetical protein 90.2 0.42 9E-06 41.6 4.3 29 147-175 99-127 (128)
34 smart00586 ZnF_DBF Zinc finger 89.8 0.21 4.6E-06 36.7 1.8 28 32-62 6-33 (49)
35 KOG4727 U1-like Zn-finger prot 89.3 0.42 9.1E-06 43.8 3.7 59 3-61 36-105 (193)
36 KOG3576 Ovo and related transc 89.2 0.29 6.3E-06 46.2 2.7 63 145-222 171-233 (267)
37 KOG2231 Predicted E3 ubiquitin 88.9 0.45 9.8E-06 51.8 4.2 80 146-229 114-211 (669)
38 COG5112 UFD2 U1-like Zn-finger 88.7 0.19 4E-06 42.7 1.0 31 32-62 56-86 (126)
39 PHA02768 hypothetical protein; 86.3 0.45 9.9E-06 35.8 1.7 26 197-227 4-29 (55)
40 PHA00616 hypothetical protein 85.2 0.44 9.4E-06 34.3 1.1 33 148-180 2-34 (44)
41 PHA00732 hypothetical protein 83.6 0.81 1.8E-05 36.7 2.1 22 32-53 2-23 (79)
42 smart00355 ZnF_C2H2 zinc finge 83.3 0.85 1.8E-05 26.9 1.7 20 200-222 2-21 (26)
43 PF05605 zf-Di19: Drought indu 82.7 2.1 4.5E-05 31.4 3.9 49 148-223 3-51 (54)
44 KOG2837 Protein containing a U 82.6 0.21 4.5E-06 48.7 -1.9 30 32-61 26-55 (309)
45 PHA00732 hypothetical protein 82.4 1.2 2.5E-05 35.8 2.6 45 149-224 3-47 (79)
46 PF13909 zf-H2C2_5: C2H2-type 81.5 0.84 1.8E-05 27.7 1.2 23 149-172 2-24 (24)
47 PF13913 zf-C2HC_2: zinc-finge 81.2 1.2 2.7E-05 27.9 1.9 21 32-53 3-23 (25)
48 KOG3032 Uncharacterized conser 81.0 1.1 2.3E-05 43.0 2.3 30 32-62 36-65 (264)
49 PF13465 zf-H2C2_2: Zinc-finge 77.4 1.1 2.3E-05 28.2 0.7 14 30-43 13-26 (26)
50 COG5188 PRP9 Splicing factor 3 76.6 1.2 2.7E-05 45.0 1.3 32 32-63 239-270 (470)
51 PF12013 DUF3505: Protein of u 76.2 1.9 4E-05 36.0 2.1 75 144-224 8-107 (109)
52 KOG2505 Ankyrin repeat protein 75.7 2.1 4.5E-05 45.3 2.6 33 31-63 66-98 (591)
53 KOG1994 Predicted RNA binding 75.6 2.5 5.5E-05 40.4 3.0 33 182-220 226-258 (268)
54 KOG0227 Splicing factor 3a, su 74.4 1.5 3.2E-05 41.0 1.1 34 30-63 52-85 (222)
55 COG5246 PRP11 Splicing factor 73.8 1.8 3.9E-05 40.2 1.5 34 30-63 52-85 (222)
56 PF05605 zf-Di19: Drought indu 73.3 3 6.4E-05 30.6 2.3 22 31-53 2-23 (54)
57 PF13909 zf-H2C2_5: C2H2-type 68.5 4.1 9E-05 24.6 1.8 21 32-53 1-21 (24)
58 PF12013 DUF3505: Protein of u 68.2 15 0.00033 30.5 5.8 28 145-172 78-109 (109)
59 KOG2462 C2H2-type Zn-finger pr 64.5 4.5 9.8E-05 39.7 2.1 31 28-58 212-242 (279)
60 PF02892 zf-BED: BED zinc fing 60.0 4.7 0.0001 28.0 1.1 22 31-52 16-41 (45)
61 PF08790 zf-LYAR: LYAR-type C2 59.8 1.2 2.5E-05 29.1 -1.9 20 32-52 1-20 (28)
62 KOG1074 Transcriptional repres 59.7 5.3 0.00012 44.6 1.9 53 144-222 602-654 (958)
63 KOG3623 Homeobox transcription 58.2 3.2 7E-05 45.7 -0.1 30 29-58 307-336 (1007)
64 KOG3623 Homeobox transcription 58.0 5.7 0.00012 43.9 1.7 74 149-227 242-335 (1007)
65 COG5236 Uncharacterized conser 56.8 3.6 7.8E-05 41.7 0.0 72 151-225 152-244 (493)
66 KOG1994 Predicted RNA binding 56.6 5.9 0.00013 38.0 1.4 21 147-167 239-259 (268)
67 smart00614 ZnF_BED BED zinc fi 55.3 7.8 0.00017 27.9 1.6 24 32-56 19-47 (50)
68 smart00734 ZnF_Rad18 Rad18-lik 52.9 11 0.00024 23.8 1.8 20 33-53 3-22 (26)
69 PF04988 AKAP95: A-kinase anch 52.9 9.5 0.00021 34.8 2.1 27 32-58 1-27 (165)
70 COG5188 PRP9 Splicing factor 3 49.1 10 0.00023 38.6 1.9 65 163-230 159-267 (470)
71 KOG1074 Transcriptional repres 48.9 7.6 0.00017 43.5 0.9 25 30-54 352-376 (958)
72 KOG2384 Major histocompatibili 47.7 11 0.00024 35.6 1.6 36 27-63 80-115 (223)
73 KOG3408 U1-like Zn-finger-cont 45.1 7.8 0.00017 33.8 0.2 29 197-228 56-84 (129)
74 PF04959 ARS2: Arsenite-resist 44.7 14 0.00031 35.1 1.9 34 27-61 73-106 (214)
75 PF14420 Clr5: Clr5 domain 44.7 11 0.00024 27.8 1.0 25 156-180 19-43 (54)
76 KOG0717 Molecular chaperone (D 43.5 12 0.00026 39.4 1.3 28 199-229 293-320 (508)
77 COG5236 Uncharacterized conser 43.5 31 0.00068 35.3 4.2 74 148-224 221-304 (493)
78 KOG3576 Ovo and related transc 42.5 7.8 0.00017 36.8 -0.1 27 148-174 213-239 (267)
79 KOG3288 OTU-like cysteine prot 40.8 23 0.0005 34.7 2.7 32 27-58 272-303 (307)
80 PF12907 zf-met2: Zinc-binding 39.9 15 0.00032 25.9 0.9 24 32-55 2-28 (40)
81 KOG3993 Transcription factor ( 39.3 19 0.00042 37.6 2.0 31 29-59 354-384 (500)
82 KOG3993 Transcription factor ( 38.5 18 0.00039 37.8 1.7 30 30-61 294-323 (500)
83 PF05443 ROS_MUCR: ROS/MUCR tr 36.5 20 0.00044 31.6 1.5 39 199-253 73-111 (132)
84 PF04780 DUF629: Protein of un 35.9 22 0.00048 37.5 1.9 27 32-59 58-84 (466)
85 COG4049 Uncharacterized protei 34.0 17 0.00038 27.6 0.6 29 29-58 15-43 (65)
86 KOG1146 Homeobox protein [Gene 33.4 44 0.00096 39.5 3.9 32 28-59 515-546 (1406)
87 PF09237 GAGA: GAGA factor; I 33.0 39 0.00085 25.3 2.3 26 28-53 21-46 (54)
88 COG5067 DBF4 Protein kinase es 30.2 18 0.00038 37.5 0.1 31 28-62 420-450 (468)
89 PF09237 GAGA: GAGA factor; I 29.1 29 0.00063 26.0 1.1 28 146-173 23-50 (54)
90 KOG3454 U1 snRNP-specific prot 28.6 40 0.00087 30.8 2.1 31 31-61 3-35 (165)
91 TIGR02026 BchE magnesium-proto 27.8 1.4E+02 0.003 31.5 6.2 89 147-235 204-309 (497)
92 PF09630 DUF2024: Domain of un 27.7 15 0.00033 29.8 -0.7 31 144-176 49-79 (81)
93 KOG4364 Chromatin assembly fac 27.2 44 0.00096 36.8 2.4 15 96-110 520-534 (811)
94 COG4822 CbiK Cobalamin biosynt 25.7 45 0.00097 32.2 1.9 45 149-193 143-190 (265)
95 PF02148 zf-UBP: Zn-finger in 23.7 22 0.00047 26.8 -0.5 44 198-250 11-55 (63)
96 KOG4167 Predicted DNA-binding 23.7 28 0.00061 38.7 0.2 30 30-59 791-820 (907)
97 KOG2593 Transcription initiati 22.4 58 0.0013 34.1 2.1 31 197-230 127-159 (436)
98 PF14475 Mso1_Sec1_bdg: Sec1-b 22.1 22 0.00048 25.2 -0.6 20 291-310 19-38 (41)
99 COG5112 UFD2 U1-like Zn-finger 22.1 27 0.00059 29.9 -0.2 29 197-228 54-82 (126)
100 PF04988 AKAP95: A-kinase anch 21.1 1.1E+02 0.0023 28.1 3.3 42 5-59 78-120 (165)
101 PF09538 FYDLN_acid: Protein o 21.1 39 0.00084 28.7 0.5 17 29-45 7-23 (108)
102 PF05443 ROS_MUCR: ROS/MUCR tr 21.1 41 0.00089 29.6 0.7 26 146-174 71-96 (132)
103 KOG2893 Zn finger protein [Gen 20.8 61 0.0013 31.6 1.8 25 198-225 10-34 (341)
104 KOG2231 Predicted E3 ubiquitin 20.4 1E+02 0.0022 34.1 3.6 71 147-222 182-260 (669)
105 KOG2636 Splicing factor 3a, su 20.3 59 0.0013 34.3 1.7 27 32-58 402-429 (497)
106 KOG2186 Cell growth-regulating 20.3 46 0.001 32.6 0.9 22 30-52 28-49 (276)
No 1
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.9e-81 Score=613.37 Aligned_cols=336 Identities=37% Similarity=0.590 Sum_probs=254.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhhcc--CCCCCccccccccCccCCHHHHHHHhhcHHHHHHHhcCCCchhhhhhhhhccc
Q 042126 1 VAGVPGVTEALFLARQAALAQEKNT--NETPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQGTSNEEKEKVIIRSIS 78 (369)
Q Consensus 1 VA~LPPVt~e~F~~k~~~~a~~~~~--~~~~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~~~~~~~~~~~i~~~~ 78 (369)
||+|||||+|+|++|+++.+.++.. .++.+.+.|.+|+|+|.|++|+.+||+||+|+.+..+..+..+.+.+.+..++
T Consensus 36 VA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r~~e~d~a~~~q~~ 115 (390)
T KOG2785|consen 36 VASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQRSEEGDSAKISQLP 115 (390)
T ss_pred hhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChhhHHHHHHHhhcchhhhhhhccccccchhhhhcc
Confidence 8999999999999998887554443 45778889999999999999999999999999998876554344444444443
Q ss_pred ccCCCCCCCCCcCCCCCCCCCcccccccCCchhhhhhhcccccccCCCCCCCCCCCccCCCCCCCCCCCCccccCCCCCC
Q 042126 79 LRDVNKPPPKREANNEESEDSDDEWEEVGPDEVLVSEATNSLTNLNVGSPADDDMEEDDDDGAFEEFDPACCFMCDLPHD 158 (369)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~d~e~eweev~~~e~~~~~~~~s~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~CLFC~~~~~ 158 (369)
.+.+. + .. ...+++..|-|++.++....+. ..+ +..+|++++.. ...+..|+.||||++.+.
