Query 009730
Match_columns 527
No_of_seqs 176 out of 212
Neff 3.4
Searched_HMMs 46136
Date Thu Mar 28 16:38:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009730.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009730hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5188 PRP9 Splicing factor 3 99.8 8.5E-22 1.8E-26 201.5 0.7 165 244-441 235-407 (470)
2 KOG2636 Splicing factor 3a, su 99.8 1.3E-20 2.9E-25 196.8 -0.9 172 244-441 246-434 (497)
3 PF11931 DUF3449: Domain of un 99.8 3.6E-20 7.7E-25 177.6 -3.2 120 308-441 8-134 (196)
4 smart00451 ZnF_U1 U1-like zinc 98.4 3.6E-07 7.9E-12 63.9 3.5 33 409-441 3-35 (35)
5 PF12874 zf-met: Zinc-finger o 98.3 3.5E-07 7.6E-12 60.1 2.5 25 410-434 1-25 (25)
6 smart00451 ZnF_U1 U1-like zinc 98.1 1.6E-06 3.5E-11 60.6 2.7 32 247-278 3-34 (35)
7 PF12874 zf-met: Zinc-finger o 98.0 3.2E-06 6.9E-11 55.6 2.3 25 248-272 1-25 (25)
8 PF12171 zf-C2H2_jaz: Zinc-fin 97.8 9.4E-06 2E-10 55.0 2.2 26 410-435 2-27 (27)
9 PF12171 zf-C2H2_jaz: Zinc-fin 97.6 3.3E-05 7.1E-10 52.3 1.8 26 248-273 2-27 (27)
10 PF06220 zf-U1: U1 zinc finger 96.7 0.0013 2.8E-08 48.9 2.8 31 410-440 4-36 (38)
11 PF06220 zf-U1: U1 zinc finger 96.7 0.0015 3.2E-08 48.6 3.0 32 247-278 3-36 (38)
12 KOG4727 U1-like Zn-finger prot 96.6 0.0016 3.4E-08 63.0 3.1 35 407-441 73-107 (193)
13 KOG0717 Molecular chaperone (D 96.5 0.0052 1.1E-07 66.8 6.4 35 247-281 292-326 (508)
14 KOG3792 Transcription factor N 95.7 0.012 2.7E-07 66.5 5.2 33 243-275 189-221 (816)
15 KOG4727 U1-like Zn-finger prot 95.7 0.0079 1.7E-07 58.3 2.9 34 245-278 73-106 (193)
16 KOG3408 U1-like Zn-finger-cont 95.1 0.012 2.5E-07 54.4 1.8 37 245-281 55-91 (129)
17 KOG2785 C2H2-type Zn-finger pr 94.6 0.025 5.5E-07 60.2 3.2 34 409-442 68-101 (390)
18 PLN02748 tRNA dimethylallyltra 94.5 0.023 4.9E-07 61.9 2.7 36 408-443 417-453 (468)
19 KOG0227 Splicing factor 3a, su 94.0 0.03 6.4E-07 55.3 2.1 36 406-441 50-85 (222)
20 PF13894 zf-C2H2_4: C2H2-type 94.0 0.042 9E-07 34.5 2.0 21 410-430 1-21 (24)
21 PF14968 CCDC84: Coiled coil p 93.9 0.052 1.1E-06 57.1 3.8 31 249-282 1-31 (336)
22 KOG3408 U1-like Zn-finger-cont 93.9 0.055 1.2E-06 50.1 3.4 37 407-443 55-91 (129)
23 KOG3032 Uncharacterized conser 93.6 0.11 2.5E-06 52.6 5.3 36 406-442 32-67 (264)
24 KOG3973 Uncharacterized conser 93.5 0.085 1.8E-06 56.2 4.3 14 153-166 356-369 (465)
25 PF00096 zf-C2H2: Zinc finger, 93.3 0.06 1.3E-06 34.5 1.8 22 410-431 1-22 (23)
26 smart00586 ZnF_DBF Zinc finger 93.1 0.057 1.2E-06 42.7 1.9 31 245-278 3-33 (49)
27 KOG0717 Molecular chaperone (D 93.1 0.06 1.3E-06 58.8 2.6 34 410-443 293-326 (508)
28 PLN02748 tRNA dimethylallyltra 93.0 0.083 1.8E-06 57.6 3.6 37 246-282 417-454 (468)
29 KOG3454 U1 snRNP-specific prot 92.9 0.057 1.2E-06 51.9 2.0 33 247-279 3-37 (165)
30 PF07535 zf-DBF: DBF zinc fing 92.6 0.082 1.8E-06 41.7 2.1 30 245-277 3-32 (49)
31 PF13912 zf-C2H2_6: C2H2-type 92.4 0.1 2.2E-06 34.7 2.1 22 409-430 1-22 (27)
32 KOG1146 Homeobox protein [Gene 92.2 0.14 3E-06 61.6 4.2 38 243-280 514-551 (1406)
33 COG5246 PRP11 Splicing factor 92.2 0.092 2E-06 51.7 2.3 44 407-450 51-94 (222)
34 smart00586 ZnF_DBF Zinc finger 92.0 0.071 1.5E-06 42.2 1.1 30 409-441 5-34 (49)
35 KOG0921 Dosage compensation co 91.5 0.36 7.9E-06 56.8 6.3 6 102-107 1168-1173(1282)
36 PF07535 zf-DBF: DBF zinc fing 91.4 0.12 2.5E-06 40.9 1.7 30 409-441 5-34 (49)
37 PF05918 API5: Apoptosis inhib 90.5 0.078 1.7E-06 59.1 0.0 11 133-143 517-527 (556)
38 KOG1596 Fibrillarin and relate 90.0 0.61 1.3E-05 48.3 5.8 17 427-443 190-206 (317)
39 COG5112 UFD2 U1-like Zn-finger 89.4 0.26 5.6E-06 45.1 2.4 36 408-443 54-89 (126)
40 KOG2785 C2H2-type Zn-finger pr 89.3 0.2 4.4E-06 53.6 1.9 39 243-281 64-102 (390)
41 PF12756 zf-C2H2_2: C2H2 type 89.2 0.19 4.2E-06 40.9 1.3 31 409-439 50-80 (100)
42 COG5188 PRP9 Splicing factor 3 89.1 0.21 4.5E-06 53.4 1.9 33 409-441 238-270 (470)
43 KOG3973 Uncharacterized conser 88.9 0.37 8E-06 51.6 3.5 13 146-158 429-441 (465)
44 KOG0227 Splicing factor 3a, su 88.9 0.3 6.5E-06 48.5 2.6 39 244-282 50-88 (222)
45 COG5112 UFD2 U1-like Zn-finger 88.7 0.36 7.7E-06 44.2 2.8 38 244-281 52-89 (126)
46 KOG0150 Spliceosomal protein F 88.4 0.26 5.7E-06 51.7 2.0 38 242-279 5-43 (336)
47 KOG3454 U1 snRNP-specific prot 88.1 0.3 6.5E-06 47.1 2.1 30 410-439 4-35 (165)
48 smart00355 ZnF_C2H2 zinc finge 87.9 0.32 7E-06 30.4 1.5 21 410-430 1-21 (26)
49 KOG0921 Dosage compensation co 87.7 0.83 1.8E-05 54.0 5.5 13 174-186 1258-1270(1282)
50 KOG3032 Uncharacterized conser 87.5 0.75 1.6E-05 46.9 4.4 39 242-281 30-68 (264)
51 KOG3262 H/ACA small nucleolar 87.1 0.89 1.9E-05 45.1 4.6 14 53-66 124-137 (215)
52 KOG1596 Fibrillarin and relate 84.7 1.9 4.1E-05 44.8 5.7 16 146-161 16-31 (317)
53 PF13909 zf-H2C2_5: C2H2-type 84.2 0.77 1.7E-05 30.0 1.8 20 410-430 1-20 (24)
54 PF13894 zf-C2H2_4: C2H2-type 83.6 0.82 1.8E-05 28.5 1.8 21 248-268 1-21 (24)
55 KOG3262 H/ACA small nucleolar 82.9 1.8 3.8E-05 43.1 4.5 19 140-158 5-23 (215)
56 COG5246 PRP11 Splicing factor 82.3 1.1 2.5E-05 44.3 3.0 39 244-282 50-88 (222)
57 PRK10590 ATP-dependent RNA hel 81.7 3.1 6.6E-05 44.3 6.1 6 153-158 402-407 (456)
58 PF00096 zf-C2H2: Zinc finger, 80.5 1.2 2.6E-05 28.5 1.7 21 248-268 1-21 (23)
59 PF13912 zf-C2H2_6: C2H2-type 80.5 1.3 2.9E-05 29.3 2.0 21 248-268 2-22 (27)
60 KOG0150 Spliceosomal protein F 80.1 1 2.2E-05 47.5 1.9 33 408-440 9-42 (336)
61 PF12756 zf-C2H2_2: C2H2 type 77.9 0.91 2E-05 37.0 0.7 31 247-277 50-80 (100)
62 PTZ00448 hypothetical protein; 76.5 1.9 4.1E-05 46.3 2.7 34 408-441 313-346 (373)
63 KOG4722 Zn-finger protein [Gen 75.8 2.4 5.2E-05 46.7 3.2 67 208-281 460-527 (672)
64 KOG4722 Zn-finger protein [Gen 74.6 1.7 3.7E-05 47.8 1.8 36 408-443 492-527 (672)
65 PRK11634 ATP-dependent RNA hel 73.8 5.6 0.00012 44.9 5.6 16 142-157 573-588 (629)
66 smart00355 ZnF_C2H2 zinc finge 72.9 2.7 5.8E-05 26.1 1.7 20 249-268 2-21 (26)
67 COG5136 U1 snRNP-specific prot 66.8 2.4 5.2E-05 41.4 0.7 32 247-278 3-36 (188)
68 PF05918 API5: Apoptosis inhib 66.8 1.9 4E-05 48.5 0.0 6 99-104 471-476 (556)
69 COG4907 Predicted membrane pro 66.5 4.6 9.9E-05 45.0 2.8 12 116-127 555-566 (595)
70 KOG2837 Protein containing a U 66.0 1.3 2.9E-05 46.0 -1.2 34 410-443 26-59 (309)
71 KOG3915 Transcription regulato 65.2 67 0.0014 36.3 11.2 43 238-280 180-226 (641)
72 PF09237 GAGA: GAGA factor; I 60.7 8.7 0.00019 31.3 2.8 25 405-429 20-44 (54)
73 PHA02768 hypothetical protein; 57.1 5.7 0.00012 32.3 1.2 25 409-435 5-29 (55)
74 KOG3293 Small nuclear ribonucl 55.6 15 0.00032 34.6 3.7 10 152-161 100-109 (134)
75 COG5136 U1 snRNP-specific prot 54.2 5.3 0.00012 39.1 0.7 29 410-438 4-34 (188)
76 KOG1146 Homeobox protein [Gene 53.2 11 0.00023 46.5 3.1 36 408-443 517-552 (1406)
77 PTZ00070 40S ribosomal protein 50.9 13 0.00029 38.4 2.9 8 174-181 20-27 (257)
78 KOG3792 Transcription factor N 50.4 6.5 0.00014 45.6 0.7 31 408-438 192-222 (816)
79 PF03194 LUC7: LUC7 N_terminus 48.6 8.7 0.00019 39.0 1.2 27 410-436 191-220 (254)
80 PF04094 DUF390: Protein of un 47.3 49 0.0011 39.0 6.8 31 124-156 56-86 (828)
81 KOG0796 Spliceosome subunit [R 46.5 12 0.00025 39.8 1.8 29 410-438 187-218 (319)
82 PHA00732 hypothetical protein 46.0 13 0.00029 31.7 1.7 21 410-430 2-22 (79)
83 KOG2837 Protein containing a U 45.9 5.8 0.00013 41.5 -0.5 36 246-281 24-59 (309)
84 PF04988 AKAP95: A-kinase anch 45.3 15 0.00033 35.8 2.2 33 410-442 1-33 (165)
85 PF12300 DUF3628: Protein of u 44.1 62 0.0013 31.9 6.0 18 110-127 37-54 (180)
86 PF14968 CCDC84: Coiled coil p 43.5 20 0.00042 38.4 2.9 38 243-280 54-97 (336)
87 PF04988 AKAP95: A-kinase anch 42.5 23 0.0005 34.6 3.0 34 248-281 1-34 (165)
88 PHA00616 hypothetical protein 41.7 14 0.0003 28.9 1.1 21 409-429 1-21 (44)
89 PF12764 Gly-rich_Ago1: Glycin 41.2 42 0.00091 30.7 4.2 12 148-159 19-30 (104)
90 KOG3576 Ovo and related transc 40.0 8.9 0.00019 39.1 -0.2 35 408-442 172-209 (267)
91 KOG1074 Transcriptional repres 35.8 12 0.00025 44.4 -0.2 26 408-433 632-657 (958)
92 PF13913 zf-C2HC_2: zinc-finge 34.9 25 0.00055 23.9 1.4 20 410-430 3-22 (25)
93 PF09237 GAGA: GAGA factor; I 34.2 41 0.00088 27.6 2.7 29 240-268 17-45 (54)
94 PF04959 ARS2: Arsenite-resist 31.3 39 0.00084 34.0 2.7 33 409-442 77-109 (214)
95 KOG2893 Zn finger protein [Gen 31.0 27 0.00058 36.4 1.5 29 404-432 5-33 (341)
96 COG1512 Beta-propeller domains 30.6 58 0.0012 33.9 3.8 24 113-136 196-220 (271)
97 COG4371 Predicted membrane pro 30.5 63 0.0014 34.1 4.0 8 484-491 306-313 (334)
98 PF12764 Gly-rich_Ago1: Glycin 29.9 49 0.0011 30.3 2.8 16 140-157 6-21 (104)
99 PF13465 zf-H2C2_2: Zinc-finge 29.7 32 0.00069 23.3 1.3 12 409-420 14-25 (26)
100 PF11931 DUF3449: Domain of un 29.2 18 0.0004 36.0 0.0 39 244-282 98-137 (196)
101 KOG2384 Major histocompatibili 29.0 13 0.00029 37.5 -0.9 34 409-443 84-117 (223)
102 TIGR01659 sex-lethal sex-letha 28.4 82 0.0018 33.4 4.6 9 111-119 210-218 (346)
103 PF11705 RNA_pol_3_Rpc31: DNA- 28.2 73 0.0016 31.6 4.0 7 213-219 32-38 (233)
104 PF12907 zf-met2: Zinc-binding 27.3 30 0.00065 26.6 0.9 26 248-274 2-30 (40)
105 COG5067 DBF4 Protein kinase es 27.1 29 0.00062 38.3 1.0 31 244-277 419-449 (468)
106 COG5200 LUC7 U1 snRNP componen 27.0 35 0.00076 35.0 1.5 30 410-439 186-218 (258)
107 PF04094 DUF390: Protein of un 26.0 1.5E+02 0.0033 35.1 6.4 8 72-79 32-39 (828)
108 KOG3428 Small nuclear ribonucl 25.1 36 0.00077 31.4 1.1 13 172-184 94-106 (109)
