Query psy6242
Match_columns 541
No_of_seqs 431 out of 1904
Neff 7.8
Searched_HMMs 46136
Date Fri Aug 16 21:23:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6242.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6242hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2084|consensus 99.9 1.7E-23 3.7E-28 226.6 22.2 390 41-461 2-424 (482)
2 PF01753 zf-MYND: MYND finger; 99.0 4.6E-11 1E-15 82.2 0.1 37 15-51 1-37 (37)
3 PF00856 SET: SET domain; Int 98.8 5.7E-09 1.2E-13 95.0 4.5 44 245-288 110-162 (162)
4 KOG1710|consensus 98.3 6.9E-08 1.5E-12 93.8 -1.9 41 12-52 319-360 (396)
5 smart00317 SET SET (Su(var)3-9 98.2 1.1E-06 2.4E-11 75.7 3.0 40 248-287 68-116 (116)
6 PF01753 zf-MYND: MYND finger; 97.7 3.1E-06 6.7E-11 58.1 -1.8 36 99-141 1-37 (37)
7 KOG2589|consensus 96.9 0.00066 1.4E-08 68.6 3.6 60 249-318 191-257 (453)
8 PF13824 zf-Mss51: Zinc-finger 96.2 0.0015 3.3E-08 48.3 0.3 39 14-52 1-43 (55)
9 KOG2061|consensus 96.0 0.0052 1.1E-07 62.7 3.3 42 11-52 135-177 (362)
10 COG2940 Proteins containing SE 95.8 0.0056 1.2E-07 66.8 3.0 66 252-317 404-478 (480)
11 KOG4442|consensus 95.5 0.01 2.2E-07 65.0 3.4 41 254-294 194-243 (729)
12 KOG1080|consensus 95.5 0.0095 2.1E-07 69.1 3.4 38 253-290 939-985 (1005)
13 KOG3612|consensus 95.4 0.0029 6.2E-08 67.2 -1.3 39 12-52 527-565 (588)
14 PF13824 zf-Mss51: Zinc-finger 93.3 0.044 9.5E-07 40.7 1.4 47 99-148 2-49 (55)
15 KOG1710|consensus 93.2 0.02 4.3E-07 56.6 -0.6 42 97-144 320-362 (396)
16 KOG1337|consensus 90.1 0.35 7.5E-06 52.8 4.6 79 224-308 197-291 (472)
17 KOG1141|consensus 90.1 0.21 4.5E-06 55.8 2.8 51 254-312 1190-1253(1262)
18 KOG1082|consensus 89.5 0.16 3.5E-06 53.4 1.3 37 256-292 275-324 (364)
19 PF04438 zf-HIT: HIT zinc fing 89.3 0.13 2.8E-06 33.4 0.3 27 97-129 3-29 (30)
20 PLN03158 methionine aminopepti 88.1 0.19 4.1E-06 53.3 0.8 42 9-50 6-54 (396)
21 PF00856 SET: SET domain; Int 86.6 0.19 4.2E-06 44.9 -0.2 28 65-92 1-28 (162)
22 PF04438 zf-HIT: HIT zinc fing 86.6 0.21 4.5E-06 32.4 0.0 29 12-41 2-30 (30)
23 KOG2857|consensus 83.5 0.44 9.6E-06 42.1 0.6 37 97-143 6-44 (157)
24 KOG4317|consensus 73.3 1.5 3.2E-05 44.0 0.9 36 97-142 8-43 (383)
25 PF09889 DUF2116: Uncharacteri 72.4 2 4.3E-05 32.6 1.2 24 96-130 3-26 (59)
26 smart00317 SET SET (Su(var)3-9 69.9 2 4.3E-05 36.2 0.8 34 57-90 3-36 (116)
27 PF14949 ARF7EP_C: ARF7 effect 67.7 2.5 5.4E-05 35.8 1.0 32 97-138 68-99 (103)
28 PRK11032 hypothetical protein; 65.2 20 0.00044 33.0 6.4 65 406-477 76-149 (160)
29 KOG1083|consensus 64.7 4.9 0.00011 46.7 2.8 33 256-288 1253-1294(1306)
30 KOG3362|consensus 59.8 4 8.7E-05 36.4 0.8 32 93-130 115-146 (156)