T Consensus 116 ~~~p~---~-l~----~~~e~e~~~~E~~~~~d~~~e~-------~~d--d~~Edi~~d~~-~e~e~~Pt~CLfC~~~~k 177 (390)
T KOG2785|consen 116 SRRPS---N-LQ----NKGESELKWYEVDSDEDSSEEE-------EED--DEEEDIEEDGD-DEDELIPTDCLFCDKKSK 177 (390)
T ss_pred ccCcc---c-cc----cCCCcccchhhcccccccchhh-------ccC--cchhhhhhccc-hhcccCCcceeecCCCcc
Confidence 22210 0 00 0112455565555442110000 000 11111111111 122345599999999999
Q ss_pred CHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhCCCccccCCCCCchH
Q 042126 159 AIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAKRHCKMHFGDGDDEE 238 (369)
Q Consensus 159 s~e~nl~HM~~~H~F~IP~~~ylvd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~dK~Hcki~~~~~~~~~ 238 (369)
+++.|+.||++.||||||+++||+|+.|||.||++||..+++|||||..|+.|+|++|||+||.+||||||+| ++ |+
T Consensus 178 ~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~HCkl~y-d~--ee 254 (390)
T KOG2785|consen 178 SLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKGHCKLPY-DG--EE 254 (390)
T ss_pred cHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhccCcccCC-Ch--HH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999 54 99
Q ss_pred HHHhhhhcccCCCCcCcccccccccCCCCCceee--CC-CeeEEEeccCCCCCCcceeeeccccccccCCCCCCCCch--
Q 042126 239 EAELEEFYDYSSSYMDEDGKQLISSSDMANTVEL--GG-GSELIITRRTDKGTSTKTFGSREYLRYYRRKPRPSPANN-- 313 (369)
Q Consensus 239 ~~e~~~FYDf~~sy~d~~~~~~~~~~~~~~~~~~--~~-g~eL~L~~~~~~~psG~~iGhR~~~ryyrQ~~~~~~~~~-- 313 (369)
++||++||||++||+|..+.+.+...++.++..+ .+ .+||+| |||++||||+|+|||||||+|+....
T Consensus 255 ~~El~efYDfsssY~d~~~~~~~~~~e~~~~~~l~~g~~~~el~l-------psga~vGhRsl~RYykQ~l~p~~~~~~~ 327 (390)
T KOG2785|consen 255 RLELAEFYDFSSSYPDIAENQDPDSAEEDPTDELEGGDELYELTL-------PSGARVGHRSLMRYYKQNLRPSSAVVRL 327 (390)
T ss_pred HhhhhhhhcCcccccCcccCCCCcchhcCCcccccccceeeeeec-------ccccccccHHHHHHHhhcCCCcchHHHH
Confidence 9999999999999999766554443443333344 11 278999 99999999999999999999998653
Q ss_pred --HHHHHHHHHhhhhcccchhhhHHHHHHHHHHHHHHhhhhhhhhhhhcccccc
Q 042126 314 --VAITAALASRYKSMGLATVQTREHMVRMKVIKEMNRTGVEAMRTRVGMKNNI 365 (369)
Q Consensus 314 --~~~~~~~~~~y~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kvg~k~N~ 365 (369)
..++.+.+..|+++||++.+...+.++.+.++.++|.+ .+|.++||+|+|.
T Consensus 328 ~~r~~~~~~~~~~~a~~~t~~~~~~~k~~~~~~k~v~R~~-~r~~~~~g~k~n~ 380 (390)
T KOG2785|consen 328 VSRRALSRVKRFYPALGWTGTTGVRAKMQARDMKFVERGR-RRFALRVGMKNNY 380 (390)
T ss_pred HHHHHHHHHHHhhhcccchhhHHHHHHHHHHHHHHHHHHH-HHHHHHhcchhhH
Confidence 33344566778899999988776666667777777765 7799999999994
No 2
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=99.80 E-value=8.6e-21 Score=153.23 Aligned_cols=99 Identities=45% Similarity=0.834 Sum_probs=28.0
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhCCCcc
Q 042126 149 CCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAKRHCK 228 (369)
Q Consensus 149 ~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~~ylvd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~dK~Hck 228 (369)
.|+||+..++++..++.||...|+|.||+..+|+++.+|++|++.+|...+.|++|+ +.|.|..+|+.||+.++|++
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 499999999999999999999999999999999999999999999999889999998 88999999999999999999
Q ss_pred ccCCCCCchHHHHhhhhccc-CCCC
Q 042126 229 MHFGDGDDEEEAELEEFYDY-SSSY 252 (369)
Q Consensus 229 i~~~~~~~~~~~e~~~FYDf-~~sy 252 (369)
+.++.+ ....++..|||| +.+|
T Consensus 78 ~~~~~~--~~~~~~~~~y~~~~~~~ 100 (100)
T PF12756_consen 78 RNSESE--ESWEEFEKFYDFWSNDY 100 (100)
T ss_dssp -S-----------------------
T ss_pred cccccc--cccccccccccccccCC
Confidence 988643 668899999999 6554
No 3
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=99.70 E-value=2.6e-18 Score=167.17 Aligned_cols=159 Identities=21% Similarity=0.373 Sum_probs=117.0
Q ss_pred cccccccCccCCHHHHHHHhhcHHHHH-HHhcCCCchhhhhh-hhhcccccCCCCCCCCCcC--C-CCCCCCCccccccc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHIM-RAAQGTSNEEKEKV-IIRSISLRDVNKPPPKREA--N-NEESEDSDDEWEEV 106 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk~-~~~~~~~~~~~~~~-~i~~~~~~~~~~~~~~~~~--~-~~~~~d~e~eweev 106 (369)
+.|.+|.|.|..+|+++.||+.|.|++ +..+. .++.. +|..+....+ ..+...+. . .+...+.+++|++|
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK~HrrinPknr----eYDkfyiINY~ev~ks-~t~~~~e~dret~~d~~E~D~~wsDw 270 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNR----EYDKFYIINYLEVGKS-WTIVHSEDDRETNEDINETDDTWSDW 270 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhccCcccCCCcc----ccceEEEEeHhhcCCc-cchhhhhhhhhhhccccccccchhhh
Confidence 579999999999999999999999999 44333 55543 5543221000 00000010 0 11223456778877
Q ss_pred CCchhhhhhhcccccccCCCCCCCCCCCccCCCCCCCCCCCCccccCCCCCCCHHHHHHHhhhhcCCCCCCcc--c---c
Q 042126 107 GPDEVLVSEATNSLTNLNVGSPADDDMEEDDDDGAFEEFDPACCFMCDLPHDAIENCMVHMHKCHGFFIPDVE--Y---L 181 (369)
Q Consensus 107 ~~~e~~~~~~~~s~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~~--y---l 181 (369)
.+++.+ -....||||.+...++...++||..+|-|+|-... | .
T Consensus 271 ~ed~a~--------------------------------a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~ 318 (423)
T KOG2482|consen 271 NEDDAE--------------------------------ALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNF 318 (423)
T ss_pred hcCCCC--------------------------------ccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccch
Confidence 654311 02268999999999999999999999999999884 4 3
Q ss_pred cCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhCCCccccC
Q 042126 182 KDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAKRHCKMHF 231 (369)
Q Consensus 182 vd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~dK~Hcki~~ 231 (369)
|....||||||++++ ...|..|. -+|.+..+++.||..-.|--|..
T Consensus 319 YqrvrviNyiRkq~~-~~~c~~cd---~~F~~e~~l~~hm~e~k~l~i~p 364 (423)
T KOG2482|consen 319 YQRVRVINYIRKQKK-KSRCAECD---LSFWKEPGLLIHMVEDKHLSILP 364 (423)
T ss_pred hhhhhHHHHHHHHhh-cccccccc---ccccCcchhhhhccccccccccC
Confidence 899999999999988 56999998 68999999999999988877764
No 4
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=99.49 E-value=2.7e-14 Score=139.43 Aligned_cols=95 Identities=24% Similarity=0.463 Sum_probs=87.7
Q ss_pred CCCCccccCCCCC-CCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHh
Q 042126 145 FDPACCFMCDLPH-DAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEA 223 (369)
Q Consensus 145 ~~~~~CLFC~~~~-~s~e~nl~HM~~~H~F~IP~~~ylvd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~d 223 (369)
+-..+||||+... ....+.+.||+..|||.|..++.||....||..|.+++. .++||||. |.|+..-.|+.||+.
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 3567899999987 589999999999999999999999999999999999987 57999998 999999999999999
Q ss_pred CCCccccCCCCCchHHHHhhhhcccC
Q 042126 224 KRHCKMHFGDGDDEEEAELEEFYDYS 249 (369)
Q Consensus 224 K~Hcki~~~~~~~~~~~e~~~FYDf~ 249 (369)
|+|.+|+.. ..||+.||-..
T Consensus 218 K~HrrinPk------nreYDkfyiIN 237 (423)
T KOG2482|consen 218 KRHRRINPK------NREYDKFYIIN 237 (423)
T ss_pred ccCcccCCC------ccccceEEEEe
Confidence 999999886 46999999764
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=98.50 E-value=4.7e-08 Score=62.45 Aligned_cols=26 Identities=35% Similarity=0.732 Sum_probs=25.0
Q ss_pred cccccccCccCCHHHHHHHhhcHHHH
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHI 57 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk 57 (369)
|.|.+|+|.|.++++|++||+|++||
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 57999999999999999999999997
No 6
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.34 E-value=2.5e-07 Score=57.66 Aligned_cols=25 Identities=40% Similarity=0.929 Sum_probs=24.0
Q ss_pred cccccccCccCCHHHHHHHhhcHHH
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSH 56 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkH 56 (369)
|.|.+|+++|+|.++|++|++|++|
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 5799999999999999999999999
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=98.20 E-value=1.4e-06 Score=58.27 Aligned_cols=32 Identities=19% Similarity=0.519 Sum_probs=29.0
Q ss_pred ccccccccCccCCHHHHHHHhhcHHHHHHHhc
Q 042126 31 TYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQ 62 (369)
Q Consensus 31 ~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~ 62 (369)
.|.|.+|++.|.+..+|++|++|++|+.++..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 36799999999999999999999999998653
No 8
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=1.6e-05 Score=81.43 Aligned_cols=31 Identities=35% Similarity=0.640 Sum_probs=28.5
Q ss_pred cccccccCccCCHHHHHHHhhcHHHHHHHhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHIMRAAQ 62 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~ 62 (369)
+.|.+|+|+|.|++|+.||.+||||+++++.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~e 323 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAE 323 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHH
Confidence 5699999999999999999999999997653
No 9
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=97.25 E-value=0.00026 Score=71.16 Aligned_cols=33 Identities=15% Similarity=0.384 Sum_probs=30.4
Q ss_pred ccccccccCccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 31 TYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 31 ~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
.|+|..|...|.+....+.|++|.||++|.+..