109 PTZ00448 hypothetical protein; 24.4 60 0.0013 35.4 2.7 34 247-280 314-347 (373)
110 KOG2505 Ankyrin repeat protein 24.3 54 0.0012 37.3 2.5 58 408-465 65-122 (591)
111 PF06397 Desulfoferrod_N: Desu 24.1 31 0.00067 26.0 0.4 13 406-418 3-16 (36)
112 PF05477 SURF2: Surfeit locus 24.1 1E+02 0.0022 31.7 4.2 41 244-284 76-117 (244)
113 PHA00616 hypothetical protein 22.5 47 0.001 26.0 1.2 20 248-267 2-21 (44)
114 PF04959 ARS2: Arsenite-resist 22.4 93 0.002 31.4 3.5 37 244-281 74-110 (214)
115 COG5152 Uncharacterized conser 21.9 73 0.0016 32.6 2.6 41 402-442 189-231 (259)
116 KOG2505 Ankyrin repeat protein 20.7 80 0.0017 36.0 2.9 33 246-278 65-97 (591)
117 PHA00733 hypothetical protein 20.1 69 0.0015 29.4 1.9 22 409-430 73-94 (128)
No 1
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=99.82 E-value=8.5e-22 Score=201.47 Aligned_cols=165 Identities=21% Similarity=0.223 Sum_probs=131.0
Q ss_pred CcCceeccccccccCCHHHHHHhhcchHHHHHHHHHHHHhhhcCCccccccccchhhhchhhhh-cCCcccccccccccc
Q 009730 244 PLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEELRKAVKPMAEIQTEQKPIAECQTEAS-ERPELAQDGEEKEAA 322 (527)
Q Consensus 244 p~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~~~K~~~~~e~~ste~~~IAe~p~E~~-~~P~l~~d~E~~~tk 322 (527)
..+.+||++|+..|..-.|++.|+.||+|.|+.+..++ ++. .|.. .+.-..++.++.+|+
T Consensus 235 ~~~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~-----------------~v~--~Ey~l~r~~kyl~d~~s~tr 295 (470)
T COG5188 235 WFPKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEE-----------------FVY--SEYVLHRYLKYLGDPVSETR 295 (470)
T ss_pred hccceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhH-----------------HHH--HHHHHHHHHHHhCChhHHHH
Confidence 34678999999999999999999999999999776553 121 2343 333445788899999
Q ss_pred cccCCccccchhhhhhcCCCCCCC--CC-CcCCCCCCCc--cccccccccccccccccccccccCCCcccccc-cccCCC
Q 009730 323 VDVPSETVNDDKEIEAEHPGNADE--QP-EVPVNESSNP--QEEKPRMDRFDNRRHGMKRKKRVGQGRKRMKS-TFEGSR 396 (527)
Q Consensus 323 vNveska~ltsher~~Elq~n~~~--k~-~~p~ee~S~~--Qe~k~~e~~~yN~~~GpKrKlp~GwdGK~I~~-t~~~~~ 396 (527)
+||.+..++|+.||-+|....... ++ ..+++...++ +.++++|+++|| +. +||+||||+|||| ++++|+
T Consensus 296 s~V~r~la~ta~ER~aei~~l~r~~~~~at~S~e~EGaeq~d~eQ~DE~~~~k----~f-dmPLG~DG~PmP~WL~klhg 370 (470)
T COG5188 296 SLVLRSLAITAKERKAEISLLSRRKKQPATKSSEKEGAEQVDGEQRDEHVSGK----SF-DMPLGPDGLPMPRWLCKLHG 370 (470)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHhhccCCCchhhcccccccccccchhhccC----cc-cCCCCCCCCCCchHHHHhcC
Confidence 999999999999998887665552 11 1111111122 233566889988 66 8999999999999 999999
Q ss_pred CCCCCCCCCccCceecccc-cccccCHHHHHHhhchhHHHHHHHhc
Q 009730 397 QSMEPPKPKVVIPLICSLC-NVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 397 q~vE~~~pk~~~~l~CEIC-NV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
+..| |.|||| |.+++++..|+.||+..+|+.-|+.+
T Consensus 371 Ld~e---------f~CEICgNyvy~GR~~FdrHF~E~rHiygl~cl 407 (470)
T COG5188 371 LDIE---------FECEICGNYVYYGRDRFDRHFEEDRHIYGLECL 407 (470)
T ss_pred CCcc---------eeeeecccccccchHHHHhhhhhhhhhhheeec
Confidence 9888 999999 89999999999999999999999876
No 2
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=99.78 E-value=1.3e-20 Score=196.79 Aligned_cols=172 Identities=20% Similarity=0.287 Sum_probs=134.4
Q ss_pred CcCceeccccccccCCHHHHHHhhcchHHHHHHHHHHHHhhh-----cCCcccccccc---------chhhhchhhhh-c
Q 009730 244 PLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEELRKA-----VKPMAEIQTEQ---------KPIAECQTEAS-E 308 (527)
Q Consensus 244 p~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~~~K~-----~~~~e~~ste~---------~~IAe~p~E~~-~ 308 (527)
....++|..|...+..-.++..|+.|+.|-++.+..++..+. .+.++..++.. .+||. .|+. +
T Consensus 246 s~Eel~~~g~erlk~al~alglk~gGt~~~ra~rlf~Tk~~~l~~L~~~~~~kn~s~~~~~~~~~~~keia~--tEa~v~ 323 (497)
T KOG2636|consen 246 SVEELYCLGCERLKSALTALGLKCGGTLHERAQRLFSTKSKSLSHLDTKLFAKNPSKKGHRREKERNKEIAR--TEALVK 323 (497)
T ss_pred HHHHHHhhchhHHHHHHHHHHHhcCCeecHHHHhhhhhcCcchhhhhhhhhccCcccchhhhhhhccchHHH--HHHHHH
Confidence 345788999999988888999999999999988777653222 11122222222 36777 6777 7
Q ss_pred CCcccccccccccccccCCccccchhhhhhcCCCCCCCCCCcCCCCCCCccccccccccccccccccccccccCCCcccc
Q 009730 309 RPELAQDGEEKEAAVDVPSETVNDDKEIEAEHPGNADEQPEVPVNESSNPQEEKPRMDRFDNRRHGMKRKKRVGQGRKRM 388 (527)
Q Consensus 309 ~P~l~~d~E~~~tkvNveska~ltsher~~Elq~n~~~k~~~p~ee~S~~Qe~k~~e~~~yN~~~GpKrKlp~GwdGK~I 388 (527)
.....+++++..|..||.++.+.|.-+++.|-++-+. +...++.|.++.+|| || +||+|||||||
T Consensus 324 k~~~iL~eeR~~t~env~rKq~~ta~e~E~E~~eq~~----------~~~e~~~de~~~~yn----p~-~lPLGwDGkPi 388 (497)
T KOG2636|consen 324 KLLAILAEERKATRENVVRKQARTAEEREEEEEEQSD----------SDEESDDDEEELIYN----PK-NLPLGWDGKPI 388 (497)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcchhhhhhhhhhhhc----------cccccccchhhccCC----cc-cCCCCCCCCcC
Confidence 7777789999999999999999998877554322111 112223445689999 88 99999999999
Q ss_pred cc-cccCCCCCCCCCCCCccCceecccc-cccccCHHHHHHhhchhHHHHHHHhc
Q 009730 389 KS-TFEGSRQSMEPPKPKVVIPLICSLC-NVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 389 ~~-t~~~~~q~vE~~~pk~~~~l~CEIC-NV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
|| ++++|++..+ |.|||| |.+++++..|++||+.++|+.-|+.+
T Consensus 389 PyWLyKLHGL~~e---------y~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCL 434 (497)
T KOG2636|consen 389 PYWLYKLHGLDIE---------YNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCL 434 (497)
T ss_pred chHHHhhcCCCcc---------cceeeccCccccCcHHHHHHhHHHHHhhcceec
Confidence 99 9999998877 999999 89999999999999999999999887
No 3
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=99.75 E-value=3.6e-20 Score=177.60 Aligned_cols=120 Identities=17% Similarity=0.255 Sum_probs=26.8
Q ss_pred cCCcccccccccccccccCCccccchhhhhhcCCCCCC-----CCCCcCCCCCCCccccccccccccccccccccccccC
Q 009730 308 ERPELAQDGEEKEAAVDVPSETVNDDKEIEAEHPGNAD-----EQPEVPVNESSNPQEEKPRMDRFDNRRHGMKRKKRVG 382 (527)
Q Consensus 308 ~~P~l~~d~E~~~tkvNveska~ltsher~~Elq~n~~-----~k~~~p~ee~S~~Qe~k~~e~~~yN~~~GpKrKlp~G 382 (527)
......+..++.+|+.||+|+.++|.+|++.|...+.. +......+..+++.++++.++.+|| ++ ++|+|
T Consensus 8 ~~~~~~L~~~~~~T~~~verk~a~T~~E~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n----p~-~lPLG 82 (196)
T PF11931_consen 8 HKLCELLSEEREDTKENVERKQARTEEERQAEEEYEEEIYSEDEYEEEEEEEESEEDSDDDEEEKIYN----PL-NLPLG 82 (196)
T ss_dssp HHHHHHTHHHHHHHHHHHHHHHT--HHHHHHHHHHTS-SS-TT--SS--B------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHhhhhhhhccccccccccccccccccccccccccCC----cc-cCCCC
Confidence 44555688899999999999999999999884222111 1111111112233334555788999 77 99999
Q ss_pred CCcccccc-cccCCCCCCCCCCCCccCceecccc-cccccCHHHHHHhhchhHHHHHHHhc
Q 009730 383 QGRKRMKS-TFEGSRQSMEPPKPKVVIPLICSLC-NVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 383 wdGK~I~~-t~~~~~q~vE~~~pk~~~~l~CEIC-NV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
|||||||| ++++|++.++ |.|||| |.+|.++.+|++||++++|+.-|+.+
T Consensus 83 ~DGkPIPyWLYKLhGL~~e---------y~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcL 134 (196)
T PF11931_consen 83 WDGKPIPYWLYKLHGLGVE---------YKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCL 134 (196)
T ss_dssp -------------------------------------------------------------
T ss_pred CCCCcccHHHHHHhCCCCe---------eeeEeCCCcceecHHHHHHhcChhHHHccChhc
Confidence 99999999 9999999998 999999 99999999999999999999999887
No 4
>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=98.36 E-value=3.6e-07 Score=63.92 Aligned_cols=33 Identities=36% Similarity=0.621 Sum_probs=30.8
Q ss_pred ceecccccccccCHHHHHHhhchhHHHHHHHhc
Q 009730 409 PLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
.|+|++|++.|++...+..|++|+||..++++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~~ 35 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHcC
Confidence 499999999999999999999999999999763
No 5
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.32 E-value=3.5e-07 Score=60.14 Aligned_cols=25 Identities=32% Similarity=0.763 Sum_probs=24.5
Q ss_pred eecccccccccCHHHHHHhhchhHH
Q 009730 410 LICSLCNVKCDTKEVFGRHLSGKKH 434 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~GKKH 434 (527)
|+|+||++.|+++..|..|++|+||
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 7999999999999999999999999
No 6
>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=98.14 E-value=1.6e-06 Score=60.63 Aligned_cols=32 Identities=38% Similarity=0.731 Sum_probs=30.3
Q ss_pred ceeccccccccCCHHHHHHhhcchHHHHHHHH
Q 009730 247 SAWCELCRVDCTSLQILEQHRNGKRHRKNLLR 278 (527)
Q Consensus 247 ~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLka 278 (527)
.++|++|++.|++...+.+|+.|++|++++++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 58999999999999999999999999999875
No 7
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.03 E-value=3.2e-06 Score=55.58 Aligned_cols=25 Identities=32% Similarity=0.692 Sum_probs=24.3
Q ss_pred eeccccccccCCHHHHHHhhcchHH
Q 009730 248 AWCELCRVDCTSLQILEQHRNGKRH 272 (527)
Q Consensus 248 ~~CeVCqV~cnSe~vy~sHl~GKKH 272 (527)
|+|++|++.|+++.+|.+|+.|+||
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 6899999999999999999999998
No 8
>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=97.85 E-value=9.4e-06 Score=54.97 Aligned_cols=26 Identities=23% Similarity=0.588 Sum_probs=25.2
Q ss_pred eecccccccccCHHHHHHhhchhHHH
Q 009730 410 LICSLCNVKCDTKEVFGRHLSGKKHI 435 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~GKKH~ 435 (527)
|+|++|++.|+++.+|+.|++|++|.