31 KOG1338|consensus 52.6 35 0.00075 35.9 6.2 69 222-290 172-261 (466)
32 KOG3612|consensus 52.2 3.2 7E-05 44.8 -1.2 41 97-147 528-570 (588)
33 PF12855 Ecl1: Life-span regul 51.9 6.6 0.00014 27.8 0.7 34 10-46 4-37 (43)
34 KOG1085|consensus 51.8 10 0.00022 37.9 2.2 39 254-292 334-381 (392)
35 PF07295 DUF1451: Protein of u 48.2 77 0.0017 28.8 7.2 54 407-465 65-124 (146)
36 PF09986 DUF2225: Uncharacteri 48.2 25 0.00053 34.1 4.3 76 350-425 46-133 (214)
37 PF04810 zf-Sec23_Sec24: Sec23 46.5 6.7 0.00014 27.2 0.0 30 327-361 3-33 (40)
38 PLN03158 methionine aminopepti 46.4 6.1 0.00013 42.0 -0.3 36 97-139 10-53 (396)
39 PF07754 DUF1610: Domain of un 46.4 13 0.00029 22.8 1.3 21 458-478 3-24 (24)
40 PF10571 UPF0547: Uncharacteri 44.6 16 0.00034 22.9 1.5 22 98-122 2-23 (26)
41 KOG0856|consensus 39.8 17 0.00036 32.4 1.5 27 454-482 55-81 (146)
42 COG4068 Uncharacterized protei 38.7 14 0.00031 27.7 0.7 24 96-130 8-31 (64)
43 PF04181 RPAP2_Rtr1: Rtr1/RPAP 38.7 16 0.00034 29.4 1.0 13 472-484 19-31 (79)
44 KOG4442|consensus 38.4 17 0.00036 40.8 1.5 45 35-83 105-149 (729)
45 PF03884 DUF329: Domain of unk 37.1 15 0.00032 27.7 0.6 9 122-130 22-30 (57)
46 KOG1079|consensus 36.9 31 0.00068 38.5 3.3 38 253-290 665-711 (739)
47 PF08189 Meleagrin: Meleagrin/ 36.7 13 0.00027 25.1 0.2 19 119-137 6-25 (39)
48 COG3024 Uncharacterized protei 35.7 17 0.00038 27.8 0.8 9 122-130 27-35 (65)
49 KOG2807|consensus 35.3 35 0.00077 34.8 3.1 86 22-130 275-361 (378)
50 PF07975 C1_4: TFIIH C1-like d 35.0 12 0.00027 27.4 -0.0 32 98-130 1-37 (51)
51 PLN03144 Carbon catabolite rep 34.6 16 0.00035 40.9 0.7 37 14-50 61-108 (606)
52 KOG2857|consensus 33.8 20 0.00044 31.9 1.1 29 453-486 5-33 (157)
53 PRK00418 DNA gyrase inhibitor; 33.1 24 0.00052 27.1 1.2 9 122-130 26-34 (62)
54 PF10083 DUF2321: Uncharacteri 32.2 1.2E+02 0.0025 27.8 5.6 30 350-381 66-95 (158)
55 PF03604 DNA_RNApol_7kD: DNA d 31.5 33 0.00072 22.6 1.5 24 455-478 2-25 (32)
56 KOG2738|consensus 31.1 20 0.00044 36.1 0.7 41 11-51 5-52 (369)
57 PF08271 TF_Zn_Ribbon: TFIIB z 30.8 33 0.00071 24.0 1.5 13 351-363 18-30 (43)
58 PRK01343 zinc-binding protein; 29.9 41 0.00089 25.3 2.0 31 10-45 7-37 (57)
59 PF14803 Nudix_N_2: Nudix N-te 28.2 30 0.00064 23.2 0.9 28 329-361 3-31 (34)
60 PF13719 zinc_ribbon_5: zinc-r 27.6 27 0.00058 23.7 0.6 32 327-363 3-36 (37)
61 COG1998 RPS31 Ribosomal protei 27.1 32 0.00069 25.0 0.9 26 327-361 20-46 (51)
62 PF02150 RNA_POL_M_15KD: RNA p 26.7 17 0.00037 24.4 -0.5 29 329-364 4-32 (35)
63 PF09538 FYDLN_acid: Protein o 26.4 52 0.0011 28.3 2.3 26 97-122 10-35 (108)
64 PF14949 ARF7EP_C: ARF7 effect 26.4 35 0.00077 29.0 1.3 7 472-478 69-75 (103)