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRk 35 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRK 35 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhH
Confidence 578999999999999999999999999987754
No 10
>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=96.91 E-value=0.00051 Score=41.62 Aligned_cols=22 Identities=36% Similarity=0.958 Sum_probs=20.7
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNS 53 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~S 53 (369)
|.|..|+|.|.+...|+.|++.
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 11
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=96.50 E-value=0.0035 Score=60.88 Aligned_cols=29 Identities=28% Similarity=0.615 Sum_probs=22.5
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCCccccC
Q 042126 199 FMCLYCNDRCHPFNSLEAVRKHMEAKRHCKMHF 231 (369)
Q Consensus 199 ~~Cl~C~~~~k~F~S~eav~~HM~dK~Hcki~~ 231 (369)
+.|-.|+ |.|.+.-.||.||+.-++.| .|
T Consensus 216 F~C~hC~---kAFADRSNLRAHmQTHS~~K-~~ 244 (279)
T KOG2462|consen 216 FSCPHCG---KAFADRSNLRAHMQTHSDVK-KH 244 (279)
T ss_pred ccCCccc---chhcchHHHHHHHHhhcCCc-cc
Confidence 5788887 88888888888888777666 44
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=96.41 E-value=0.002 Score=38.53 Aligned_cols=22 Identities=41% Similarity=1.038 Sum_probs=18.4
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNS 53 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~S 53 (369)
|.|.+|+++|.+..+|+.|++.
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=96.30 E-value=0.0022 Score=40.28 Aligned_cols=24 Identities=38% Similarity=0.750 Sum_probs=21.6
Q ss_pred ccccccccCccCCHHHHHHHhhcH
Q 042126 31 TYSCGLCGKGYRSSKALAQHLNSR 54 (369)
Q Consensus 31 ~~~C~~C~K~F~S~nA~~nHl~Sk 54 (369)
+|.|..|+++|.+..+|..|+++.
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 368999999999999999999764
No 14
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.81 E-value=0.0041 Score=49.65 Aligned_cols=30 Identities=37% Similarity=0.799 Sum_probs=26.1
Q ss_pred ccccccccCccCCHHHHHHHhhcHHHHHHH
Q 042126 31 TYSCGLCGKGYRSSKALAQHLNSRSHIMRA 60 (369)
Q Consensus 31 ~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~ 60 (369)
.+.|.+|++.|.|..+++.||+++.|+...
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 15
>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=95.63 E-value=0.01 Score=41.20 Aligned_cols=30 Identities=27% Similarity=0.369 Sum_probs=19.2
Q ss_pred cccccccCcc--CCHHHHHHHhhcHHHHHHHh
Q 042126 32 YSCGLCGKGY--RSSKALAQHLNSRSHIMRAA 61 (369)
Q Consensus 32 ~~C~~C~K~F--~S~nA~~nHl~SkkHk~~~~ 61 (369)
|.|.+|++.| .|...-++|.++.+|+.++.
T Consensus 4 yyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~ 35 (38)
T PF06220_consen 4 YYCDYCKKYLTHDSPSIRKQHERGWKHKENVK 35 (38)
T ss_dssp -B-TTT--B-S--SHHHHHHHT--THHHHHHH
T ss_pred eecccccceecCCChHHHHHhhccHHHHHHHH
Confidence 6799999999 55578899999999999865
No 16
>PTZ00448 hypothetical protein; Provisional
Probab=95.56 E-value=0.0084 Score=60.50 Aligned_cols=33 Identities=24% Similarity=0.407 Sum_probs=30.3
Q ss_pred ccccccccCccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 31 TYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 31 ~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
.|.|..|+-.|.+.+.++.|++|.||++|.+..
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRk 346 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRN 346 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHH
Confidence 578999999999999999999999999987754
No 17
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.47 E-value=0.012 Score=35.37 Aligned_cols=21 Identities=43% Similarity=0.947 Sum_probs=19.7
Q ss_pred cccccccCccCCHHHHHHHhh
Q 042126 32 YSCGLCGKGYRSSKALAQHLN 52 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~ 52 (369)
+.|..|+++|.+...+..|++
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 469999999999999999998
No 18
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=95.29 E-value=0.0095 Score=51.37 Aligned_cols=34 Identities=24% Similarity=0.432 Sum_probs=30.8
Q ss_pred CccccccccCccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 30 MTYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 30 ~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
..|+|..|.+.|.+..+++-|.++|.||.|+++.
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l 89 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKTKVHKRRVKEL 89 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhccHHHHHHHhc
Confidence 3468999999999999999999999999988754
No 19
>PLN02748 tRNA dimethylallyltransferase
Probab=95.05 E-value=0.014 Score=61.14 Aligned_cols=34 Identities=29% Similarity=0.531 Sum_probs=30.1
Q ss_pred CccccccccC-ccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 30 MTYSCGLCGK-GYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 30 ~~~~C~~C~K-~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
..|.|.+|++ ++..+..|+.|++|++||.++...
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~ 451 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRL 451 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHH
Confidence 4578999997 899999999999999999976644
No 20
>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=94.47 E-value=0.004 Score=39.51 Aligned_cols=25 Identities=36% Similarity=0.824 Sum_probs=23.0
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCC
Q 042126 199 FMCLYCNDRCHPFNSLEAVRKHMEAKRH 226 (369)
Q Consensus 199 ~~Cl~C~~~~k~F~S~eav~~HM~dK~H 226 (369)
+.|..|+ +.|.+..++++||+.|.|
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 999999999999999877
No 21
>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=93.93 E-value=0.03 Score=35.07 Aligned_cols=25 Identities=44% Similarity=0.953 Sum_probs=21.7
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCCcc
Q 042126 199 FMCLYCNDRCHPFNSLEAVRKHMEAKRHCK 228 (369)
Q Consensus 199 ~~Cl~C~~~~k~F~S~eav~~HM~dK~Hck 228 (369)
+.|..|+ +.|.+..++..|| +.||+
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 9999999999999 66664
No 22
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.91 E-value=0.011 Score=36.30 Aligned_cols=24 Identities=38% Similarity=0.866 Sum_probs=22.0
Q ss_pred eeeecCCCCCCCCCHHHHHHHHHhCCC
Q 042126 200 MCLYCNDRCHPFNSLEAVRKHMEAKRH 226 (369)
Q Consensus 200 ~Cl~C~~~~k~F~S~eav~~HM~dK~H 226 (369)
.|-.|+ +.|.|...+++||+.+.|
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 23
>PHA00733 hypothetical protein
Probab=93.87 E-value=0.088 Score=45.82 Aligned_cols=49 Identities=18% Similarity=0.425 Sum_probs=38.6
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhC
Q 042126 148 ACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAK 224 (369)
Q Consensus 148 ~~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~~ylvd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~dK 224 (369)
..|-.|+..+.+......||.. |. . .+.|-.|+ +.|.....+..||..|
T Consensus 74 y~C~~Cgk~Fss~s~L~~H~r~-h~-----------------------~-~~~C~~Cg---K~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 74 YVCPLCLMPFSSSVSLKQHIRY-TE-----------------------H-SKVCPVCG---KEFRNTDSTLDHVCKK 122 (128)
T ss_pred ccCCCCCCcCCCHHHHHHHHhc-CC-----------------------c-CccCCCCC---CccCCHHHHHHHHHHh
Confidence 4588899999988888888874 21 0 14888897 8899999999998876
No 24
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=93.14 E-value=0.11 Score=38.99 Aligned_cols=31 Identities=23% Similarity=0.585 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHH
Q 042126 183 DPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRK 219 (369)
Q Consensus 183 d~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~ 219 (369)
-+..||.|||.+ .+-|+||+ -+|.|.+.+..
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 67888877753
No 25
>PHA02768 hypothetical protein; Provisional
Probab=92.96 E-value=0.059 Score=40.48 Aligned_cols=24 Identities=33% Similarity=0.791 Sum_probs=22.2
Q ss_pred ccccccccCccCCHHHHHHHhhcH
Q 042126 31 TYSCGLCGKGYRSSKALAQHLNSR 54 (369)
Q Consensus 31 ~~~C~~C~K~F~S~nA~~nHl~Sk 54 (369)
.|.|..|+|.|....++..|+++.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H 28 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKH 28 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhc
Confidence 478999999999999999999983
No 26
>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=92.91 E-value=0.041 Score=33.09 Aligned_cols=22 Identities=27% Similarity=0.762 Sum_probs=19.9
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHh
Q 042126 199 FMCLYCNDRCHPFNSLEAVRKHMEA 223 (369)
Q Consensus 199 ~~Cl~C~~~~k~F~S~eav~~HM~d 223 (369)
+.|-.|+ +.|.+...++.||+.
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 999999999999985
No 27
>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=92.12 E-value=0.15 Score=37.40 Aligned_cols=28 Identities=29% Similarity=0.496 Sum_probs=24.2
Q ss_pred ccccccCccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 33 SCGLCGKGYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 33 ~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
+|..|...|.+ |..|+.|++|+.-+.+.
T Consensus 7 YCE~C~~ky~~---l~~Hi~s~~Hr~FA~~~ 34 (49)
T PF07535_consen 7 YCENCRVKYDD---LEEHIQSEKHRKFAEND 34 (49)
T ss_pred cCccccchhhh---HHHHhCCHHHHHHHcCc
Confidence 49999999986 88999999999976543
No 28
>PHA00616 hypothetical protein
Probab=91.68 E-value=0.078 Score=38.09 Aligned_cols=22 Identities=41% Similarity=0.765 Sum_probs=20.5
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNS 53 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~S 53 (369)
|.|.-|+|.|.....+..|+++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~ 23 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLS 23 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHH
Confidence 6899999999999999999954
No 29
>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=91.64 E-value=0.1 Score=30.84 Aligned_cols=22 Identities=36% Similarity=0.822 Sum_probs=17.9
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHh
Q 042126 199 FMCLYCNDRCHPFNSLEAVRKHMEA 223 (369)
Q Consensus 199 ~~Cl~C~~~~k~F~S~eav~~HM~d 223 (369)
+.|..|+ +.|.+..+++.||..