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 89999999999999999999999995
No 9
>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=97.60 E-value=3.3e-05 Score=52.33 Aligned_cols=26 Identities=31% Similarity=0.621 Sum_probs=25.2
Q ss_pred eeccccccccCCHHHHHHhhcchHHH
Q 009730 248 AWCELCRVDCTSLQILEQHRNGKRHR 273 (527)
Q Consensus 248 ~~CeVCqV~cnSe~vy~sHl~GKKHk 273 (527)
++|++|++.|+++.++..|+.|++|+
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 68999999999999999999999996
No 10
>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=96.72 E-value=0.0013 Score=48.88 Aligned_cols=31 Identities=29% Similarity=0.518 Sum_probs=20.6
Q ss_pred eecccccccc--cCHHHHHHhhchhHHHHHHHh
Q 009730 410 LICSLCNVKC--DTKEVFGRHLSGKKHIAKLKR 440 (527)
Q Consensus 410 l~CEICNV~C--nS~~v~~~Hl~GKKH~~kLKk 440 (527)
|||+.|++.+ ++..+-..|..|+||+.++++
T Consensus 4 yyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 4 YYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp -B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred eecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 9999999999 566777999999999999976
No 11
>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=96.71 E-value=0.0015 Score=48.61 Aligned_cols=32 Identities=31% Similarity=0.631 Sum_probs=21.0
Q ss_pred ceecccccccc--CCHHHHHHhhcchHHHHHHHH
Q 009730 247 SAWCELCRVDC--TSLQILEQHRNGKRHRKNLLR 278 (527)
Q Consensus 247 ~~~CeVCqV~c--nSe~vy~sHl~GKKHkKnLka 278 (527)
..||+.|++.+ .+..+-+.|..|.||+.++++
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 58999999999 466777999999999999875
No 12
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=96.59 E-value=0.0016 Score=63.03 Aligned_cols=35 Identities=26% Similarity=0.389 Sum_probs=31.7
Q ss_pred cCceecccccccccCHHHHHHhhchhHHHHHHHhc
Q 009730 407 VIPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 407 ~~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
..-|+|.|||-++.-..+|-.|+|||+|+.+|-.+
T Consensus 73 ~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred cCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 46699999999999999999999999999999544
No 13
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=96.46 E-value=0.0052 Score=66.76 Aligned_cols=35 Identities=26% Similarity=0.612 Sum_probs=33.5
Q ss_pred ceeccccccccCCHHHHHHhhcchHHHHHHHHHHH
Q 009730 247 SAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEE 281 (527)
Q Consensus 247 ~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~ 281 (527)
.++|-||..+|.|+.++..|-+.|||+++|..|..
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrq 326 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQ 326 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHHHHHHHH
Confidence 39999999999999999999999999999999986
No 14
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=95.74 E-value=0.012 Score=66.50 Aligned_cols=33 Identities=21% Similarity=0.572 Sum_probs=30.8
Q ss_pred CCcCceeccccccccCCHHHHHHhhcchHHHHH
Q 009730 243 QPLKSAWCELCRVDCTSLQILEQHRNGKRHRKN 275 (527)
Q Consensus 243 kp~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKn 275 (527)
...+.++|++|+++|+....+..|+.+.||+++
T Consensus 189 ~laqL~~~kw~k~~a~G~qs~re~lr~~r~l~k 221 (816)
T KOG3792|consen 189 RLAQLHYCKWCKISAAGPQTYREHLRGQKHLKK 221 (816)
T ss_pred HHHHhhhhHHHHHhccccHHHHHHHHHHHHHHh
Confidence 456789999999999999999999999999997
No 15
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=95.68 E-value=0.0079 Score=58.33 Aligned_cols=34 Identities=26% Similarity=0.482 Sum_probs=31.1
Q ss_pred cCceeccccccccCCHHHHHHhhcchHHHHHHHH
Q 009730 245 LKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLR 278 (527)
Q Consensus 245 ~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLka 278 (527)
...+||.||+-.+.--.+|-.|++||+|+++|.-
T Consensus 73 ~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgm 106 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGM 106 (193)
T ss_pred cCceeeeecceeehhhHHHHHHhccHHHHHHHhh
Confidence 3589999999999999999999999999999864
No 16
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=95.06 E-value=0.012 Score=54.40 Aligned_cols=37 Identities=19% Similarity=0.314 Sum_probs=34.5
Q ss_pred cCceeccccccccCCHHHHHHhhcchHHHHHHHHHHH
Q 009730 245 LKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEE 281 (527)
Q Consensus 245 ~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~ 281 (527)
...+||-.|-..|.+..+|..|+.+|.|+++|+.|++
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELRE 91 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhccHHHHHHHhccc
Confidence 3679999999999999999999999999999999884
No 17
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=94.64 E-value=0.025 Score=60.23 Aligned_cols=34 Identities=26% Similarity=0.557 Sum_probs=31.9
Q ss_pred ceecccccccccCHHHHHHhhchhHHHHHHHhcc
Q 009730 409 PLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFE 442 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~ 442 (527)
++.|++||.++-|...+..|++.+||..++.++.
T Consensus 68 ~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~ 101 (390)
T KOG2785|consen 68 VVYCEACNKSFASPKAHENHLKSKKHVENLSNHQ 101 (390)
T ss_pred ceehHHhhccccChhhHHHHHHHhhcchhhhhhh
Confidence 4899999999999999999999999999998864
No 18
>PLN02748 tRNA dimethylallyltransferase
Probab=94.54 E-value=0.023 Score=61.87 Aligned_cols=36 Identities=17% Similarity=0.452 Sum_probs=32.2
Q ss_pred Cceecccccc-cccCHHHHHHhhchhHHHHHHHhccC
Q 009730 408 IPLICSLCNV-KCDTKEVFGRHLSGKKHIAKLKRFEG 443 (527)
Q Consensus 408 ~~l~CEICNV-~CnS~~v~~~Hl~GKKH~~kLKk~~g 443 (527)
..|.||+|+. +++++...+.|++|++|.+++++..-
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 5588999987 89999999999999999999987753
No 19
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=94.03 E-value=0.03 Score=55.33 Aligned_cols=36 Identities=28% Similarity=0.403 Sum_probs=32.1
Q ss_pred ccCceecccccccccCHHHHHHhhchhHHHHHHHhc
Q 009730 406 VVIPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 406 ~~~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
..++|.|.+|+-.-|++..|..|..||||..||-+.
T Consensus 50 h~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarr 85 (222)
T KOG0227|consen 50 HLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARR 85 (222)
T ss_pred cCcceeehhhhhhhcchhhhhhhhccchhhHHHHHH
Confidence 346699999999999999999999999999998554
No 20
>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=93.96 E-value=0.042 Score=34.47 Aligned_cols=21 Identities=19% Similarity=0.605 Sum_probs=17.6
Q ss_pred eecccccccccCHHHHHHhhc
Q 009730 410 LICSLCNVKCDTKEVFGRHLS 430 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~ 430 (527)
|.|++|+..|.+...|..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 689999999999999999985
No 21
>PF14968 CCDC84: Coiled coil protein 84
Probab=93.93 E-value=0.052 Score=57.12 Aligned_cols=31 Identities=26% Similarity=0.517 Sum_probs=26.7
Q ss_pred eccccccccCCHHHHHHhhcchHHHHHHHHHHHH
Q 009730 249 WCELCRVDCTSLQILEQHRNGKRHRKNLLRIEEL 282 (527)
Q Consensus 249 ~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~~ 282 (527)
||+||++.+.. -..|.-+++|+++|..+...
T Consensus 1 yC~vCr~~h~~---gr~H~Y~~~Hq~~L~~~L~r 31 (336)
T PF14968_consen 1 YCEVCRRNHDQ---GRRHVYSPKHQKSLSAFLSR 31 (336)
T ss_pred CcchhhCcccc---cCCCccCHHHHHHHHHHHHH
Confidence 79999998876 67899999999999987653
No 22
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=93.89 E-value=0.055 Score=50.07 Aligned_cols=37 Identities=16% Similarity=0.234 Sum_probs=34.5
Q ss_pred cCceecccccccccCHHHHHHhhchhHHHHHHHhccC
Q 009730 407 VIPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFEG 443 (527)
Q Consensus 407 ~~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~g 443 (527)
...|+|-.|...|-++.+|..|+.+|.|.++||++.+
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELRE 91 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhccHHHHHHHhccc
Confidence 3559999999999999999999999999999999986
No 23
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.57 E-value=0.11 Score=52.55 Aligned_cols=36 Identities=25% Similarity=0.540 Sum_probs=32.1
Q ss_pred ccCceecccccccccCHHHHHHhhchhHHHHHHHhcc
Q 009730 406 VVIPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFE 442 (527)
Q Consensus 406 ~~~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~ 442 (527)
..+.+.|-|||+... +.....|.+||||..++.++.