65 KOG1081|consensus 26.4 20 0.00044 38.9 -0.2 43 249-291 366-418 (463)
66 PF13248 zf-ribbon_3: zinc-rib 26.1 43 0.00094 20.7 1.3 24 454-480 3-26 (26)
67 PF13717 zinc_ribbon_4: zinc-r 24.7 38 0.00082 22.8 0.9 31 327-362 3-35 (36)
68 COG1996 RPC10 DNA-directed RNA 24.7 41 0.00089 24.5 1.1 27 310-341 8-34 (49)
69 PF14446 Prok-RING_1: Prokaryo 23.8 48 0.001 24.7 1.4 32 96-129 5-36 (54)
70 COG2888 Predicted Zn-ribbon RN 23.7 61 0.0013 24.6 1.9 47 310-361 11-59 (61)
71 KOG1085|consensus 23.6 35 0.00076 34.2 0.8 35 48-84 252-286 (392)
72 PRK00398 rpoP DNA-directed RNA 23.5 52 0.0011 23.3 1.5 11 352-362 21-31 (46)
73 TIGR02098 MJ0042_CXXC MJ0042 f 23.5 35 0.00075 23.0 0.6 32 327-363 3-36 (38)
74 PF13240 zinc_ribbon_2: zinc-r 23.1 50 0.0011 19.9 1.1 21 98-121 1-21 (23)
75 PF07282 OrfB_Zn_ribbon: Putat 23.1 78 0.0017 24.3 2.6 40 321-368 23-62 (69)
76 smart00154 ZnF_AN1 AN1-like Zi 22.3 56 0.0012 22.5 1.4 24 99-125 1-24 (39)
77 PF04423 Rad50_zn_hook: Rad50 22.1 1.1E+02 0.0024 22.3 3.2 28 354-381 22-49 (54)
78 KOG4850|consensus 22.0 32 0.00069 31.3 0.2 19 113-131 149-167 (190)
79 KOG4215|consensus 21.5 29 0.00062 36.0 -0.2 37 10-52 17-59 (432)
80 PF09862 DUF2089: Protein of u 20.9 1E+02 0.0023 26.6 3.1 11 384-394 48-58 (113)
81 PF13453 zf-TFIIB: Transcripti 20.9 54 0.0012 22.6 1.1 9 310-318 1-9 (41)
82 KOG3507|consensus 20.4 44 0.00096 25.2 0.6 26 453-478 20-45 (62)
83 PF08772 NOB1_Zn_bind: Nin one 20.1 46 0.001 26.4 0.7 23 97-121 10-32 (73)
84 PF12760 Zn_Tnp_IS1595: Transp 20.0 66 0.0014 22.8 1.5 31 323-361 15-46 (46)
No 1
>KOG2084|consensus
Probab=99.91 E-value=1.7e-23 Score=226.63 Aligned_cols=390 Identities=22% Similarity=0.308 Sum_probs=240.8
Q ss_pred hhcccccccCCCCCCcc-ccCCcccchhhccccCCCCCccccccCCeeeccccCCCCcccccccCCCCCCCCCCcCCCCC
Q psy6242 41 KEHWKLHKPKCKKLPYE-IKSSPLLGRYLQATLDLHPGDRIARESPLIVGPKLALAEPICLGCHKPLNPNLADNARCPRC 119 (541)
Q Consensus 41 ~~~w~~Hk~~C~~~~~~-i~~s~~~GR~l~A~~~i~~Ge~I~~e~plv~~p~~~~~~~~C~~C~~~~~~~~~~~~~C~~C 119 (541)
..+|..++.... .+. +...+..||+++|+++|+.|++|+.|.|++.+|... .|..|+... ...|.+|
T Consensus 2 ~~~~~~~~~~~~--~~~~~~~~~~~Gr~~~a~~~i~~g~~i~~e~p~~~~p~~~----~~~~c~~~~------~~~C~~~ 69 (482)
T KOG2084|consen 2 TKDLKSDPRNGL--NVEEVANSPELGRGLVATQAIEAGEVILEEEPLVVGPASK----SCSRCLGCS------CDHCRRC 69 (482)
T ss_pred cchhccCccccC--CcccccCccccCcceeeecccCCCceEEecCcceeeeccc----CCccccccc------hhhhhcC
Confidence 456666444332 222 223358899999999999999999999999999983 344444321 3467777
Q ss_pred Ccc-ccChhhhccccCCCCHhhhhhhhhcchhhhccCccchhcHHHHHHHHHhcC---ChhhH--HHHHHhhhhhccCCC