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 30
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=91.16 E-value=0.24 Score=50.07 Aligned_cols=64 Identities=19% Similarity=0.310 Sum_probs=55.0
Q ss_pred CCCcccc--CCCCCCCHHHHHHHhhhhc-CCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHH
Q 042126 146 DPACCFM--CDLPHDAIENCMVHMHKCH-GFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHME 222 (369)
Q Consensus 146 ~~~~CLF--C~~~~~s~e~nl~HM~~~H-~F~IP~~~ylvd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~ 222 (369)
+.-.|-| |.....+......||.+.| ||.-| .+.|-+|. |.|.+=.+|-.|++
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 4457888 9999999999999999999 76533 24899998 88999999999999
Q ss_pred hCCCccccCCC
Q 042126 223 AKRHCKMHFGD 233 (369)
Q Consensus 223 dK~Hcki~~~~ 233 (369)
.|.-.+||++-
T Consensus 374 kkH~f~~PsGh 384 (467)
T KOG3608|consen 374 KKHGFRLPSGH 384 (467)
T ss_pred HhhcccCCCCC
Confidence 99999999863
No 31
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=90.55 E-value=0.29 Score=49.48 Aligned_cols=71 Identities=17% Similarity=0.280 Sum_probs=53.1
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCCCCCCc----ccc----cCHHHHHHHHHHHhcCCceeee--cCCCCCCCCCHHHH
Q 042126 148 ACCFMCDLPHDAIENCMVHMHKCHGFFIPDV----EYL----KDPKGLLTYLGLKVKRDFMCLY--CNDRCHPFNSLEAV 217 (369)
Q Consensus 148 ~~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~----~yl----vd~~gLl~yL~~kI~~~~~Cl~--C~~~~k~F~S~eav 217 (369)
-.|..|+...+.....-.||...|+=+=|-. +|+ .|+.+-+.|=.+-+ +.|-. |. -.|++.-.+
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~---y~C~h~~C~---~s~r~~~q~ 337 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTV---YQCEHPDCH---YSVRTYTQM 337 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccc---eecCCCCCc---HHHHHHHHH
Confidence 3589999999999999999999999877765 332 35555555444333 47877 87 467899999
Q ss_pred HHHHHhC
Q 042126 218 RKHMEAK 224 (369)
Q Consensus 218 ~~HM~dK 224 (369)
+.||+.-
T Consensus 338 ~~H~~ev 344 (467)
T KOG3608|consen 338 RRHFLEV 344 (467)
T ss_pred HHHHHHh
Confidence 9999974
No 32
>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=90.33 E-value=0.14 Score=33.79 Aligned_cols=28 Identities=36% Similarity=0.708 Sum_probs=25.0
Q ss_pred CceeeecCCCCCCCCCHHHHHHHHHhCCCcc
Q 042126 198 DFMCLYCNDRCHPFNSLEAVRKHMEAKRHCK 228 (369)
Q Consensus 198 ~~~Cl~C~~~~k~F~S~eav~~HM~dK~Hck 228 (369)
.+.|..|+ +.|.+..++++|+..+.|-+
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 33
>PHA00733 hypothetical protein
Probab=90.24 E-value=0.42 Score=41.61 Aligned_cols=29 Identities=17% Similarity=0.419 Sum_probs=25.6
Q ss_pred CCccccCCCCCCCHHHHHHHhhhhcCCCC
Q 042126 147 PACCFMCDLPHDAIENCMVHMHKCHGFFI 175 (369)
Q Consensus 147 ~~~CLFC~~~~~s~e~nl~HM~~~H~F~I 175 (369)
+..|-.|+..+........||.+.|+.-+
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~~~~ 127 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHNICV 127 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcCccc
Confidence 35899999999999999999999998643
No 34
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=89.80 E-value=0.21 Score=36.67 Aligned_cols=28 Identities=32% Similarity=0.419 Sum_probs=23.5
Q ss_pred cccccccCccCCHHHHHHHhhcHHHHHHHhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHIMRAAQ 62 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~ 62 (369)
.+|..|...|. .|..|+.|++|+.-+..
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 35999999998 57889999999996553
No 35
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=89.33 E-value=0.42 Score=43.76 Aligned_cols=59 Identities=19% Similarity=0.257 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHH---HHHH-Hhhhcc-------CCCCCccccccccCccCCHHHHHHHhhcHHHHHHHh
Q 042126 3 GVPGVTEALFLAR---QAAL-AQEKNT-------NETPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRAA 61 (369)
Q Consensus 3 ~LPPVt~e~F~~k---~~~~-a~~~~~-------~~~~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~ 61 (369)
.=|||+.|....| +..- .-.+.. .+....|+|.+|+-+|...-.|-.|++=|+|..+..
T Consensus 36 ~~~~vqre~L~~rdykvdl~sKLgkt~vitk~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlg 105 (193)
T KOG4727|consen 36 DGPPVQREHLKHRDYKVDLESKLGKTVVITKSTPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLG 105 (193)
T ss_pred cCCchhHHHHhhhhhhhHhHhhccceeEeccCCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHh
Confidence 4589998887765 1111 111111 134456899999999999999999999999999743
No 36
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=89.21 E-value=0.29 Score=46.21 Aligned_cols=63 Identities=21% Similarity=0.386 Sum_probs=40.7
Q ss_pred CCCCccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHH
Q 042126 145 FDPACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHME 222 (369)
Q Consensus 145 ~~~~~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~~ylvd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~ 222 (369)
+-|-.|-.|++.+...-..-.|..+.||- ..-..|-.++-. -++|--|+ -.-...+..-.|..
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 45667888888888777777888888884 122345555544 46888886 34445555555554
No 37
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.89 E-value=0.45 Score=51.78 Aligned_cols=80 Identities=20% Similarity=0.394 Sum_probs=60.4
Q ss_pred CCCccccCCCCCCCHHHHHHHhhhhcCCCCCCc-----cc------ccCHHHHHHHHH-----HHhcCC-ceeeecCCCC
Q 042126 146 DPACCFMCDLPHDAIENCMVHMHKCHGFFIPDV-----EY------LKDPKGLLTYLG-----LKVKRD-FMCLYCNDRC 208 (369)
Q Consensus 146 ~~~~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~-----~y------lvd~~gLl~yL~-----~kI~~~-~~Cl~C~~~~ 208 (369)
.-..|++| ..+.+++..-.||...|+++.-.. .+ +|=...|++.+. .+...| -+|.+|.
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 44679999 888999999999999999987432 11 355566777664 455555 6899998
Q ss_pred CCCCCHHHHHHHHHh-CCCccc
Q 042126 209 HPFNSLEAVRKHMEA-KRHCKM 229 (369)
Q Consensus 209 k~F~S~eav~~HM~d-K~Hcki 229 (369)
..|-....++.||+- .-+|.+
T Consensus 190 ~~fld~~el~rH~~~~h~~chf 211 (669)
T KOG2231|consen 190 ERFLDDDELYRHLRFDHEFCHF 211 (669)
T ss_pred hhhccHHHHHHhhccceeheee
Confidence 778999999999984 445544
No 38
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=88.73 E-value=0.19 Score=42.69 Aligned_cols=31 Identities=29% Similarity=0.465 Sum_probs=28.7
Q ss_pred cccccccCccCCHHHHHHHhhcHHHHHHHhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHIMRAAQ 62 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~ 62 (369)
++|--|.+-|-|+.|+..|.++|-|+.++..
T Consensus 56 hYCieCaryf~t~~aL~~HkkgkvHkRR~Ke 86 (126)
T COG5112 56 HYCIECARYFITEKALMEHKKGKVHKRRAKE 86 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhccchhHHHHHH
Confidence 5699999999999999999999999998764
No 39
>PHA02768 hypothetical protein; Provisional
Probab=86.27 E-value=0.45 Score=35.76 Aligned_cols=26 Identities=15% Similarity=0.437 Sum_probs=23.3
Q ss_pred CCceeeecCCCCCCCCCHHHHHHHHHhCCCc
Q 042126 197 RDFMCLYCNDRCHPFNSLEAVRKHMEAKRHC 227 (369)
Q Consensus 197 ~~~~Cl~C~~~~k~F~S~eav~~HM~dK~Hc 227 (369)
.|+.|-.|+ +.|....+++.||+. |-
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 367999998 999999999999998 55
No 40
>PHA00616 hypothetical protein
Probab=85.23 E-value=0.44 Score=34.28 Aligned_cols=33 Identities=18% Similarity=0.270 Sum_probs=27.5
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCCCCCCccc
Q 042126 148 ACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEY 180 (369)
Q Consensus 148 ~~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~~y 180 (369)
-.|+.|+..+........||.+.||=.--..+|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 479999999999999999999999974444444
No 41
>PHA00732 hypothetical protein
Probab=83.56 E-value=0.81 Score=36.68 Aligned_cols=22 Identities=32% Similarity=0.567 Sum_probs=20.2
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNS 53 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~S 53 (369)
|.|..|+++|.+..+++.|++.
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 42
>smart00355 ZnF_C2H2 zinc finger.
Probab=83.28 E-value=0.85 Score=26.92 Aligned_cols=20 Identities=35% Similarity=0.707 Sum_probs=18.5
Q ss_pred eeeecCCCCCCCCCHHHHHHHHH
Q 042126 200 MCLYCNDRCHPFNSLEAVRKHME 222 (369)
Q Consensus 200 ~Cl~C~~~~k~F~S~eav~~HM~ 222 (369)
.|..|+ +.|.+...++.||+
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 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=82.68 E-value=2.1 Score=31.39 Aligned_cols=49 Identities=14% Similarity=0.317 Sum_probs=37.2
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHh
Q 042126 148 ACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEA 223 (369)
Q Consensus 148 ~~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~~ylvd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~d 223 (369)
-.|.||+. .-++...+.|....|... . ....|..|.. . ....+..||.-
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
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=82.60 E-value=0.21 Score=48.74 Aligned_cols=30 Identities=27% Similarity=0.472 Sum_probs=27.6
Q ss_pred cccccccCccCCHHHHHHHhhcHHHHHHHh
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHIMRAA 61 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~ 61 (369)
++|.+|+|.|+++|.|+-|..|..|.....
T Consensus 26 wyCqmCQkQcrDeNGFkCH~~SeSHqRql~ 55 (309)
T KOG2837|consen 26 WYCQMCQKQCRDENGFKCHTMSESHQRQLL 55 (309)
T ss_pred HHHHHHHHHhccccccccccCCHHHHHHHH
Confidence 679999999999999999999999998543
No 45
>PHA00732 hypothetical protein
Probab=82.44 E-value=1.2 Score=35.78 Aligned_cols=45 Identities=18% Similarity=0.424 Sum_probs=36.4
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHHhC
Q 042126 149 CCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHMEAK 224 (369)
Q Consensus 149 ~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~~ylvd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~dK 224 (369)
.|-.|+..+.+......||...|. +..|-.|+ +.|. .+..|+..|
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 588888766
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=81.55 E-value=0.84 Score=27.70 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=18.7
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcC
Q 042126 149 CCFMCDLPHDAIENCMVHMHKCHG 172 (369)
Q Consensus 149 ~CLFC~~~~~s~e~nl~HM~~~H~ 172 (369)
.|-+|+..+. ......||...|+
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 4999999987 8899999999986
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=81.17 E-value=1.2 Score=27.90 Aligned_cols=21 Identities=24% Similarity=0.725 Sum_probs=18.0
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNS 53 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~S 53 (369)
..|..|+.+| ...++..|++.