T Consensus 32 ~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lK 67 (264)
T KOG3032|consen 32 ESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLK 67 (264)
T ss_pred CCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHH
Confidence 346689999999998 999999999999999888776
No 24
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=93.46 E-value=0.085 Score=56.21 Aligned_cols=14 Identities=14% Similarity=0.216 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCCCC
Q 009730 153 GAGHKNFGPRHSNP 166 (527)
Q Consensus 153 gggrg~~g~~~~~~ 166 (527)
||+||+.|.+|+.+
T Consensus 356 gg~Rgg~Gg~~gGr 369 (465)
T KOG3973|consen 356 GGSRGGSGGNWGGR 369 (465)
T ss_pred cCCCCCCCCCCCCC
Confidence 67788877766633
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=93.26 E-value=0.06 Score=34.55 Aligned_cols=22 Identities=23% Similarity=0.584 Sum_probs=20.2
Q ss_pred eecccccccccCHHHHHHhhch
Q 009730 410 LICSLCNVKCDTKEVFGRHLSG 431 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~G 431 (527)
|.|++|+..|.+...|..|+.-
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 6899999999999999999863
No 26
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=93.10 E-value=0.057 Score=42.70 Aligned_cols=31 Identities=32% Similarity=0.517 Sum_probs=26.7
Q ss_pred cCceeccccccccCCHHHHHHhhcchHHHHHHHH
Q 009730 245 LKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLR 278 (527)
Q Consensus 245 ~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLka 278 (527)
++..|||.|.+.|. .|+.|+.+++|.+-++.
T Consensus 3 ~k~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~~ 33 (49)
T smart00586 3 KKPGYCENCREKYD---DLETHLLSEKHRRFAEN 33 (49)
T ss_pred CCCcccccHhHHHh---hHHHHhccHHHHHHHcC
Confidence 46789999999997 78899999999997543
No 27
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=93.06 E-value=0.06 Score=58.84 Aligned_cols=34 Identities=24% Similarity=0.505 Sum_probs=32.4
Q ss_pred eecccccccccCHHHHHHhhchhHHHHHHHhccC
Q 009730 410 LICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFEG 443 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~g 443 (527)
++|-+||++|-|+.+|.-|.+.|||..||.++..
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrq 326 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQ 326 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999988864
No 28
>PLN02748 tRNA dimethylallyltransferase
Probab=93.01 E-value=0.083 Score=57.63 Aligned_cols=37 Identities=30% Similarity=0.513 Sum_probs=32.8
Q ss_pred Cceecccccc-ccCCHHHHHHhhcchHHHHHHHHHHHH
Q 009730 246 KSAWCELCRV-DCTSLQILEQHRNGKRHRKNLLRIEEL 282 (527)
Q Consensus 246 k~~~CeVCqV-~cnSe~vy~sHl~GKKHkKnLkaL~~~ 282 (527)
+...|++|+. .+.++..-+.|++|++|+++++++...
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~ 454 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQK 454 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhh
Confidence 5566999998 799999999999999999999987643
No 29
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=92.92 E-value=0.057 Score=51.92 Aligned_cols=33 Identities=27% Similarity=0.624 Sum_probs=29.3
Q ss_pred ceeccccccccC--CHHHHHHhhcchHHHHHHHHH
Q 009730 247 SAWCELCRVDCT--SLQILEQHRNGKRHRKNLLRI 279 (527)
Q Consensus 247 ~~~CeVCqV~cn--Se~vy~sHl~GKKHkKnLkaL 279 (527)
..||+.|+...+ |.+|=+.|+.|+||+++++.-
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~Y 37 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDY 37 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHH
Confidence 478999998776 899999999999999998754
No 30
>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=92.65 E-value=0.082 Score=41.73 Aligned_cols=30 Identities=40% Similarity=0.653 Sum_probs=26.2
Q ss_pred cCceeccccccccCCHHHHHHhhcchHHHHHHH
Q 009730 245 LKSAWCELCRVDCTSLQILEQHRNGKRHRKNLL 277 (527)
Q Consensus 245 ~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLk 277 (527)
.+..|||.|.+.|. .|+.|+.+.+|++-+.
T Consensus 3 ~k~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA~ 32 (49)
T PF07535_consen 3 KKPGYCENCRVKYD---DLEEHIQSEKHRKFAE 32 (49)
T ss_pred CCCccCccccchhh---hHHHHhCCHHHHHHHc
Confidence 46789999999997 5899999999999753
No 31
>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=92.45 E-value=0.1 Score=34.73 Aligned_cols=22 Identities=18% Similarity=0.469 Sum_probs=20.4
Q ss_pred ceecccccccccCHHHHHHhhc
Q 009730 409 PLICSLCNVKCDTKEVFGRHLS 430 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~ 430 (527)
+|.|++|+..|.+...|..|+.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHC
T ss_pred CCCCCccCCccCChhHHHHHhH
Confidence 4899999999999999999984
No 32
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=92.19 E-value=0.14 Score=61.59 Aligned_cols=38 Identities=29% Similarity=0.336 Sum_probs=33.6
Q ss_pred CCcCceeccccccccCCHHHHHHhhcchHHHHHHHHHH
Q 009730 243 QPLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIE 280 (527)
Q Consensus 243 kp~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~ 280 (527)
-+.+..-|.+|.+.++....|..|+..-+|+.+|+..+
T Consensus 514 ~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~ 551 (1406)
T KOG1146|consen 514 CPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAE 551 (1406)
T ss_pred CCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHH
Confidence 46678889999999999999999999999999976544
No 33
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=92.17 E-value=0.092 Score=51.72 Aligned_cols=44 Identities=27% Similarity=0.416 Sum_probs=35.9
Q ss_pred cCceecccccccccCHHHHHHhhchhHHHHHHHhccCCccccCC
Q 009730 407 VIPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFEGHQAMYGP 450 (527)
Q Consensus 407 ~~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~g~~~~~G~ 450 (527)
...|.|.+|+-.-.++..|..|+.||||..++-+.+..+...|.
T Consensus 51 ~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~eksslgr 94 (222)
T COG5246 51 TGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSEEKSSLGR 94 (222)
T ss_pred CCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHHHhhcccc
Confidence 35599999999999999999999999999998766554444444
No 34
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=92.05 E-value=0.071 Score=42.19 Aligned_cols=30 Identities=30% Similarity=0.403 Sum_probs=25.0
Q ss_pred ceecccccccccCHHHHHHhhchhHHHHHHHhc
Q 009730 409 PLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
+-+||+|.+.|. .|+.|+.++||..=.+..
T Consensus 5 ~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~~~ 34 (49)
T smart00586 5 PGYCENCREKYD---DLETHLLSEKHRRFAENN 34 (49)
T ss_pred CcccccHhHHHh---hHHHHhccHHHHHHHcCc
Confidence 378999999986 799999999998765443
No 35
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=91.45 E-value=0.36 Score=56.81 Aligned_cols=6 Identities=33% Similarity=0.335 Sum_probs=3.1
Q ss_pred hcCCCC
Q 009730 102 SAYYPA 107 (527)
Q Consensus 102 ~~~~~~ 107 (527)
|+|||-
T Consensus 1168 maryDn 1173 (1282)
T KOG0921|consen 1168 MARYDN 1173 (1282)
T ss_pred cccccC
Confidence 455554
No 36
>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=91.37 E-value=0.12 Score=40.90 Aligned_cols=30 Identities=30% Similarity=0.468 Sum_probs=25.1
Q ss_pred ceecccccccccCHHHHHHhhchhHHHHHHHhc
Q 009730 409 PLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
+-+||+|.+.|. .|+.|+.+++|..=.+..
T Consensus 5 ~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA~~~ 34 (49)
T PF07535_consen 5 PGYCENCRVKYD---DLEEHIQSEKHRKFAEND 34 (49)
T ss_pred CccCccccchhh---hHHHHhCCHHHHHHHcCc
Confidence 368999999997 599999999998766443
No 37
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=90.51 E-value=0.078 Score=59.06 Aligned_cols=11 Identities=36% Similarity=1.108 Sum_probs=0.0
Q ss_pred CCCCCCCCCCC
Q 009730 133 TPGGQFPNKGG 143 (527)
Q Consensus 133 ~~~g~~~~~gg 143 (527)
+|.|.....||
T Consensus 517 ~p~~k~ss~~~ 527 (556)
T PF05918_consen 517 PPSGKYSSNGG 527 (556)
T ss_dssp -----------
T ss_pred CCCCCCcCCCC
Confidence 44444443333
No 38
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=89.99 E-value=0.61 Score=48.26 Aligned_cols=17 Identities=29% Similarity=0.350 Sum_probs=11.1
Q ss_pred HhhchhHHHHHHHhccC
Q 009730 427 RHLSGKKHIAKLKRFEG 443 (527)
Q Consensus 427 ~Hl~GKKH~~kLKk~~g 443 (527)
+|..|+.-+.+.|+...
T Consensus 190 s~rsGRdL~nmAkkRtN 206 (317)
T KOG1596|consen 190 SHRSGRDLINMAKKRTN 206 (317)
T ss_pred cccchHHHHHHhhccCC
Confidence 67777776666666543
No 39
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=89.44 E-value=0.26 Score=45.11 Aligned_cols=36 Identities=22% Similarity=0.262 Sum_probs=33.1
Q ss_pred CceecccccccccCHHHHHHhhchhHHHHHHHhccC
Q 009730 408 IPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFEG 443 (527)
Q Consensus 408 ~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~g 443 (527)
+.++|--|...|.++.+|..|+.|+-|..++|++.+
T Consensus 54 GqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRe 89 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKGKVHKRRAKELRE 89 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhc
Confidence 348888899999999999999999999999999976
No 40
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=89.34 E-value=0.2 Score=53.62 Aligned_cols=39 Identities=26% Similarity=0.444 Sum_probs=34.4
Q ss_pred CCcCceeccccccccCCHHHHHHhhcchHHHHHHHHHHH
Q 009730 243 QPLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEE 281 (527)
Q Consensus 243 kp~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~ 281 (527)
......+|++|+..|.++..++.|+..|||..++.++..
T Consensus 64 ~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 64 EAESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred hcccceehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 344578999999999999999999999999999888663
No 41
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=89.15 E-value=0.19 Score=40.93 Aligned_cols=31 Identities=23% Similarity=0.537 Sum_probs=26.1
Q ss_pred ceecccccccccCHHHHHHhhchhHHHHHHH
Q 009730 409 PLICSLCNVKCDTKEVFGRHLSGKKHIAKLK 439 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLK 439 (527)
.+.|.+|++.|.+...|..|+..+.|.....
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 4999999999999999999999999987643
No 42
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=89.13 E-value=0.21 Score=53.40 Aligned_cols=33 Identities=27% Similarity=0.504 Sum_probs=29.2
Q ss_pred ceecccccccccCHHHHHHhhchhHHHHHHHhc
Q 009730 409 PLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
.++|+.|...|....||+.|+.||.|-+..++.
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~ 270 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGK 270 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhh
Confidence 389999999999999999999999998766543
No 43
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=88.93 E-value=0.37 Score=51.55 Aligned_cols=13 Identities=23% Similarity=0.475 Sum_probs=6.5
Q ss_pred CCCCCccCCCCCC
Q 009730 146 QGGRPFQGAGHKN 158 (527)
Q Consensus 146 ~gg~~~rgggrg~ 158 (527)
|+|++-+||||++
T Consensus 429 rdggg~~gggr~g 441 (465)
T KOG3973|consen 429 RDGGGRDGGGRDG 441 (465)
T ss_pred CCCCCCCCCCCCC
Confidence 3444445555555
No 44
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=88.92 E-value=0.3 Score=48.52 Aligned_cols=39 Identities=28% Similarity=0.363 Sum_probs=34.1
Q ss_pred CcCceeccccccccCCHHHHHHhhcchHHHHHHHHHHHH
Q 009730 244 PLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEEL 282 (527)
Q Consensus 244 p~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~~ 282 (527)
-....-|.+|.-.-+++..|..|+.||||+-||.+....