Q psy6242 120 FWP-ACSARCSGLSDAHTHAPECAILKLGCETLLAYNDYKYEAILPLRCLILQRR---SPKKY--QELKDMEAHMSKRGP 193 (541)
Q Consensus 120 ~~~-yCS~~C~~~~~~~~H~~EC~~l~~~~~~~~~~~~~~~~~~l~lR~l~~~~~---~~~~~--~~v~~L~sh~~~~~~ 193 (541)
..+ +|+. |.+..++.-+..+|.. ........ ........-++...... .++.+ ..+..+....+.. +
T Consensus 70 ~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 142 (482)
T KOG2084|consen 70 LEAIECNK-CQQRGWALCGKFACSA-DLAKLECE----PLKLVGAPEECLALSSLHEESREAIVLLSLLEECSLSAEK-P 142 (482)
T ss_pred CccHhhhh-hhccCccccchhhcch-hhcccccc----chhhccchHHHHHhhcCCccccchHHHHHHHHHhhhhccc-c
Confidence 766 7764 4443556666666655 22211100 00000111111111111 11111 1111111111111 1
Q ss_pred CchhHHHHHHHHHHHHHHHhhhCCCCCCCcCCHHHHHHHHhhhhcccccc-----C----CceeEEecccccccCCCCCC
Q psy6242 194 GTEVYEEIDSIVKYLRSNFLEKLPGDVLDDTSAKCLHWICGVIEVNGVDI-----G----RYTQGLYSVICLMEHNCLPN 264 (541)
Q Consensus 194 ~~~~~~~~~~i~~~L~~~~~~~l~~~~l~~~~~~~i~~i~~~l~~Naf~i-----~----~~g~glYp~~Sl~NHSC~PN 264 (541)
....+.... -....... ... .........+..+...+..|++.+ . ..+.|+||..+++||||.||
T Consensus 143 ~~~~~~~~~--~~~~~~~~--~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~hsC~pn 216 (482)
T KOG2084|consen 143 RLRLDLSYL--EHGATEDD--QSH--LLLVLAADCISKLFPSLLCNSITNASSLRVPEPLFLGRGLFPGSSLFNHSCFPN 216 (482)
T ss_pred cHhHHHhhH--HHHhhHHh--hcc--ccchhHHHHHHHHHHHHHHhhhhhhhhhhccccccceeeecccchhcccCCCCC
Confidence 100000000 00000000 000 000012223333344444444444 2 48999999999999999999
Q ss_pred ceeeeeCCeEEEE-e----cC-CeeeeeccCCCCChHHHHHHHhcCCCeEEeccCCCCCCccccccccccccccCCCCCc
Q psy6242 265 AKHSNMMQSKLFV-F----RD-THISTMYTNALWGTQPRREHLAITKYFNCSCERCSDPTELGTYFSAMKCLNEHKDQGD 338 (541)
Q Consensus 265 ~~~~f~~~~~i~v-r----~G-eEItisY~d~~~~~~~Rr~~L~~~y~F~C~C~rC~~~~e~~~~l~~~~C~~~~~~~C~ 338 (541)
+...|++...+.+ . ++ +||+++|++.++++..||.+|+..|+|.|.|+||.|+++.++++++++|... +|.
T Consensus 217 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~y~~~~~~~~~r~~~l~~~~~f~c~c~rc~d~~~~~~~~~~~~c~~~---~~~ 293 (482)
T KOG2084|consen 217 ISVIFDGRGLALLVPAGIDAGEEELTISYTDPLLSTASRQKQLRQSKLFSCQCPRCLDPTELGTFLSSLRCENC---TCG 293 (482)
T ss_pred eEEEECCceeEEEeecccCCCCCEEEEeecccccCHHHHHHHHhhccceeeecCCCCCCCccccchhhhhhcCC---CCC
Confidence 9999988643322 2 44 4999999999999999999999999999999999999999999999999884 366
Q ss_pred eeeecCCCCCCCCCcccCcCcCccCHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhcccCCCChhHHHHHHHHHH
Q psy6242 339 CWILPVNPLDNDSDWTCGSCSARLNARDVHLVTSQLGEQVDKLVQENPNVKSLEEMLTKLEAMFHPHHYHCYAVKHSLIQ 418 (541)
Q Consensus 339 g~~lp~~~~~~~~~w~C~~C~~~~~~~~v~~~l~~~~~~~~~~~~~~~~~~~le~~l~~~~~~Lhp~h~~~~~~~~~L~~ 418 (541)
+.+.+..+..+...|.|..|........+....+....++.. ........+.+..+...+++++|+........+..