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 48
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=80.98 E-value=1.1 Score=42.98 Aligned_cols=30 Identities=20% Similarity=0.395 Sum_probs=27.1
Q ss_pred cccccccCccCCHHHHHHHhhcHHHHHHHhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHIMRAAQ 62 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~ 62 (369)
..|.+|+--.. ++-|.-|+.||+|++++.+
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 47999999999 9999999999999997554
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=77.43 E-value=1.1 Score=28.20 Aligned_cols=14 Identities=36% Similarity=1.046 Sum_probs=11.9
Q ss_pred CccccccccCccCC
Q 042126 30 MTYSCGLCGKGYRS 43 (369)
Q Consensus 30 ~~~~C~~C~K~F~S 43 (369)
..|.|..|+|+|.+
T Consensus 13 k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 13 KPYKCPYCGKSFSN 26 (26)
T ss_dssp SSEEESSSSEEESS
T ss_pred CCCCCCCCcCeeCc
Confidence 45899999999974
No 50
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=76.64 E-value=1.2 Score=45.01 Aligned_cols=32 Identities=25% Similarity=0.516 Sum_probs=28.2
Q ss_pred cccccccCccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
++|..|++-|.....|+.|+.+|.|..+....
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 45999999999999999999999999865443
No 51
>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=76.17 E-value=1.9 Score=36.02 Aligned_cols=75 Identities=25% Similarity=0.428 Sum_probs=49.3
Q ss_pred CCCCCccccCCCCCCCHHHHHHHhhhhcCCCC------------------CCcccc---cCHHHHHHHHHHHhcCCcee-
Q 042126 144 EFDPACCFMCDLPHDAIENCMVHMHKCHGFFI------------------PDVEYL---KDPKGLLTYLGLKVKRDFMC- 201 (369)
Q Consensus 144 ~~~~~~CLFC~~~~~s~e~nl~HM~~~H~F~I------------------P~~~yl---vd~~gLl~yL~~kI~~~~~C- 201 (369)
+.....|.-|.+.-.. .+...|+.+.|.-.- ++.+-+ -+...=|..| .|+.|+.|
T Consensus 8 ~~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gL--p~~~G~~C~ 84 (109)
T PF12013_consen 8 EYRVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGL--PVYDGYRCQ 84 (109)
T ss_pred cCCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCC--CCCCCeeee
Confidence 3466789999886644 888899998776431 111111 1111122222 56789999
Q ss_pred ---eecCCCCCCCCCHHHHHHHHHhC
Q 042126 202 ---LYCNDRCHPFNSLEAVRKHMEAK 224 (369)
Q Consensus 202 ---l~C~~~~k~F~S~eav~~HM~dK 224 (369)
..|++. ..+...++.|++.+
T Consensus 85 ~~~~~C~y~---~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 85 CDPPHCGYI---TRSKKTMRKHWRKE 107 (109)
T ss_pred cCCCCCCcE---eccHHHHHHHHHHh
Confidence 999854 47999999999875
No 52
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=75.72 E-value=2.1 Score=45.30 Aligned_cols=33 Identities=18% Similarity=0.354 Sum_probs=29.8
Q ss_pred ccccccccCccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 31 TYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 31 ~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
...|.+|+-.|.|.+..+.|.+|.||+.|..+.
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 357999999999999999999999999987654
No 53
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=75.60 E-value=2.5 Score=40.44 Aligned_cols=33 Identities=15% Similarity=0.517 Sum_probs=27.4
Q ss_pred cCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHH
Q 042126 182 KDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKH 220 (369)
Q Consensus 182 vd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~H 220 (369)
-++..|..||+.- .+-||||+ -.|.+.+++-.|
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 678999999876
No 54
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=74.40 E-value=1.5 Score=40.97 Aligned_cols=34 Identities=21% Similarity=0.332 Sum_probs=30.8
Q ss_pred CccccccccCccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 30 MTYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 30 ~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
-.|.|.+|.-.-.++++|..|.+=|||+.|.+.+
T Consensus 52 G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarr 85 (222)
T KOG0227|consen 52 GKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARR 85 (222)
T ss_pred cceeehhhhhhhcchhhhhhhhccchhhHHHHHH
Confidence 3479999999999999999999999999987654
No 55
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=73.76 E-value=1.8 Score=40.18 Aligned_cols=34 Identities=18% Similarity=0.347 Sum_probs=30.4
Q ss_pred CccccccccCccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 30 MTYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 30 ~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
-.|.|.+|.-+--|+++|..|+.-|||+.|.+.+
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 3478999999999999999999999999986644
No 56
>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=73.26 E-value=3 Score=30.58 Aligned_cols=22 Identities=32% Similarity=0.718 Sum_probs=18.9
Q ss_pred ccccccccCccCCHHHHHHHhhc
Q 042126 31 TYSCGLCGKGYRSSKALAQHLNS 53 (369)
Q Consensus 31 ~~~C~~C~K~F~S~nA~~nHl~S 53 (369)
.|.|.+|+| ..|..+|..|+..
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 7889999999863
No 57
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=68.51 E-value=4.1 Score=24.56 Aligned_cols=21 Identities=29% Similarity=0.629 Sum_probs=16.4
Q ss_pred cccccccCccCCHHHHHHHhhc
Q 042126 32 YSCGLCGKGYRSSKALAQHLNS 53 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~S 53 (369)
|.|..|.-+.. ...+++|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 57999998887 9999999875
No 58
>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=68.21 E-value=15 Score=30.49 Aligned_cols=28 Identities=25% Similarity=0.399 Sum_probs=25.1
Q ss_pred CCCCcc----ccCCCCCCCHHHHHHHhhhhcC
Q 042126 145 FDPACC----FMCDLPHDAIENCMVHMHKCHG 172 (369)
Q Consensus 145 ~~~~~C----LFC~~~~~s~e~nl~HM~~~H~ 172 (369)
++--.| ..|++...+....-.|+...||
T Consensus 78 ~~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 78 YDGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 355679 9999999999999999999997
No 59
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=64.45 E-value=4.5 Score=39.73 Aligned_cols=31 Identities=26% Similarity=0.623 Sum_probs=26.5
Q ss_pred CCCccccccccCccCCHHHHHHHhhcHHHHH
Q 042126 28 TPMTYSCGLCGKGYRSSKALAQHLNSRSHIM 58 (369)
Q Consensus 28 ~~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~ 58 (369)
+...|.|..|+|.|.++.-|+.||+..-+..
T Consensus 212 GEKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 212 GEKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred CCCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 3446899999999999999999999876655
No 60
>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=60.02 E-value=4.7 Score=27.99 Aligned_cols=22 Identities=32% Similarity=0.662 Sum_probs=15.4
Q ss_pred ccccccccCccCC----HHHHHHHhh
Q 042126 31 TYSCGLCGKGYRS----SKALAQHLN 52 (369)
Q Consensus 31 ~~~C~~C~K~F~S----~nA~~nHl~ 52 (369)
...|.+|++.|.. ...+..||+
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 3479999999976 488999994
No 61
>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=59.82 E-value=1.2 Score=29.11 Aligned_cols=20 Identities=25% Similarity=0.642 Sum_probs=15.0
Q ss_pred cccccccCccCCHHHHHHHhh
Q 042126 32 YSCGLCGKGYRSSKALAQHLN 52 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~ 52 (369)
|+|.-|+|+| +...|++|.+
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 7888888853
No 62
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=59.70 E-value=5.3 Score=44.63 Aligned_cols=53 Identities=23% Similarity=0.471 Sum_probs=36.6
Q ss_pred CCCCCccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHHHHHHHHhcCCceeeecCCCCCCCCCHHHHHHHHH
Q 042126 144 EFDPACCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLLTYLGLKVKRDFMCLYCNDRCHPFNSLEAVRKHME 222 (369)
Q Consensus 144 ~~~~~~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~~ylvd~~gLl~yL~~kI~~~~~Cl~C~~~~k~F~S~eav~~HM~ 222 (369)
.-++..|+||-+.-+=...+-.|-.. |+= ++ -+.|-.|+ |.|.+.-.|+.||-
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrt-HtG-------------------ER---PFkCKiCg---RAFtTkGNLkaH~~ 654 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRT-HTG-------------------ER---PFKCKICG---RAFTTKGNLKAHMS 654 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhc-ccC-------------------cC---cccccccc---chhccccchhhccc
Confidence 34789999998877666666666654 441 12 35777786 78888888888873
No 63
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=58.16 E-value=3.2 Score=45.73 Aligned_cols=30 Identities=23% Similarity=0.525 Sum_probs=26.7
Q ss_pred CCccccccccCccCCHHHHHHHhhcHHHHH
Q 042126 29 PMTYSCGLCGKGYRSSKALAQHLNSRSHIM 58 (369)
Q Consensus 29 ~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~ 58 (369)
...|.|.-|+|.|+-.+.|-.||.|||=.-
T Consensus 307 EKPfeCpnCkKRFSHSGSySSHmSSKKCIs 336 (1007)
T KOG3623|consen 307 EKPFECPNCKKRFSHSGSYSSHMSSKKCIS 336 (1007)
T ss_pred CCCcCCcccccccccCCcccccccccchhh
Confidence 345889999999999999999999999884
No 64
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=58.01 E-value=5.7 Score=43.91 Aligned_cols=74 Identities=23% Similarity=0.414 Sum_probs=41.9
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcCCCCCCcccccCHHHHH------------HH---HH--HHhcCC---ceeeecCCCC
Q 042126 149 CCFMCDLPHDAIENCMVHMHKCHGFFIPDVEYLKDPKGLL------------TY---LG--LKVKRD---FMCLYCNDRC 208 (369)
Q Consensus 149 ~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~~ylvd~~gLl------------~y---L~--~kI~~~---~~Cl~C~~~~ 208 (369)
.|..|.++|.....+=.||.. |.-- ++.---++..+++ .| |. .+|+.| +.|--|.
T Consensus 242 sC~lCsytFAyRtQLErhm~~-hkpg-~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCk--- 316 (1007)
T KOG3623|consen 242 SCMLCSYTFAYRTQLERHMQL-HKPG-GDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCK--- 316 (1007)
T ss_pred cchhhhhhhhhHHHHHHHHHh-hcCC-CcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccc---
Confidence 399999999999999999974 4422 2221112223322 22 22 233333 3566665
Q ss_pred CCCCCHHHHHHHHHhCCCc
Q 042126 209 HPFNSLEAVRKHMEAKRHC 227 (369)
Q Consensus 209 k~F~S~eav~~HM~dK~Hc 227 (369)
|+|+-.-+.-.||.+|.=.