T Consensus 50 h~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa~ 88 (222)
T KOG0227|consen 50 HLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAAK 88 (222)
T ss_pred cCcceeehhhhhhhcchhhhhhhhccchhhHHHHHHHHH
Confidence 445778999999999999999999999999999876554
No 45
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=88.67 E-value=0.36 Score=44.23 Aligned_cols=38 Identities=24% Similarity=0.453 Sum_probs=34.9
Q ss_pred CcCceeccccccccCCHHHHHHhhcchHHHHHHHHHHH
Q 009730 244 PLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEE 281 (527)
Q Consensus 244 p~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~ 281 (527)
-...+||--|...|-++.+|..|+.||-|+++++.|.+
T Consensus 52 GlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRe 89 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELRE 89 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhc
Confidence 34679999999999999999999999999999998875
No 46
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=88.37 E-value=0.26 Score=51.66 Aligned_cols=38 Identities=21% Similarity=0.506 Sum_probs=31.9
Q ss_pred CCCcCceeccccccccC-CHHHHHHhhcchHHHHHHHHH
Q 009730 242 QQPLKSAWCELCRVDCT-SLQILEQHRNGKRHRKNLLRI 279 (527)
Q Consensus 242 ~kp~k~~~CeVCqV~cn-Se~vy~sHl~GKKHkKnLkaL 279 (527)
|+.....||++|++.+. ++..-..|-.|+||+-+|++.
T Consensus 5 WkS~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Kr 43 (336)
T KOG0150|consen 5 WKSQPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAKR 43 (336)
T ss_pred hhhccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHH
Confidence 44556789999999876 788888999999999998753
No 47
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=88.14 E-value=0.3 Score=47.12 Aligned_cols=30 Identities=30% Similarity=0.618 Sum_probs=26.1
Q ss_pred eeccccc--ccccCHHHHHHhhchhHHHHHHH
Q 009730 410 LICSLCN--VKCDTKEVFGRHLSGKKHIAKLK 439 (527)
Q Consensus 410 l~CEICN--V~CnS~~v~~~Hl~GKKH~~kLK 439 (527)
|.|+-|+ ..=.|-.|=..|++|+||+.++|
T Consensus 4 YyCDYCdt~LthDslsvRK~H~~GrkH~~nvk 35 (165)
T KOG3454|consen 4 YYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVK 35 (165)
T ss_pred chhhhhhhhhhcccHHHHHhhhhhHHHHHHHH
Confidence 8999998 44568889999999999999884
No 48
>smart00355 ZnF_C2H2 zinc finger.
Probab=87.87 E-value=0.32 Score=30.41 Aligned_cols=21 Identities=19% Similarity=0.474 Sum_probs=19.5
Q ss_pred eecccccccccCHHHHHHhhc
Q 009730 410 LICSLCNVKCDTKEVFGRHLS 430 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~ 430 (527)
|.|.+|+..|.+...|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 579999999999999999986
No 49
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=87.71 E-value=0.83 Score=54.01 Aligned_cols=13 Identities=54% Similarity=1.012 Sum_probs=5.5
Q ss_pred CcCCCCcCCCCCC
Q 009730 174 HGRGRGRGRGGSR 186 (527)
Q Consensus 174 rgrgrg~g~g~~~ 186 (527)
||+|||.|+||+.
T Consensus 1258 rgggrgagggGgf 1270 (1282)
T KOG0921|consen 1258 RGGGRGAGGGGGF 1270 (1282)
T ss_pred CCCCCCCCCCCCC
Confidence 4444444444333
No 50
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.46 E-value=0.75 Score=46.90 Aligned_cols=39 Identities=21% Similarity=0.417 Sum_probs=35.9
Q ss_pred CCCcCceeccccccccCCHHHHHHhhcchHHHHHHHHHHH
Q 009730 242 QQPLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEE 281 (527)
Q Consensus 242 ~kp~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~ 281 (527)
..+...+.|-||++-.. +.+...|.+||||.-++..|..
T Consensus 30 yn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs 68 (264)
T KOG3032|consen 30 YNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKS 68 (264)
T ss_pred cCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHh
Confidence 36778899999999999 9999999999999999999995
No 51
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=87.05 E-value=0.89 Score=45.11 Aligned_cols=14 Identities=14% Similarity=0.297 Sum_probs=9.4
Q ss_pred ccccccccCCcccc
Q 009730 53 SYYSTAYQSLPHQQ 66 (527)
Q Consensus 53 ~~y~~~~~~~~~q~ 66 (527)
.+|..++--||..-
T Consensus 124 k~fi~p~KllPl~R 137 (215)
T KOG3262|consen 124 KLFIDPDKLLPLDR 137 (215)
T ss_pred eEEecccccCcHhh
Confidence 55777777777654
No 52
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=84.69 E-value=1.9 Score=44.84 Aligned_cols=16 Identities=38% Similarity=0.540 Sum_probs=6.7
Q ss_pred CCCCCccCCCCCCCCC
Q 009730 146 QGGRPFQGAGHKNFGP 161 (527)
Q Consensus 146 ~gg~~~rgggrg~~g~ 161 (527)
+||+...||+||.||+
T Consensus 16 ~gg~gg~gg~rg~~gg 31 (317)
T KOG1596|consen 16 RGGRGGFGGGRGTSGG 31 (317)
T ss_pred ccCcCCCCCCccccCC
Confidence 3334444444444443
No 53
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=84.18 E-value=0.77 Score=29.96 Aligned_cols=20 Identities=30% Similarity=0.604 Sum_probs=16.3
Q ss_pred eecccccccccCHHHHHHhhc
Q 009730 410 LICSLCNVKCDTKEVFGRHLS 430 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~ 430 (527)
|.|..|+..++ +..|..|+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLK 20 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHH
Confidence 68999999998 999999975
No 54
>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=83.65 E-value=0.82 Score=28.47 Aligned_cols=21 Identities=29% Similarity=0.420 Sum_probs=17.1
Q ss_pred eeccccccccCCHHHHHHhhc
Q 009730 248 AWCELCRVDCTSLQILEQHRN 268 (527)
Q Consensus 248 ~~CeVCqV~cnSe~vy~sHl~ 268 (527)
+-|++|...|.+...|..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 469999999999999999974
No 55
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=82.90 E-value=1.8 Score=43.11 Aligned_cols=19 Identities=37% Similarity=0.686 Sum_probs=12.5
Q ss_pred CCCCCCCCCCCccCCCCCC
Q 009730 140 NKGGCRQGGRPFQGAGHKN 158 (527)
Q Consensus 140 ~~gg~~~gg~~~rgggrg~ 158 (527)
..||+.+|++.||||+++.
T Consensus 5 rgggg~~g~~gfRgg~ggg 23 (215)
T KOG3262|consen 5 RGGGGGGGGGGFRGGGGGG 23 (215)
T ss_pred cCCCCCCCCCCcccCCCCC
Confidence 5566666677778776654
No 56
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=82.32 E-value=1.1 Score=44.32 Aligned_cols=39 Identities=28% Similarity=0.420 Sum_probs=34.2
Q ss_pred CcCceeccccccccCCHHHHHHhhcchHHHHHHHHHHHH
Q 009730 244 PLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEEL 282 (527)
Q Consensus 244 p~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~~ 282 (527)
-...+-|.+|+-.-.++..|..|+.||||+-|+.+-++.
T Consensus 50 h~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~e 88 (222)
T COG5246 50 HTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSEE 88 (222)
T ss_pred CCCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHHH
Confidence 445778999999999999999999999999999887543
No 57
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=81.66 E-value=3.1 Score=44.34 Aligned_cols=6 Identities=33% Similarity=0.772 Sum_probs=2.6
Q ss_pred CCCCCC
Q 009730 153 GAGHKN 158 (527)
Q Consensus 153 gggrg~ 158 (527)
|||||.
T Consensus 402 ~~~~~~ 407 (456)
T PRK10590 402 GGGRGQ 407 (456)
T ss_pred CCCCCC
Confidence 444443
No 58
>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=80.54 E-value=1.2 Score=28.45 Aligned_cols=21 Identities=24% Similarity=0.428 Sum_probs=19.0
Q ss_pred eeccccccccCCHHHHHHhhc
Q 009730 248 AWCELCRVDCTSLQILEQHRN 268 (527)
Q Consensus 248 ~~CeVCqV~cnSe~vy~sHl~ 268 (527)
+-|+.|...|+++..|..|..
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 469999999999999999975
No 59
>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=80.49 E-value=1.3 Score=29.31 Aligned_cols=21 Identities=29% Similarity=0.556 Sum_probs=19.4
Q ss_pred eeccccccccCCHHHHHHhhc
Q 009730 248 AWCELCRVDCTSLQILEQHRN 268 (527)
Q Consensus 248 ~~CeVCqV~cnSe~vy~sHl~ 268 (527)
+.|++|++.|.+...|..|..
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHC
T ss_pred CCCCccCCccCChhHHHHHhH
Confidence 579999999999999999984
No 60
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=80.09 E-value=1 Score=47.52 Aligned_cols=33 Identities=21% Similarity=0.428 Sum_probs=27.6
Q ss_pred Cceecccccccc-cCHHHHHHhhchhHHHHHHHh
Q 009730 408 IPLICSLCNVKC-DTKEVFGRHLSGKKHIAKLKR 440 (527)
Q Consensus 408 ~~l~CEICNV~C-nS~~v~~~Hl~GKKH~~kLKk 440 (527)
...||++|+|.+ +.+..-+.|-.|++|..+|.+
T Consensus 9 ~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K 42 (336)
T KOG0150|consen 9 PKKFCDYCKIWIKDNPASVRFHERGKRHKENVAK 42 (336)
T ss_pred cchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence 448999998654 789999999999999888743
No 61
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=77.91 E-value=0.91 Score=36.99 Aligned_cols=31 Identities=29% Similarity=0.459 Sum_probs=26.4
Q ss_pred ceeccccccccCCHHHHHHhhcchHHHHHHH
Q 009730 247 SAWCELCRVDCTSLQILEQHRNGKRHRKNLL 277 (527)
Q Consensus 247 ~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLk 277 (527)
.+.|.+|.+.|.+...+..|+..+.|++...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 6899999999999999999999999998743
No 62
>PTZ00448 hypothetical protein; Provisional
Probab=76.48 E-value=1.9 Score=46.34 Aligned_cols=34 Identities=29% Similarity=0.502 Sum_probs=32.2
Q ss_pred CceecccccccccCHHHHHHhhchhHHHHHHHhc
Q 009730 408 IPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRF 441 (527)
Q Consensus 408 ~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~ 441 (527)
.+|.|..|++.|.+...+..|+..-=|.+|||+.
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRk 346 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRN 346 (373)
T ss_pred CCccccccccccCCHHHHHHHhhhhHHHHHHHHH
Confidence 4689999999999999999999999999999986
No 63
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=75.76 E-value=2.4 Score=46.67 Aligned_cols=67 Identities=24% Similarity=0.369 Sum_probs=44.4
Q ss_pred CCCCCCCCCchhhhhccCCCCcccccccCCCCCCCCCc-CceeccccccccCCHHHHHHhhcchHHHHHHHHHHH
Q 009730 208 AEPADPSPNATEKAAQFLPEPLLSTAAAGKVEPSQQPL-KSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEE 281 (527)
Q Consensus 208 ~~~~~p~~~~pe~~~~~~~~t~~s~~~~~~~~p~~kp~-k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~ 281 (527)
++...|+.-.+++-.+- .+++. +-+|+--|. ...-|.+|+|-.+|+.-|=+|..|.||+.+|..+.-
T Consensus 460 ~ek~e~~ke~aadl~qg-----rhant--dyapkltpyerkkqcslcnvlissevylfshvkgrkhqqal~e~~~ 527 (672)
T KOG4722|consen 460 GEKEEPAKEAAADLLQG-----RHANT--DYAPKLTPYERKKQCSLCNVLISSEVYLFSHVKGRKHQQALNELLL 527 (672)
T ss_pred hcccCcccccHHHHhcc-----ccccc--ccccccChHHhhhccchhhhhhhhhhhhhhhhcchhHHHHHHHHhc
Confidence 34556666666655443 23332 223333222 233599999999999999999999999999887653
No 64
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=74.64 E-value=1.7 Score=47.77 Aligned_cols=36 Identities=31% Similarity=0.435 Sum_probs=32.0
Q ss_pred CceecccccccccCHHHHHHhhchhHHHHHHHhccC
Q 009730 408 IPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFEG 443 (527)
Q Consensus 408 ~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~g 443 (527)
..-.|.+|||-..|++-+-+|..|.||+.-|+.+.-
T Consensus 492 rkkqcslcnvlissevylfshvkgrkhqqal~e~~~ 527 (672)
T KOG4722|consen 492 RKKQCSLCNVLISSEVYLFSHVKGRKHQQALNELLL 527 (672)
T ss_pred hhhccchhhhhhhhhhhhhhhhcchhHHHHHHHHhc
Confidence 345799999999999999999999999999988754
No 65
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=73.76 E-value=5.6 Score=44.93 Aligned_cols=16 Identities=31% Similarity=0.435 Sum_probs=7.0
Q ss_pred CCCCCCCCCccCCCCC
Q 009730 142 GGCRQGGRPFQGAGHK 157 (527)
Q Consensus 142 gg~~~gg~~~rgggrg 157 (527)
||+++.|+.-|+|||+
T Consensus 573 ~~~~~~~~~~~~~~~~ 588 (629)
T PRK11634 573 GGGRGFGGERREGGRN 588 (629)
T ss_pred CCCCCCCCCCCCCCcC
Confidence 3333334444455444
No 66
>smart00355 ZnF_C2H2 zinc finger.
Probab=72.92 E-value=2.7 Score=26.13 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=18.6
Q ss_pred eccccccccCCHHHHHHhhc
Q 009730 249 WCELCRVDCTSLQILEQHRN 268 (527)
Q Consensus 249 ~CeVCqV~cnSe~vy~sHl~ 268 (527)
-|..|...|.+...+..|..
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 59999999999999999986
No 67
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=66.81 E-value=2.4 Score=41.39 Aligned_cols=32 Identities=25% Similarity=0.404 Sum_probs=28.2
Q ss_pred ceeccccccccC--CHHHHHHhhcchHHHHHHHH
Q 009730 247 SAWCELCRVDCT--SLQILEQHRNGKRHRKNLLR 278 (527)
Q Consensus 247 ~~~CeVCqV~cn--Se~vy~sHl~GKKHkKnLka 278 (527)
..+||.|++..+ +.+|-+.|+.|++|..+.+.
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~d 36 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKD 36 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHH
Confidence 468999999888 78899999999999988664
No 68
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=66.78 E-value=1.9 Score=48.53 Aligned_cols=6 Identities=17% Similarity=0.490 Sum_probs=0.0
Q ss_pred hhhhcC
Q 009730 99 QQHSAY 104 (527)
Q Consensus 99 ~~~~~~ 104 (527)
.+|..+
T Consensus 471 k~~~~~ 476 (556)
T PF05918_consen 471 KKHQPI 476 (556)
T ss_dssp ------
T ss_pred cccCCc
Confidence 444443
No 69
>COG4907 Predicted membrane protein [Function unknown]
Probab=66.47 E-value=4.6 Score=44.98 Aligned_cols=12 Identities=17% Similarity=0.077 Sum_probs=5.0
Q ss_pred Hhhhhhhhhhhc
Q 009730 116 QFAGTMQAAEGA 127 (527)
Q Consensus 116 ~~~~~~~~~~~~ 127 (527)
.|--+.+.|-.|
T Consensus 555 r~~~~~~raysa 566 (595)
T COG4907 555 RSFNNLNRAYSA 566 (595)
T ss_pred hhhcccchhhhc
Confidence 333444444443
No 70
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=65.97 E-value=1.3 Score=46.02 Aligned_cols=34 Identities=24% Similarity=0.502 Sum_probs=31.5
Q ss_pred eecccccccccCHHHHHHhhchhHHHHHHHhccC
Q 009730 410 LICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFEG 443 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~g 443 (527)
|+|.+|...|+.+.-|.+|....-|++.|..+..
T Consensus 26 wyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~ 59 (309)
T KOG2837|consen 26 WYCQMCQKQCRDENGFKCHTMSESHQRQLLLFAL 59 (309)
T ss_pred HHHHHHHHHhccccccccccCCHHHHHHHHHHHh
Confidence 8899999999999999999999999999976654
No 71
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=65.15 E-value=67 Score=36.32 Aligned_cols=43 Identities=23% Similarity=0.348 Sum_probs=30.3
Q ss_pred CCCCCCCcCceeccccccccCCH--HHHHHhhcchHHH--HHHHHHH
Q 009730 238 VEPSQQPLKSAWCELCRVDCTSL--QILEQHRNGKRHR--KNLLRIE 280 (527)
Q Consensus 238 ~~p~~kp~k~~~CeVCqV~cnSe--~vy~sHl~GKKHk--KnLkaL~ 280 (527)
|+..-.++-.|.-+=|.+.|--+ .+|-.|+.|--|- -+|++|+
T Consensus 180 Vd~rG~kVAsF~i~g~emiCLPQafdlFLKhlVGGLHTVYTKLKRLd 226 (641)
T KOG3915|consen 180 VDLRGAKVASFTIEGCELICLPQAFDLFLKHLVGGLHTVYTKLKRLD 226 (641)
T ss_pred eeecCceeeEEEecCceEEecHHHHHHHHHHHhchHHHHHHHhhccc
Confidence 34444677788888899999865 5677899998885 3455554
No 72
>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=60.70 E-value=8.7 Score=31.33 Aligned_cols=25 Identities=24% Similarity=0.535 Sum_probs=18.0
Q ss_pred CccCceecccccccccCHHHHHHhh
Q 009730 405 KVVIPLICSLCNVKCDTKEVFGRHL 429 (527)
Q Consensus 405 k~~~~l~CEICNV~CnS~~v~~~Hl 429 (527)
.++.+-.|-||..+|.+..+|..||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHl 44 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHL 44 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHH
T ss_pred ccCCCCCCCcchhhccchhhHHHHH
Confidence 4567789999999999999999997
No 73
>PHA02768 hypothetical protein; Provisional
Probab=57.14 E-value=5.7 Score=32.32 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=22.0
Q ss_pred ceecccccccccCHHHHHHhhchhHHH
Q 009730 409 PLICSLCNVKCDTKEVFGRHLSGKKHI 435 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~GKKH~ 435 (527)
-|.|++|+..|.....|..|+.- |.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~--H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK--HN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh--cC
Confidence 38999999999999999999853 66
No 74
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=55.61 E-value=15 Score=34.56 Aligned_cols=10 Identities=40% Similarity=0.660 Sum_probs=4.4
Q ss_pred cCCCCCCCCC
Q 009730 152 QGAGHKNFGP 161 (527)
Q Consensus 152 rgggrg~~g~ 161 (527)
||+|+|++++
T Consensus 100 rG~gng~~~~ 109 (134)
T KOG3293|consen 100 RGRGNGNRGG 109 (134)
T ss_pred cCCCCCCCCC
Confidence 3444444443
No 75
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=54.15 E-value=5.3 Score=39.07 Aligned_cols=29 Identities=31% Similarity=0.396 Sum_probs=24.1
Q ss_pred eecccccccc--cCHHHHHHhhchhHHHHHH
Q 009730 410 LICSLCNVKC--DTKEVFGRHLSGKKHIAKL 438 (527)
Q Consensus 410 l~CEICNV~C--nS~~v~~~Hl~GKKH~~kL 438 (527)
|.||.|++.. .+-.|-..|+.|++|..+.
T Consensus 4 Y~CeyC~~~LthD~lsvRk~H~~G~~H~~~~ 34 (188)
T COG5136 4 YFCEYCNKMLTHDRLSVRKMHCGGAKHGLMR 34 (188)
T ss_pred hHHHHHHHHHhccHHHHHHHhhhhHHHHHHH
Confidence 8999998765 4567888999999998765
No 76
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=53.20 E-value=11 Score=46.47 Aligned_cols=36 Identities=28% Similarity=0.433 Sum_probs=33.2
Q ss_pred CceecccccccccCHHHHHHhhchhHHHHHHHhccC
Q 009730 408 IPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFEG 443 (527)
Q Consensus 408 ~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~g 443 (527)
..|.|++||+.+.+...+-+|+..-+|..+|+....
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~ 552 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEE 552 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHh
Confidence 569999999999999999999999999999887765
No 77
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=50.86 E-value=13 Score=38.38 Aligned_cols=8 Identities=88% Similarity=1.709 Sum_probs=3.8
Q ss_pred CcCCCCcC
Q 009730 174 HGRGRGRG 181 (527)
Q Consensus 174 rgrgrg~g 181 (527)
||||||+|
T Consensus 20 ~g~~~~~~ 27 (257)
T PTZ00070 20 RGRGRGRG 27 (257)
T ss_pred CCCCCCCC
Confidence 45544444
No 78
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=50.38 E-value=6.5 Score=45.60 Aligned_cols=31 Identities=26% Similarity=0.583 Sum_probs=28.3
Q ss_pred CceecccccccccCHHHHHHhhchhHHHHHH
Q 009730 408 IPLICSLCNVKCDTKEVFGRHLSGKKHIAKL 438 (527)
Q Consensus 408 ~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kL 438 (527)
+-.+|++|++.|++...+..|+.+.||+++-
T Consensus 192 qL~~~kw~k~~a~G~qs~re~lr~~r~l~kr 222 (816)
T KOG3792|consen 192 QLHYCKWCKISAAGPQTYREHLRGQKHLKKE 222 (816)
T ss_pred HhhhhHHHHHhccccHHHHHHHHHHHHHHhc
Confidence 4567999999999999999999999999875
No 79
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=48.56 E-value=8.7 Score=39.05 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=22.1
Q ss_pred eeccccc---ccccCHHHHHHhhchhHHHH
Q 009730 410 LICSLCN---VKCDTKEVFGRHLSGKKHIA 436 (527)
Q Consensus 410 l~CEICN---V~CnS~~v~~~Hl~GKKH~~ 436 (527)
-.|+||. +...+..-++.||.||-|+-
T Consensus 191 ~VCeVCGA~Ls~~D~d~RladH~~GK~HlG 220 (254)
T PF03194_consen 191 EVCEVCGAFLSVGDNDRRLADHFGGKQHLG 220 (254)
T ss_pred cchhhhhhHHhccchHHHHHHHhccchhhh
Confidence 5799996 45567778999999999964
No 80
>PF04094 DUF390: Protein of unknown function (DUF390); InterPro: IPR007228 This domain is found in a family of long proteins that are currently found only in rice. They have no known function. However they may be some kind of transposable element. There is a putative gypsy type transposon domain (IPR007321 from INTERPRO) towards the N terminus of the proteins.
Probab=47.32 E-value=49 Score=38.96 Aligned_cols=31 Identities=35% Similarity=0.587 Sum_probs=13.1
Q ss_pred hhhccCCCCCCCCCCCCCCCCCCCCCCccCCCC
Q 009730 124 AEGAMGGMHTPGGQFPNKGGCRQGGRPFQGAGH 156 (527)
Q Consensus 124 ~~~~~~~~~~~~g~~~~~gg~~~gg~~~rgggr 156 (527)
|-|+.++ +.|-|.+. .||+++|+....||||
T Consensus 56 AVGAsr~-Ra~RG~dG-AGGsr~G~~stpGGgr 86 (828)
T PF04094_consen 56 AVGASRE-RAPRGHDG-AGGSRRGEQSTPGGGR 86 (828)
T ss_pred Hhccccc-ccccccCC-ccccCCCCCCCCCCCC
Confidence 3555544 33444442 3334444443344433
No 81
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=46.54 E-value=12 Score=39.84 Aligned_cols=29 Identities=24% Similarity=0.613 Sum_probs=23.8
Q ss_pred eeccccc---ccccCHHHHHHhhchhHHHHHH
Q 009730 410 LICSLCN---VKCDTKEVFGRHLSGKKHIAKL 438 (527)
Q Consensus 410 l~CEICN---V~CnS~~v~~~Hl~GKKH~~kL 438 (527)
-.|+||. +...+..=++.||+||=|+--+
T Consensus 187 ~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~ 218 (319)
T KOG0796|consen 187 RVCEVCGAFLSVNDADRRLADHFGGKLHLGYV 218 (319)
T ss_pred hHHHhhhHHHhccchHHHHHHhhcchHHHHHH
Confidence 3699995 6677888899999999997544
No 82
>PHA00732 hypothetical protein
Probab=45.99 E-value=13 Score=31.69 Aligned_cols=21 Identities=19% Similarity=0.428 Sum_probs=19.6
Q ss_pred eecccccccccCHHHHHHhhc
Q 009730 410 LICSLCNVKCDTKEVFGRHLS 430 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~ 430 (527)
|.|++|+..|.+...|..|+.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhh
Confidence 789999999999999999975
No 83
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=45.93 E-value=5.8 Score=41.50 Aligned_cols=36 Identities=19% Similarity=0.485 Sum_probs=32.7
Q ss_pred CceeccccccccCCHHHHHHhhcchHHHHHHHHHHH
Q 009730 246 KSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEE 281 (527)
Q Consensus 246 k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~ 281 (527)
-.|||-.|+..|.-++-|.-|++.--|++.|.....