T Consensus 317 KRFSHSGSySSHmSSKKCI 335 (1007)
T KOG3623|consen 317 KRFSHSGSYSSHMSSKKCI 335 (1007)
T ss_pred cccccCCcccccccccchh
Confidence 6666666666777776433
No 65
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=56.83 E-value=3.6 Score=41.74 Aligned_cols=72 Identities=21% Similarity=0.439 Sum_probs=49.1
Q ss_pred ccCCCC-----CCCHHHHHHHhhhhcCCCCCCc------cc-----ccCHHHHHHHHH--H---HhcCCceeeecCCCCC
Q 042126 151 FMCDLP-----HDAIENCMVHMHKCHGFFIPDV------EY-----LKDPKGLLTYLG--L---KVKRDFMCLYCNDRCH 209 (369)
Q Consensus 151 LFC~~~-----~~s~e~nl~HM~~~H~F~IP~~------~y-----lvd~~gLl~yL~--~---kI~~~~~Cl~C~~~~k 209 (369)
+||+.. ...|-+.-.|....|+|+|-+. .| |.-..+|-+.-- . =.....+|++|+ +
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~---~ 228 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCK---I 228 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhcc---c
Confidence 555543 4569999999999999998765 12 233333333210 0 111246899999 7
Q ss_pred CCCCHHHHHHHHHhCC
Q 042126 210 PFNSLEAVRKHMEAKR 225 (369)
Q Consensus 210 ~F~S~eav~~HM~dK~ 225 (369)
.|++-+.|..||+.+.
T Consensus 229 ~FYdDDEL~~HcR~~H 244 (493)
T COG5236 229 YFYDDDELRRHCRLRH 244 (493)
T ss_pred eecChHHHHHHHHhhh
Confidence 8999999999999873
No 66
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=56.64 E-value=5.9 Score=38.03 Aligned_cols=21 Identities=24% Similarity=0.520 Sum_probs=18.6
Q ss_pred CCccccCCCCCCCHHHHHHHh
Q 042126 147 PACCFMCDLPHDAIENCMVHM 167 (369)
Q Consensus 147 ~~~CLFC~~~~~s~e~nl~HM 167 (369)
.--||||+..+.+-++.+.|-
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 67
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=55.28 E-value=7.8 Score=27.89 Aligned_cols=24 Identities=33% Similarity=0.702 Sum_probs=19.3
Q ss_pred cccccccCccCC-----HHHHHHHhhcHHH
Q 042126 32 YSCGLCGKGYRS-----SKALAQHLNSRSH 56 (369)
Q Consensus 32 ~~C~~C~K~F~S-----~nA~~nHl~SkkH 56 (369)
-.|..|+|.+.- ...|.+||++ +|
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 369999999954 4799999997 44
No 68
>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=52.95 E-value=11 Score=23.84 Aligned_cols=20 Identities=25% Similarity=0.605 Sum_probs=17.3
Q ss_pred ccccccCccCCHHHHHHHhhc
Q 042126 33 SCGLCGKGYRSSKALAQHLNS 53 (369)
Q Consensus 33 ~C~~C~K~F~S~nA~~nHl~S 53 (369)
.|.+|++.+ +......|+.+
T Consensus 3 ~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 3 QCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHHH
Confidence 599999999 78899999863
No 69
>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=52.90 E-value=9.5 Score=34.77 Aligned_cols=27 Identities=26% Similarity=0.548 Sum_probs=24.2
Q ss_pred cccccccCccCCHHHHHHHhhcHHHHH
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHIM 58 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk~ 58 (369)
|.|.+|.-.-.......+||.|+-|++
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E 27 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKE 27 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHH
Confidence 579999977777888999999999998
No 70
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=49.05 E-value=10 Score=38.58 Aligned_cols=65 Identities=29% Similarity=0.520 Sum_probs=46.0
Q ss_pred HHHHhhhhcCCC-CCCcc----cccCHHHHHHHHHHHhc---------------------------------------CC
Q 042126 163 CMVHMHKCHGFF-IPDVE----YLKDPKGLLTYLGLKVK---------------------------------------RD 198 (369)
Q Consensus 163 nl~HM~~~H~F~-IP~~~----ylvd~~gLl~yL~~kI~---------------------------------------~~ 198 (369)
.++.+.+-|-|. ||.+. |+--+-.|-.||+.=+. .+
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 66653 56556666666553221 13
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCCcccc
Q 042126 199 FMCLYCNDRCHPFNSLEAVRKHMEAKRHCKMH 230 (369)
Q Consensus 199 ~~Cl~C~~~~k~F~S~eav~~HM~dK~Hcki~ 230 (369)
.-|..|+ |-|+...-...|...|.|||-.
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 3588886 8899999999999999999864
No 71
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=48.92 E-value=7.6 Score=43.47 Aligned_cols=25 Identities=36% Similarity=0.644 Sum_probs=21.2
Q ss_pred CccccccccCccCCHHHHHHHhhcH
Q 042126 30 MTYSCGLCGKGYRSSKALAQHLNSR 54 (369)
Q Consensus 30 ~~~~C~~C~K~F~S~nA~~nHl~Sk 54 (369)
+...|.+|.|.|.|..|++-|++|.
T Consensus 352 ~khkCr~CakvfgS~SaLqiHlRSH 376 (958)
T KOG1074|consen 352 FKHKCRFCAKVFGSDSALQIHLRSH 376 (958)
T ss_pred ccchhhhhHhhcCchhhhhhhhhcc
Confidence 3357999999999999999999884
No 72
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=47.66 E-value=11 Score=35.58 Aligned_cols=36 Identities=17% Similarity=0.444 Sum_probs=27.9
Q ss_pred CCCCccccccccCccCCHHHHHHHhhcHHHHHHHhcC
Q 042126 27 ETPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQG 63 (369)
Q Consensus 27 ~~~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~~ 63 (369)
.....++|.+|+. |.-.+++-||..|--|..+..+.
T Consensus 80 ~~e~lfyCE~Cd~-~ip~~~~snH~tSttHllsl~~~ 115 (223)
T KOG2384|consen 80 RDEALFYCEVCDI-YIPNSKKSNHFTSTTHLLSLQHI 115 (223)
T ss_pred CCCccchhhhhhh-hccCCCCccchhhHHHHhhhccC
Confidence 3456678999975 45567788999999999976554
No 73
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=45.07 E-value=7.8 Score=33.78 Aligned_cols=29 Identities=28% Similarity=0.635 Sum_probs=26.7
Q ss_pred CCceeeecCCCCCCCCCHHHHHHHHHhCCCcc
Q 042126 197 RDFMCLYCNDRCHPFNSLEAVRKHMEAKRHCK 228 (369)
Q Consensus 197 ~~~~Cl~C~~~~k~F~S~eav~~HM~dK~Hck 228 (369)
..+.||-|. |-|.+..+++.|-+.|-|-+
T Consensus 56 GqfyCi~Ca---RyFi~~~~l~~H~ktK~HKr 84 (129)
T KOG3408|consen 56 GQFYCIECA---RYFIDAKALKTHFKTKVHKR 84 (129)
T ss_pred ceeehhhhh---hhhcchHHHHHHHhccHHHH
Confidence 468999998 89999999999999999975
No 74
>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=44.74 E-value=14 Score=35.09 Aligned_cols=34 Identities=24% Similarity=0.544 Sum_probs=25.5
Q ss_pred CCCCccccccccCccCCHHHHHHHhhcHHHHHHHh
Q 042126 27 ETPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRAA 61 (369)
Q Consensus 27 ~~~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~ 61 (369)
.+...|-|.+|+|.|....=.+.|+. +||-+.+.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve 106 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVE 106 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHh-hcCHHHHH
Confidence 35566899999999999999999998 46888644
No 75
>PF14420 Clr5: Clr5 domain
Probab=44.69 E-value=11 Score=27.77 Aligned_cols=25 Identities=28% Similarity=0.481 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhhhhcCCCCCCccc
Q 042126 156 PHDAIENCMVHMHKCHGFFIPDVEY 180 (369)
Q Consensus 156 ~~~s~e~nl~HM~~~H~F~IP~~~y 180 (369)
..-++++...||...|||..-...|
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 76
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=43.51 E-value=12 Score=39.40 Aligned_cols=28 Identities=29% Similarity=0.689 Sum_probs=25.7
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCCccc
Q 042126 199 FMCLYCNDRCHPFNSLEAVRKHMEAKRHCKM 229 (369)
Q Consensus 199 ~~Cl~C~~~~k~F~S~eav~~HM~dK~Hcki 229 (369)
..|+.|+ |.|+|.-++.-|-.+|.|-+.
T Consensus 293 lyC~vCn---KsFKseKq~kNHEnSKKHken 320 (508)
T KOG0717|consen 293 LYCVVCN---KSFKSEKQLKNHENSKKHKEN 320 (508)
T ss_pred eEEeecc---ccccchHHHHhhHHHHHHHHH
Confidence 5899999 999999999999999999754
No 77
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=43.49 E-value=31 Score=35.25 Aligned_cols=74 Identities=18% Similarity=0.353 Sum_probs=54.2
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCC-CC------CCcccccCHHHHHHHHHHHhcCCceeee--c-CCCCCCCCCHHHH
Q 042126 148 ACCFMCDLPHDAIENCMVHMHKCHGF-FI------PDVEYLKDPKGLLTYLGLKVKRDFMCLY--C-NDRCHPFNSLEAV 217 (369)
Q Consensus 148 ~~CLFC~~~~~s~e~nl~HM~~~H~F-~I------P~~~ylvd~~gLl~yL~~kI~~~~~Cl~--C-~~~~k~F~S~eav 217 (369)
-.|.||...+-+=++...||...|.- +| |..+|..+.+.|-.....- ...|.+ | ..+.-.|..--.|
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 3347888888888877644 234432 4 2334578888899
Q ss_pred HHHHHhC
Q 042126 218 RKHMEAK 224 (369)
Q Consensus 218 ~~HM~dK 224 (369)
+.|+..-
T Consensus 298 ~~h~~~~ 304 (493)
T COG5236 298 LEHLTRF 304 (493)
T ss_pred HHHHHHH
Confidence 9998764
No 78
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=42.53 E-value=7.8 Score=36.84 Aligned_cols=27 Identities=22% Similarity=0.378 Sum_probs=23.7
Q ss_pred CccccCCCCCCCHHHHHHHhhhhcCCC
Q 042126 148 ACCFMCDLPHDAIENCMVHMHKCHGFF 174 (369)
Q Consensus 148 ~~CLFC~~~~~s~e~nl~HM~~~H~F~ 174 (369)
-+|-=|++++...+..+.|....|-|.