T Consensus 24 lRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~ 59 (309)
T KOG2837|consen 24 LRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFAL 59 (309)
T ss_pred HHHHHHHHHHHhccccccccccCCHHHHHHHHHHHh
Confidence 479999999999999999999999999999876553
No 84
>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=45.32 E-value=15 Score=35.84 Aligned_cols=33 Identities=27% Similarity=0.537 Sum_probs=29.2
Q ss_pred eecccccccccCHHHHHHhhchhHHHHHHHhcc
Q 009730 410 LICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFE 442 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~ 442 (527)
|.|.+|++----+..++.||-++=|..-|+-++
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i~ 33 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYIQ 33 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHHH
Confidence 679999999999999999999999997776553
No 85
>PF12300 DUF3628: Protein of unknown function (DUF3628); InterPro: IPR022077 Proteins in this entry are DEAD Box RhlB RNA Helicases found in Xanthomonadaceae bacteria.; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=44.08 E-value=62 Score=31.87 Aligned_cols=18 Identities=17% Similarity=0.169 Sum_probs=10.9
Q ss_pred hhhHHHHhhhhhhhhhhc
Q 009730 110 PLSQLAQFAGTMQAAEGA 127 (527)
Q Consensus 110 ~~~~~~~~~~~~~~~~~~ 127 (527)
...++|--|-..-+|+-.
T Consensus 37 SVG~IfreAReqraA~E~ 54 (180)
T PF12300_consen 37 SVGTIFREAREQRAADEQ 54 (180)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 455677666666666543
No 86
>PF14968 CCDC84: Coiled coil protein 84
Probab=43.50 E-value=20 Score=38.38 Aligned_cols=38 Identities=21% Similarity=0.416 Sum_probs=31.2
Q ss_pred CCcCceeccccccccCCH------HHHHHhhcchHHHHHHHHHH
Q 009730 243 QPLKSAWCELCRVDCTSL------QILEQHRNGKRHRKNLLRIE 280 (527)
Q Consensus 243 kp~k~~~CeVCqV~cnSe------~vy~sHl~GKKHkKnLkaL~ 280 (527)
.....+||-+|......- ..+-.||.+.-|.|++++--
T Consensus 54 ~~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLaS~eH~k~vk~F~ 97 (336)
T PF14968_consen 54 EHRNRFWCVFCDCEVREHDSSFACGGAIEHLASPEHRKNVKKFW 97 (336)
T ss_pred cccceeEeeCccchhhhccchhhhccHHhhcCCHHHHHHHHHHH
Confidence 566789999999987744 34559999999999999874
No 87
>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=42.53 E-value=23 Score=34.62 Aligned_cols=34 Identities=24% Similarity=0.437 Sum_probs=31.0
Q ss_pred eeccccccccCCHHHHHHhhcchHHHHHHHHHHH
Q 009730 248 AWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEE 281 (527)
Q Consensus 248 ~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~ 281 (527)
+.|.+|+...-.+..++.|+.++=|+..++-+..
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i~t 34 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYIQT 34 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHHHh
Confidence 4699999999999999999999999999998843
No 88
>PHA00616 hypothetical protein
Probab=41.70 E-value=14 Score=28.91 Aligned_cols=21 Identities=24% Similarity=0.270 Sum_probs=19.6
Q ss_pred ceecccccccccCHHHHHHhh
Q 009730 409 PLICSLCNVKCDTKEVFGRHL 429 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl 429 (527)
+|.|..|+..|.....|..|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH
Confidence 378999999999999999998
No 89
>PF12764 Gly-rich_Ago1: Glycine-rich region of argonaut; InterPro: IPR024357 This domain is found in the N terminus of some argonaut proteins. Argonaut (AGO) proteins are involved in RNA-mediated post-transcriptional gene silencing [].
Probab=41.18 E-value=42 Score=30.69 Aligned_cols=12 Identities=42% Similarity=0.567 Sum_probs=4.9
Q ss_pred CCCccCCCCCCC
Q 009730 148 GRPFQGAGHKNF 159 (527)
Q Consensus 148 g~~~rgggrg~~ 159 (527)
|++..|||||++
T Consensus 19 G~~~yGggrgg~ 30 (104)
T PF12764_consen 19 GRPGYGGGRGGG 30 (104)
T ss_pred CCCCCCCCCCCC
Confidence 333444444433
No 90
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=39.99 E-value=8.9 Score=39.07 Aligned_cols=35 Identities=29% Similarity=0.466 Sum_probs=26.8
Q ss_pred CceecccccccccCHHHHHHhhc---hhHHHHHHHhcc
Q 009730 408 IPLICSLCNVKCDTKEVFGRHLS---GKKHIAKLKRFE 442 (527)
Q Consensus 408 ~~l~CEICNV~CnS~~v~~~Hl~---GKKH~~kLKk~~ 442 (527)
.+|+|++|++.|+-+-.|++|+. |-.|..--|+..
T Consensus 172 rpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr 209 (267)
T KOG3576|consen 172 RPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERR 209 (267)
T ss_pred cccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhh
Confidence 34999999999999999999974 455555555443
No 91
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=35.82 E-value=12 Score=44.39 Aligned_cols=26 Identities=31% Similarity=0.548 Sum_probs=23.5
Q ss_pred CceecccccccccCHHHHHHhhchhH
Q 009730 408 IPLICSLCNVKCDTKEVFGRHLSGKK 433 (527)
Q Consensus 408 ~~l~CEICNV~CnS~~v~~~Hl~GKK 433 (527)
.+|+|+||.--|.++.+|..|+.+-|
T Consensus 632 RPFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 632 RPFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred Cccccccccchhccccchhhcccccc
Confidence 56999999999999999999998754
No 92
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=34.86 E-value=25 Score=23.94 Aligned_cols=20 Identities=20% Similarity=0.567 Sum_probs=16.5
Q ss_pred eecccccccccCHHHHHHhhc
Q 009730 410 LICSLCNVKCDTKEVFGRHLS 430 (527)
Q Consensus 410 l~CEICNV~CnS~~v~~~Hl~ 430 (527)
..|.+|+-.| ..+.+..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4699999999 6778888864
No 93
>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=34.23 E-value=41 Score=27.61 Aligned_cols=29 Identities=21% Similarity=0.339 Sum_probs=19.8
Q ss_pred CCCCCcCceeccccccccCCHHHHHHhhc
Q 009730 240 PSQQPLKSAWCELCRVDCTSLQILEQHRN 268 (527)
Q Consensus 240 p~~kp~k~~~CeVCqV~cnSe~vy~sHl~ 268 (527)
-..+..+...|.+|...|.....|.-|+.
T Consensus 17 ~~~~S~~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 17 SKSQSEQPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp CCCTTS--EE-TTT--EESSHHHHHHHHH
T ss_pred HhhccCCCCCCCcchhhccchhhHHHHHH
Confidence 34467788999999999999999988874
No 94
>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=31.26 E-value=39 Score=34.04 Aligned_cols=33 Identities=24% Similarity=0.457 Sum_probs=26.6
Q ss_pred ceecccccccccCHHHHHHhhchhHHHHHHHhcc
Q 009730 409 PLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFE 442 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~ 442 (527)
.|.|.+|.+.|....=-.+|+. +||..+|+.+.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~ 109 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVK 109 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHH
T ss_pred EECCCCCCcccCChHHHHHHHh-hcCHHHHHHHH
Confidence 4999999999999999999996 78999987764
No 95
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=30.99 E-value=27 Score=36.45 Aligned_cols=29 Identities=28% Similarity=0.405 Sum_probs=24.3
Q ss_pred CCccCceecccccccccCHHHHHHhhchh
Q 009730 404 PKVVIPLICSLCNVKCDTKEVFGRHLSGK 432 (527)
Q Consensus 404 pk~~~~l~CEICNV~CnS~~v~~~Hl~GK 432 (527)
.|++..-||=.||..|..+..|-.|.+-|
T Consensus 5 kkk~~kpwcwycnrefddekiliqhqkak 33 (341)
T KOG2893|consen 5 KKKVDKPWCWYCNREFDDEKILIQHQKAK 33 (341)
T ss_pred ccccCCceeeecccccchhhhhhhhhhhc
Confidence 35566689999999999999999998754
No 96
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=30.57 E-value=58 Score=33.89 Aligned_cols=24 Identities=29% Similarity=0.335 Sum_probs=10.0
Q ss_pred HHHHhhhhhhh-hhhccCCCCCCCC
Q 009730 113 QLAQFAGTMQA-AEGAMGGMHTPGG 136 (527)
Q Consensus 113 ~~~~~~~~~~~-~~~~~~~~~~~~g 136 (527)
-++.|.+-+-+ --+.|=|..-..|
T Consensus 196 ~~~~~~~~~~~~~~~~~~g~~~~~~ 220 (271)
T COG1512 196 VFILFGGATRAIISGPMFGRSLYLG 220 (271)
T ss_pred HHHHHHHHHHhhccccccceeeecc
Confidence 34444444443 2234434444444
No 97
>COG4371 Predicted membrane protein [Function unknown]
Probab=30.54 E-value=63 Score=34.07 Aligned_cols=8 Identities=38% Similarity=0.704 Sum_probs=4.3
Q ss_pred ccccchhh
Q 009730 484 LTKLWPHQ 491 (527)
Q Consensus 484 ~~~~~~~~ 491 (527)
+|-+|+-|
T Consensus 306 ~EVlWtPq 313 (334)
T COG4371 306 AEVLWTPQ 313 (334)
T ss_pred eEEeecCc
Confidence 45555555
No 98
>PF12764 Gly-rich_Ago1: Glycine-rich region of argonaut; InterPro: IPR024357 This domain is found in the N terminus of some argonaut proteins. Argonaut (AGO) proteins are involved in RNA-mediated post-transcriptional gene silencing [].
Probab=29.93 E-value=49 Score=30.30 Aligned_cols=16 Identities=38% Similarity=0.673 Sum_probs=6.3
Q ss_pred CCCCCCCCCCCccCCCCC
Q 009730 140 NKGGCRQGGRPFQGAGHK 157 (527)
Q Consensus 140 ~~gg~~~gg~~~rgggrg 157 (527)
|-|.| |||.+-+ |||+
T Consensus 6 YqgrG-RGgp~~q-gG~~ 21 (104)
T PF12764_consen 6 YQGRG-RGGPPQQ-GGRP 21 (104)
T ss_pred ccccC-CCCCccc-CCCC
Confidence 34443 3333334 4444
No 99
>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=29.70 E-value=32 Score=23.27 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=10.2
Q ss_pred ceeccccccccc
Q 009730 409 PLICSLCNVKCD 420 (527)
Q Consensus 409 ~l~CEICNV~Cn 420 (527)
+|.|++|+..|.
T Consensus 14 ~~~C~~C~k~F~ 25 (26)
T PF13465_consen 14 PYKCPYCGKSFS 25 (26)
T ss_dssp SEEESSSSEEES
T ss_pred CCCCCCCcCeeC
Confidence 499999998875
No 100
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=29.17 E-value=18 Score=35.99 Aligned_cols=39 Identities=21% Similarity=0.195 Sum_probs=0.0
Q ss_pred CcCceecccccc-ccCCHHHHHHhhcchHHHHHHHHHHHH
Q 009730 244 PLKSAWCELCRV-DCTSLQILEQHRNGKRHRKNLLRIEEL 282 (527)
Q Consensus 244 p~k~~~CeVCqV-~cnSe~vy~sHl~GKKHkKnLkaL~~~ 282 (527)
....+.|+||.= ++.++.+|+.|....||..-|+.|--.