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 79
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=40.80 E-value=23 Score=34.69 Aligned_cols=32 Identities=25% Similarity=0.499 Sum_probs=28.8
Q ss_pred CCCCccccccccCccCCHHHHHHHhhcHHHHH
Q 042126 27 ETPMTYSCGLCGKGYRSSKALAQHLNSRSHIM 58 (369)
Q Consensus 27 ~~~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~ 58 (369)
.++++..|.+|++.|--+..-..|.++..|+.
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 46788899999999999999999999999964
No 80
>PF12907 zf-met2: Zinc-binding
Probab=39.90 E-value=15 Score=25.94 Aligned_cols=24 Identities=17% Similarity=0.573 Sum_probs=19.0
Q ss_pred cccccccCcc---CCHHHHHHHhhcHH
Q 042126 32 YSCGLCGKGY---RSSKALAQHLNSRS 55 (369)
Q Consensus 32 ~~C~~C~K~F---~S~nA~~nHl~Skk 55 (369)
+.|.+|.-+| .+..+|++|..+|-
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 4799999666 56789999988763
No 81
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=39.28 E-value=19 Score=37.56 Aligned_cols=31 Identities=26% Similarity=0.470 Sum_probs=24.2
Q ss_pred CCccccccccCccCCHHHHHHHhhcHHHHHH
Q 042126 29 PMTYSCGLCGKGYRSSKALAQHLNSRSHIMR 59 (369)
Q Consensus 29 ~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~ 59 (369)
...|.|.+|.|+|....-|+-|+-+..-..+
T Consensus 354 ~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~ 384 (500)
T KOG3993|consen 354 SGIFSCHTCGKKFRRQAYLRKHQLTHQRAPL 384 (500)
T ss_pred CceeecHHhhhhhHHHHHHHHhHHhhhcccc
Confidence 3468999999999999999999766433333
No 82
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=38.49 E-value=18 Score=37.79 Aligned_cols=30 Identities=33% Similarity=0.564 Sum_probs=24.9
Q ss_pred CccccccccCccCCHHHHHHHhhcHHHHHHHh
Q 042126 30 MTYSCGLCGKGYRSSKALAQHLNSRSHIMRAA 61 (369)
Q Consensus 30 ~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~ 61 (369)
-.|.|.-|+|.|+-..-|..|- +|||-|.+
T Consensus 294 vEYrCPEC~KVFsCPANLASHR--RWHKPR~e 323 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHR--RWHKPRPE 323 (500)
T ss_pred eeecCCcccccccCchhhhhhh--cccCCchh
Confidence 3489999999999999999996 58888644
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=36.50 E-value=20 Score=31.58 Aligned_cols=39 Identities=21% Similarity=0.583 Sum_probs=24.9
Q ss_pred ceeeecCCCCCCCCCHHHHHHHHHhCCCccccCCCCCchHHHHhhhhcccCCCCc
Q 042126 199 FMCLYCNDRCHPFNSLEAVRKHMEAKRHCKMHFGDGDDEEEAELEEFYDYSSSYM 253 (369)
Q Consensus 199 ~~Cl~C~~~~k~F~S~eav~~HM~dK~Hcki~~~~~~~~~~~e~~~FYDf~~sy~ 253 (369)
-+||-|| |.|+++ ..|.+.. ..|. ..||..=|.+...||
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 8898875 2232 469999999998886
No 84
>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=35.93 E-value=22 Score=37.54 Aligned_cols=27 Identities=19% Similarity=0.520 Sum_probs=23.8
Q ss_pred cccccccCccCCHHHHHHHhhcHHHHHH
Q 042126 32 YSCGLCGKGYRSSKALAQHLNSRSHIMR 59 (369)
Q Consensus 32 ~~C~~C~K~F~S~nA~~nHl~SkkHk~~ 59 (369)
+.|..|.+.|.+..++.+||-+ +|...
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~-eH~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ-EHPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH-hhhhh
Confidence 4899999999999999999986 47764
No 85
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=33.98 E-value=17 Score=27.61 Aligned_cols=29 Identities=28% Similarity=0.519 Sum_probs=23.3
Q ss_pred CCccccccccCccCCHHHHHHHhhcHHHHH
Q 042126 29 PMTYSCGLCGKGYRSSKALAQHLNSRSHIM 58 (369)
Q Consensus 29 ~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~ 58 (369)
...+.|.-|++.|..+..|-.|.+ |.|-.
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHVN-KaH~~ 43 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHVN-KAHGW 43 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHhh-HHhhh
Confidence 344689999999999999999987 34444
No 86
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=33.43 E-value=44 Score=39.48 Aligned_cols=32 Identities=25% Similarity=0.410 Sum_probs=29.1
Q ss_pred CCCccccccccCccCCHHHHHHHhhcHHHHHH
Q 042126 28 TPMTYSCGLCGKGYRSSKALAQHLNSRSHIMR 59 (369)
Q Consensus 28 ~~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~ 59 (369)
....|.|..|.-+|.+...+-+||+|-+|+.+
T Consensus 515 ~~~p~~C~~C~~stttng~LsihlqS~~h~~~ 546 (1406)
T KOG1146|consen 515 PGKPYPCRACNYSTTTNGNLSIHLQSDLHRNE 546 (1406)
T ss_pred CCCcccceeeeeeeecchHHHHHHHHHhhHHH
Confidence 34457899999999999999999999999997
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=33.01 E-value=39 Score=25.30 Aligned_cols=26 Identities=31% Similarity=0.632 Sum_probs=18.0
Q ss_pred CCCccccccccCccCCHHHHHHHhhc
Q 042126 28 TPMTYSCGLCGKGYRSSKALAQHLNS 53 (369)
Q Consensus 28 ~~~~~~C~~C~K~F~S~nA~~nHl~S 53 (369)
+...-+|.+|+-++.+...++-||..
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHH
T ss_pred cCCCCCCCcchhhccchhhHHHHHHH
Confidence 33445799999999999999999965
No 88
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=30.24 E-value=18 Score=37.47 Aligned_cols=31 Identities=39% Similarity=0.578 Sum_probs=24.9
Q ss_pred CCCccccccccCccCCHHHHHHHhhcHHHHHHHhc
Q 042126 28 TPMTYSCGLCGKGYRSSKALAQHLNSRSHIMRAAQ 62 (369)
Q Consensus 28 ~~~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~~~~ 62 (369)
++..| |.-|.-.|.| |++|+.|++|+.-+.+
T Consensus 420 tk~GY-CENCreky~~---lE~Hi~s~~HrrFAEn 450 (468)
T COG5067 420 TKKGY-CENCREKYES---LEQHIVSEKHRRFAEN 450 (468)
T ss_pred cccch-hHHHHHHHHH---HHHHhhhhhhhhhhhc
Confidence 33445 9999999965 7899999999996654
No 89
>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=29.10 E-value=29 Score=25.95 Aligned_cols=28 Identities=25% Similarity=0.312 Sum_probs=21.0
Q ss_pred CCCccccCCCCCCCHHHHHHHhhhhcCC
Q 042126 146 DPACCFMCDLPHDAIENCMVHMHKCHGF 173 (369)
Q Consensus 146 ~~~~CLFC~~~~~s~e~nl~HM~~~H~F 173 (369)
.|..|.-|+.....-...-.||...|+.
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 6778999999999999999999999974
No 90
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=28.60 E-value=40 Score=30.82 Aligned_cols=31 Identities=23% Similarity=0.344 Sum_probs=25.7
Q ss_pred cccccccc--CccCCHHHHHHHhhcHHHHHHHh
Q 042126 31 TYSCGLCG--KGYRSSKALAQHLNSRSHIMRAA 61 (369)
Q Consensus 31 ~~~C~~C~--K~F~S~nA~~nHl~SkkHk~~~~ 61 (369)
-|.|.+|+ -+=.|...=+.|+.=+||+.+++
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk 35 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVK 35 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHH
Confidence 37799999 45567888899999999999764
No 91
>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=27.85 E-value=1.4e+02 Score=31.54 Aligned_cols=89 Identities=13% Similarity=0.172 Sum_probs=49.2
Q ss_pred CCccccCCCCC-------CCHHHH---HHHhhhhcC---CCCCCcccccCHHHHHHHHHHHhcCC--ceeeecCCCCCCC
Q 042126 147 PACCFMCDLPH-------DAIENC---MVHMHKCHG---FFIPDVEYLKDPKGLLTYLGLKVKRD--FMCLYCNDRCHPF 211 (369)
Q Consensus 147 ~~~CLFC~~~~-------~s~e~n---l~HM~~~H~---F~IP~~~ylvd~~gLl~yL~~kI~~~--~~Cl~C~~~~k~F 211 (369)
|-.|-||.... .+++.. |+++...|| |+|-+-.+.++...++.++..-+..+ .+=..|..+.-..
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 45799997542 355544 444445565 45555566677776666666544332 2334565322111
Q ss_pred CCHHHHHHHHHhCCCcc--ccCCCCC
Q 042126 212 NSLEAVRKHMEAKRHCK--MHFGDGD 235 (369)
Q Consensus 212 ~S~eav~~HM~dK~Hck--i~~~~~~ 235 (369)
..-+.+-+.|++-|-.+ |..|+.+
T Consensus 284 ~~d~ell~~l~~aG~~~v~iGiES~~ 309 (497)
T TIGR02026 284 VRDADILHLYRRAGLVHISLGTEAAA 309 (497)
T ss_pred cCCHHHHHHHHHhCCcEEEEccccCC
Confidence 11256778898887544 4456543
No 92
>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=27.68 E-value=15 Score=29.76 Aligned_cols=31 Identities=19% Similarity=0.369 Sum_probs=17.4
Q ss_pred CCCCCccccCCCCCCCHHHHHHHhhhhcCCCCC
Q 042126 144 EFDPACCFMCDLPHDAIENCMVHMHKCHGFFIP 176 (369)
Q Consensus 144 ~~~~~~CLFC~~~~~s~e~nl~HM~~~H~F~IP 176 (369)
.+....|-||--... ...+.-=-+.|||||-
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 467788999966543 3333333457899874
No 93
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=27.19 E-value=44 Score=36.82 Aligned_cols=15 Identities=60% Similarity=1.026 Sum_probs=10.7
Q ss_pred CCCCcccccccCCch
Q 042126 96 SEDSDDEWEEVGPDE 110 (369)
Q Consensus 96 ~~d~e~eweev~~~e 110 (369)
+-|+++|||+-.+++
T Consensus 520 EVdSDeEWEEEepGE 534 (811)
T KOG4364|consen 520 EVDSDEEWEEEEPGE 534 (811)
T ss_pred cccCcccccccCCCc
Confidence 456888998766655
No 94
>COG4822 CbiK Cobalamin biosynthesis protein CbiK, Co2+ chelatase [Coenzyme metabolism]
Probab=25.74 E-value=45 Score=32.16 Aligned_cols=45 Identities=24% Similarity=0.302 Sum_probs=29.3
Q ss_pred ccccCCCCCCCHHHHHHHhhhhcCC---CCCCcccccCHHHHHHHHHH
Q 042126 149 CCFMCDLPHDAIENCMVHMHKCHGF---FIPDVEYLKDPKGLLTYLGL 193 (369)
Q Consensus 149 ~CLFC~~~~~s~e~nl~HM~~~H~F---~IP~~~ylvd~~gLl~yL~~ 193 (369)
+|-=-.|.+.+--.+|+||.+.||| |+--.+-.-+++.||.||+.
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 3433345566788999999999999 33333333456667777764
No 95
>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=23.73 E-value=22 Score=26.81 Aligned_cols=44 Identities=20% Similarity=0.310 Sum_probs=26.5
Q ss_pred CceeeecCCCCCCCCCHHHHHHHHHhCCCcc-ccCCCCCchHHHHhhhhcccCC
Q 042126 198 DFMCLYCNDRCHPFNSLEAVRKHMEAKRHCK-MHFGDGDDEEEAELEEFYDYSS 250 (369)
Q Consensus 198 ~~~Cl~C~~~~k~F~S~eav~~HM~dK~Hck-i~~~~~~~~~~~e~~~FYDf~~ 250 (369)
-.+||.|+..|=.-.+..-.+.|+++.+|.- |...+. .+|.|.-
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 3589999754422233467899999999975 555442 2677753
No 96
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=23.70 E-value=28 Score=38.69 Aligned_cols=30 Identities=20% Similarity=0.424 Sum_probs=25.7
Q ss_pred CccccccccCccCCHHHHHHHhhcHHHHHH
Q 042126 30 MTYSCGLCGKGYRSSKALAQHLNSRSHIMR 59 (369)
Q Consensus 30 ~~~~C~~C~K~F~S~nA~~nHl~SkkHk~~ 59 (369)
..|.|..|+|.|.-.++...||++..-+++
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~q~~ 820 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQQEE 820 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 347999999999999999999988766663
No 97
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.39 E-value=58 Score=34.09 Aligned_cols=31 Identities=26% Similarity=0.580 Sum_probs=23.0
Q ss_pred CCceeeecCCCCCCCCCHHHHHHHH--HhCCCcccc
Q 042126 197 RDFMCLYCNDRCHPFNSLEAVRKHM--EAKRHCKMH 230 (369)
Q Consensus 197 ~~~~Cl~C~~~~k~F~S~eav~~HM--~dK~Hcki~ 230 (369)
.++.|..|+ ++|.+++|+|-== ...=||-.-
T Consensus 127 ~~Y~Cp~C~---kkyt~Lea~~L~~~~~~~F~C~~C 159 (436)
T KOG2593|consen 127 AGYVCPNCQ---KKYTSLEALQLLDNETGEFHCENC 159 (436)
T ss_pred ccccCCccc---cchhhhHHHHhhcccCceEEEecC
Confidence 368999998 8999999998543 334477554
No 98
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=22.14 E-value=22 Score=25.24 Aligned_cols=20 Identities=40% Similarity=0.620 Sum_probs=15.6
Q ss_pred ceeeeccccccccCCCCCCC
Q 042126 291 KTFGSREYLRYYRRKPRPSP 310 (369)
Q Consensus 291 ~~iGhR~~~ryyrQ~~~~~~ 310 (369)
-++=||.|++||....+|-+
T Consensus 19 dT~v~r~l~~yY~~k~~~~P 38 (41)
T PF14475_consen 19 DTHVHRVLRKYYTEKGRPFP 38 (41)
T ss_pred hhHHHHHHHHHHHHcCCCCC
Confidence 45669999999998876644
No 99
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=22.10 E-value=27 Score=29.87 Aligned_cols=29 Identities=24% Similarity=0.473 Sum_probs=26.3
Q ss_pred CCceeeecCCCCCCCCCHHHHHHHHHhCCCcc
Q 042126 197 RDFMCLYCNDRCHPFNSLEAVRKHMEAKRHCK 228 (369)
Q Consensus 197 ~~~~Cl~C~~~~k~F~S~eav~~HM~dK~Hck 228 (369)
..+-|+-|. |-|-|..+|..|.+.|-|-+
T Consensus 54 GqhYCieCa---ryf~t~~aL~~HkkgkvHkR 82 (126)
T COG5112 54 GQHYCIECA---RYFITEKALMEHKKGKVHKR 82 (126)
T ss_pred ceeeeehhH---HHHHHHHHHHHHhccchhHH
Confidence 367999998 89999999999999999976
No 100
>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=21.09 E-value=1.1e+02 Score=28.15 Aligned_cols=42 Identities=21% Similarity=0.429 Sum_probs=31.6
Q ss_pred CCCCHHHHHHHHHHHHhhhccCCCCCccccccccCcc-CCHHHHHHHhhcHHHHHH
Q 042126 5 PGVTEALFLARQAALAQEKNTNETPMTYSCGLCGKGY-RSSKALAQHLNSRSHIMR 59 (369)
Q Consensus 5 PPVt~e~F~~k~~~~a~~~~~~~~~~~~~C~~C~K~F-~S~nA~~nHl~SkkHk~~ 59 (369)
-.|+.|.|..|+.+. .|.+|+--- ......+.|++|--|..|
T Consensus 78 ~gig~ehfm~KVEa~-------------hCsACd~~IP~~~~~vQ~Hl~S~~H~~N 120 (165)
T PF04988_consen 78 EGIGQEHFMKKVEAA-------------HCSACDVFIPMQHSSVQKHLKSQDHNKN 120 (165)
T ss_pred hhcCHHHHHHHHHHh-------------hhhHhhhhccCcHHHHHHHhccHHHHhh
Confidence 356777777776542 499998654 446789999999999995
No 101
>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=21.08 E-value=39 Score=28.73 Aligned_cols=17 Identities=18% Similarity=0.481 Sum_probs=13.4
Q ss_pred CCccccccccCccCCHH
Q 042126 29 PMTYSCGLCGKGYRSSK 45 (369)
Q Consensus 29 ~~~~~C~~C~K~F~S~n 45 (369)
.....|..|++.|+.-|
T Consensus 7 GtKR~Cp~CG~kFYDLn 23 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLN 23 (108)
T ss_pred CCcccCCCCcchhccCC
Confidence 34467999999999865
No 102
>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=21.06 E-value=41 Score=29.65 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=17.7
Q ss_pred CCCccccCCCCCCCHHHHHHHhhhhcCCC
Q 042126 146 DPACCFMCDLPHDAIENCMVHMHKCHGFF 174 (369)
Q Consensus 146 ~~~~CLFC~~~~~s~e~nl~HM~~~H~F~ 174 (369)
+-..||-||..+.++ -.|....||+.
T Consensus 71 d~i~clecGk~~k~L---krHL~~~~glt 96 (132)
T PF05443_consen 71 DYIICLECGKKFKTL---KRHLRTHHGLT 96 (132)
T ss_dssp S-EE-TBT--EESBH---HHHHHHTT-S-
T ss_pred CeeEEccCCcccchH---HHHHHHccCCC
Confidence 457899999999998 78999999986
No 103
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=20.77 E-value=61 Score=31.61 Aligned_cols=25 Identities=32% Similarity=0.671 Sum_probs=22.2
Q ss_pred CceeeecCCCCCCCCCHHHHHHHHHhCC
Q 042126 198 DFMCLYCNDRCHPFNSLEAVRKHMEAKR 225 (369)
Q Consensus 198 ~~~Cl~C~~~~k~F~S~eav~~HM~dK~ 225 (369)
.--|.||| |.|..-.-|-+|.+.|.
T Consensus 10 kpwcwycn---refddekiliqhqkakh 34 (341)
T KOG2893|consen 10 KPWCWYCN---REFDDEKILIQHQKAKH 34 (341)
T ss_pred Cceeeecc---cccchhhhhhhhhhhcc
Confidence 45799999 99999999999999873
No 104
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.38 E-value=1e+02 Score=34.11 Aligned_cols=71 Identities=18% Similarity=0.283 Sum_probs=52.8
Q ss_pred CCccccCCCCCCCHHHHHHHhhhhcCCCCCCc------ccccCHHHHHHHHHHHhcCCceee--ecCCCCCCCCCHHHHH
Q 042126 147 PACCFMCDLPHDAIENCMVHMHKCHGFFIPDV------EYLKDPKGLLTYLGLKVKRDFMCL--YCNDRCHPFNSLEAVR 218 (369)
Q Consensus 147 ~~~CLFC~~~~~s~e~nl~HM~~~H~F~IP~~------~ylvd~~gLl~yL~~kI~~~~~Cl--~C~~~~k~F~S~eav~ 218 (369)
...|.||...+-+-++.+.||...|=|-+--. +|.-+-.+|=...++. .++|= .|. +++|.....+-
T Consensus 182 hp~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~---HflCE~~~C~--~~~f~~~~~~e 256 (669)
T KOG2231|consen 182 HPLCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKG---HFLCEEEFCR--TKKFYVAFELE 256 (669)
T ss_pred CccchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhc---Cccccccccc--cceeeehhHHH
Confidence 35799999999999999999999998865442 3444666776666666 35787 887 36777776666
Q ss_pred HHHH
Q 042126 219 KHME 222 (369)
Q Consensus 219 ~HM~ 222 (369)
.||+
T Consensus 257 i~lk 260 (669)
T KOG2231|consen 257 IELK 260 (669)
T ss_pred HHHH
Confidence 6666
No 105
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=20.31 E-value=59 Score=34.27 Aligned_cols=27 Identities=37% Similarity=0.845 Sum_probs=25.9
Q ss_pred ccccccc-CccCCHHHHHHHhhcHHHHH
Q 042126 32 YSCGLCG-KGYRSSKALAQHLNSRSHIM 58 (369)
Q Consensus 32 ~~C~~C~-K~F~S~nA~~nHl~SkkHk~ 58 (369)
|.|.+|+ ++|.-..||+-|-+--.|..
T Consensus 402 y~CEICGNy~Y~GrkaF~RHF~EwRH~h 429 (497)
T KOG2636|consen 402 YNCEICGNYVYKGRKAFDRHFNEWRHAH 429 (497)
T ss_pred cceeeccCccccCcHHHHHHhHHHHHhh
Confidence 7999998 99999999999999999988
No 106
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=20.27 E-value=46 Score=32.59 Aligned_cols=22 Identities=27% Similarity=0.582 Sum_probs=19.7
Q ss_pred CccccccccCccCCHHHHHHHhh
Q 042126 30 MTYSCGLCGKGYRSSKALAQHLN 52 (369)
Q Consensus 30 ~~~~C~~C~K~F~S~nA~~nHl~ 52 (369)
..|+|.-|+|+|.- -.|+||.+
T Consensus 28 ~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 28 AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred CeeEEeeccccccc-chhhhhhh
Confidence 45899999999999 89999986
Done!