T Consensus 98 L~~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI~ 137 (196)
T PF11931_consen 98 LGVEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGIP 137 (196)
T ss_dssp ----------------------------------------
T ss_pred CCCeeeeEeCCCcceecHHHHHHhcChhHHHccChhcCCC
Confidence 557888999975 777999999999999999999998764
No 101
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=29.02 E-value=13 Score=37.46 Aligned_cols=34 Identities=15% Similarity=0.458 Sum_probs=26.2
Q ss_pred ceecccccccccCHHHHHHhhchhHHHHHHHhccC
Q 009730 409 PLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFEG 443 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~g 443 (527)
.|+||||++.+.-- .--.|+++--|+.+++....
T Consensus 84 lfyCE~Cd~~ip~~-~~snH~tSttHllsl~~~pa 117 (223)
T KOG2384|consen 84 LFYCEVCDIYIPNS-KKSNHFTSTTHLLSLQHIPA 117 (223)
T ss_pred cchhhhhhhhccCC-CCccchhhHHHHhhhccCCC
Confidence 49999999877641 23469999999999987763
No 102
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=28.43 E-value=82 Score=33.37 Aligned_cols=9 Identities=22% Similarity=0.191 Sum_probs=4.0
Q ss_pred hhHHHHhhh
Q 009730 111 LSQLAQFAG 119 (527)
Q Consensus 111 ~~~~~~~~~ 119 (527)
|..||.-.|
T Consensus 210 L~~~F~~fG 218 (346)
T TIGR01659 210 LDTIFGKYG 218 (346)
T ss_pred HHHHHHhcC
Confidence 444554434
No 103
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=28.22 E-value=73 Score=31.63 Aligned_cols=7 Identities=29% Similarity=0.472 Sum_probs=2.9
Q ss_pred CCCCchh
Q 009730 213 PSPNATE 219 (527)
Q Consensus 213 p~~~~pe 219 (527)
|..++|.
T Consensus 32 P~~lfP~ 38 (233)
T PF11705_consen 32 PPPLFPP 38 (233)
T ss_pred CCCCCCC
Confidence 3344444
No 104
>PF12907 zf-met2: Zinc-binding
Probab=27.29 E-value=30 Score=26.60 Aligned_cols=26 Identities=35% Similarity=0.702 Sum_probs=20.8
Q ss_pred eeccccc---cccCCHHHHHHhhcchHHHH
Q 009730 248 AWCELCR---VDCTSLQILEQHRNGKRHRK 274 (527)
Q Consensus 248 ~~CeVCq---V~cnSe~vy~sHl~GKKHkK 274 (527)
+-|.||. +..+++.+|..|...| |-|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enK-HpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENK-HPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHcc-CCC
Confidence 5699999 7778999999998764 443
No 105
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=27.08 E-value=29 Score=38.25 Aligned_cols=31 Identities=35% Similarity=0.569 Sum_probs=25.9
Q ss_pred CcCceeccccccccCCHHHHHHhhcchHHHHHHH
Q 009730 244 PLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLL 277 (527)
Q Consensus 244 p~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLk 277 (527)
..+..|||-|.+.|- .|++|+.|+||.+-.+
T Consensus 419 etk~GYCENCreky~---~lE~Hi~s~~HrrFAE 449 (468)
T COG5067 419 ETKKGYCENCREKYE---SLEQHIVSEKHRRFAE 449 (468)
T ss_pred ccccchhHHHHHHHH---HHHHHhhhhhhhhhhh
Confidence 345589999999985 5899999999998754
No 106
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=27.02 E-value=35 Score=34.97 Aligned_cols=30 Identities=30% Similarity=0.692 Sum_probs=23.8
Q ss_pred eeccccc---ccccCHHHHHHhhchhHHHHHHH
Q 009730 410 LICSLCN---VKCDTKEVFGRHLSGKKHIAKLK 439 (527)
Q Consensus 410 l~CEICN---V~CnS~~v~~~Hl~GKKH~~kLK 439 (527)
-.|+||. +-..+..-++.||+||=|+--++
T Consensus 186 qvC~iCgayLsrlDtdrrladHf~GklHlGy~~ 218 (258)
T COG5200 186 QVCGICGAYLSRLDTDRRLADHFNGKLHLGYLL 218 (258)
T ss_pred hhhhhhhhHHHhcchhhHHHHHhccchhhhHHH
Confidence 3699996 44677888999999999975543
No 107
>PF04094 DUF390: Protein of unknown function (DUF390); InterPro: IPR007228 This domain is found in a family of long proteins that are currently found only in rice. They have no known function. However they may be some kind of transposable element. There is a putative gypsy type transposon domain (IPR007321 from INTERPRO) towards the N terminus of the proteins.
Probab=26.05 E-value=1.5e+02 Score=35.13 Aligned_cols=8 Identities=38% Similarity=0.737 Sum_probs=3.5
Q ss_pred CCCCCCCC
Q 009730 72 TLNPPGVS 79 (527)
Q Consensus 72 ~~~ppgv~ 79 (527)
+|-|-||-
T Consensus 32 sLIP~GiL 39 (828)
T PF04094_consen 32 SLIPQGIL 39 (828)
T ss_pred hccccccc
Confidence 34444443
No 108
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=25.07 E-value=36 Score=31.37 Aligned_cols=13 Identities=69% Similarity=1.158 Sum_probs=7.5
Q ss_pred CcCcCCCCcCCCC
Q 009730 172 SFHGRGRGRGRGG 184 (527)
Q Consensus 172 ~~rgrgrg~g~g~ 184 (527)
.|||||||+|+|+
T Consensus 94 ~~rgrgrg~Grg~ 106 (109)
T KOG3428|consen 94 VGRGRGRGRGRGR 106 (109)
T ss_pred cccccccccccCC
Confidence 4566666655553
No 109
>PTZ00448 hypothetical protein; Provisional
Probab=24.38 E-value=60 Score=35.39 Aligned_cols=34 Identities=21% Similarity=0.312 Sum_probs=30.8
Q ss_pred ceeccccccccCCHHHHHHhhcchHHHHHHHHHH
Q 009730 247 SAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIE 280 (527)
Q Consensus 247 ~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~ 280 (527)
.+.|..|++.|.+......|++.-=|.=||++..
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl 347 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNA 347 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHHh
Confidence 4669999999999999999999999999998743
No 110
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=24.30 E-value=54 Score=37.26 Aligned_cols=58 Identities=14% Similarity=0.185 Sum_probs=44.9
Q ss_pred CceecccccccccCHHHHHHhhchhHHHHHHHhccCCccccCCCcccccCCCCCcccc
Q 009730 408 IPLICSLCNVKCDTKEVFGRHLSGKKHIAKLKRFEGHQAMYGPEGVQALYPPNPVVHT 465 (527)
Q Consensus 408 ~~l~CEICNV~CnS~~v~~~Hl~GKKH~~kLKk~~g~~~~~G~~gl~a~~p~n~~~~~ 465 (527)
..+.|..|++.|-+......|+..-=|..|+|+.--.+.++-..-.-+++..+++.++
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krkl~~~~ils~edFe~i~s~d~ssiS 122 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRKLRGKPILSEEDFEGIISSDLSSIS 122 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhhccccccc
Confidence 3478999999999999999999999999999988766666665444455544444444
No 111
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=24.12 E-value=31 Score=26.02 Aligned_cols=13 Identities=23% Similarity=0.332 Sum_probs=7.9
Q ss_pred ccCceecccc-ccc
Q 009730 406 VVIPLICSLC-NVK 418 (527)
Q Consensus 406 ~~~~l~CEIC-NV~ 418 (527)
....|+|++| |++
T Consensus 3 ~~~~YkC~~CGniV 16 (36)
T PF06397_consen 3 KGEFYKCEHCGNIV 16 (36)
T ss_dssp TTEEEE-TTT--EE
T ss_pred cccEEEccCCCCEE
Confidence 3456999999 654
No 112
>PF05477 SURF2: Surfeit locus protein 2 (SURF2); InterPro: IPR008833 Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown [].
Probab=24.08 E-value=1e+02 Score=31.75 Aligned_cols=41 Identities=34% Similarity=0.484 Sum_probs=31.6
Q ss_pred CcCceeccccccccC-CHHHHHHhhcchHHHHHHHHHHHHhh
Q 009730 244 PLKSAWCELCRVDCT-SLQILEQHRNGKRHRKNLLRIEELRK 284 (527)
Q Consensus 244 p~k~~~CeVCqV~cn-Se~vy~sHl~GKKHkKnLkaL~~~~K 284 (527)
.+..+||.|=....| .+....-|++|||.+++|++.++..+
T Consensus 76 ~~~~LfCkLT~~~iNk~pe~V~rHv~GKRf~kaLek~ee~~~ 117 (244)
T PF05477_consen 76 NPHKLFCKLTGRHINKSPEHVERHVNGKRFQKALEKYEECQK 117 (244)
T ss_pred CCceeEEechHhHhccCHHHHHHHhhhHHHHHHHHHHHHHHh
Confidence 344667776655555 78888899999999999999887543
No 113
>PHA00616 hypothetical protein
Probab=22.52 E-value=47 Score=26.05 Aligned_cols=20 Identities=15% Similarity=0.092 Sum_probs=18.4
Q ss_pred eeccccccccCCHHHHHHhh
Q 009730 248 AWCELCRVDCTSLQILEQHR 267 (527)
Q Consensus 248 ~~CeVCqV~cnSe~vy~sHl 267 (527)
.-|..|...|.....|..|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CccchhhHHHhhHHHHHHHH
Confidence 35999999999999999998
No 114
>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=22.38 E-value=93 Score=31.40 Aligned_cols=37 Identities=14% Similarity=0.285 Sum_probs=27.6
Q ss_pred CcCceeccccccccCCHHHHHHhhcchHHHHHHHHHHH
Q 009730 244 PLKSAWCELCRVDCTSLQILEQHRNGKRHRKNLLRIEE 281 (527)
Q Consensus 244 p~k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLkaL~~ 281 (527)
....|.|.+|.+.|..+.=-.-|+. +||...|+.+.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ 110 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKK 110 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHH
Confidence 3346889999999999999989987 678888887653
No 115
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=21.87 E-value=73 Score=32.56 Aligned_cols=41 Identities=20% Similarity=0.420 Sum_probs=33.0
Q ss_pred CCCCccCceecccccccccCHHHHH--HhhchhHHHHHHHhcc
Q 009730 402 PKPKVVIPLICSLCNVKCDTKEVFG--RHLSGKKHIAKLKRFE 442 (527)
Q Consensus 402 ~~pk~~~~l~CEICNV~CnS~~v~~--~Hl~GKKH~~kLKk~~ 442 (527)
..+....+|.|.||+..|-|..+-. .||.+.=-+.++++-.
T Consensus 189 ~~~~e~IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~ 231 (259)
T COG5152 189 SGPGEKIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGD 231 (259)
T ss_pred cCCCCCCceeehhchhhccchhhhhcchhHHHHHHHHHhccCC
Confidence 3456778999999999999999877 6888887777776543
No 116
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=20.70 E-value=80 Score=35.99 Aligned_cols=33 Identities=30% Similarity=0.414 Sum_probs=30.8
Q ss_pred CceeccccccccCCHHHHHHhhcchHHHHHHHH
Q 009730 246 KSAWCELCRVDCTSLQILEQHRNGKRHRKNLLR 278 (527)
Q Consensus 246 k~~~CeVCqV~cnSe~vy~sHl~GKKHkKnLka 278 (527)
..+.|..|++.|-+......|+..-=|.=|+++
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Kr 97 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKR 97 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHH
Confidence 678899999999999999999999999999876
No 117
>PHA00733 hypothetical protein
Probab=20.14 E-value=69 Score=29.43 Aligned_cols=22 Identities=23% Similarity=0.689 Sum_probs=18.1
Q ss_pred ceecccccccccCHHHHHHhhc
Q 009730 409 PLICSLCNVKCDTKEVFGRHLS 430 (527)
Q Consensus 409 ~l~CEICNV~CnS~~v~~~Hl~ 430 (527)
+|.|++|...|.+...|..|..
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHh
Confidence 4888888888888888888765
Done!