T Consensus 294 ~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~ 370 (482)
T KOG2084|consen 294 GLLGTSFLDKEDLQWPCTECALVRLKAYVVESREELQNELLD---AFSDLLIEELLLLRQESLELPNDFEVLLLKLHLLF 370 (482)
T ss_pred CccCCCcccccCCCccccccccchhHHHHHHHHHHHHhhccc---cCChhhhHHHHHHHHHhhhCcchHHHHHHHHHHHH
Confidence 655555443356799999999998888787776666544111 12344556677778889999999999999999999
Q ss_pred HHhcCCCCccccCCHHHHHhhcce-----------eeccccccCcccccccccc
Q psy6242 419 LYGTQPGYAYTQLSSSLLERKISY-----------VMSPNLKATDEPICLGCHK 461 (541)
Q Consensus 419 ly~~~~~~~~~~~~~~~l~rk~~~-----------~~~Pg~~~~~~~~c~ec~~ 461 (541)
+++...+..+...+...+.++..+ .+.||.....+...++...
T Consensus 371 il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 (482)
T KOG2084|consen 371 ILGSLLGAFLSCSPNAELERLLNLFECRELLKALRDVKPGEEPLIAYLDYELGK 424 (482)
T ss_pred HHHHHHhhhhccchhhHHHHHHHhhhhhHHHHHHHhhcchhhhhhHHHHHHHHH
Confidence 999876654566666666666655 7888877666666655544
No 2
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=99.02 E-value=4.6e-11 Score=82.21 Aligned_cols=37 Identities=49% Similarity=1.141 Sum_probs=34.0
Q ss_pred cccccCCcCCCCccCcccccCCchhhhhcccccccCC
Q psy6242 15 CAVCRETALHKCSACKEVAYCGKQHQKEHWKLHKPKC 51 (541)
Q Consensus 15 C~~C~~~~~~~Cs~C~~v~YCs~~hQ~~~w~~Hk~~C 51 (541)
|++|+++++.+|++|+.++|||++||+.||+.|+.+|
T Consensus 1 C~~C~~~~~~~C~~C~~~~YCs~~Cq~~~w~~Hk~~C 37 (37)
T PF01753_consen 1 CAVCGKPALKRCSRCKSVYYCSEECQRADWPYHKFEC 37 (37)
T ss_dssp -TTTSSCSSEEETTTSSSEESSHHHHHHHHHHHCCTH
T ss_pred CcCCCCCcCCcCCCCCCEEecCHHHHHHHHHHHhhhC
Confidence 7899999888999999999999999999998899876
No 3
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=98.77 E-value=5.7e-09 Score=94.96 Aligned_cols=44 Identities=27% Similarity=0.325 Sum_probs=38.6
Q ss_pred CceeEEecccccccCCCCCCceeeee---CCeEEEEe------cCCeeeeecc
Q psy6242 245 RYTQGLYSVICLMEHNCLPNAKHSNM---MQSKLFVF------RDTHISTMYT 288 (541)
Q Consensus 245 ~~g~glYp~~Sl~NHSC~PN~~~~f~---~~~~i~vr------~GeEItisY~ 288 (541)
..+.+|||.++|+||||.||+.+.|+ ++..++|| +||||||||+
T Consensus 110 ~~~~~l~p~~d~~NHsc~pn~~~~~~~~~~~~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 110 RDGIALYPFADMLNHSCDPNCEVSFDFDGDGGCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp EEEEEEETGGGGSEEESSTSEEEEEEEETTTTEEEEEESS-B-TTSBEEEEST
T ss_pred ccccccCcHhHheccccccccceeeEeecccceEEEEECCccCCCCEEEEEEC
Confidence 46899999999999999999999998 34566665 9999999996
No 4
>KOG1710|consensus
Probab=98.30 E-value=6.9e-08 Score=93.84 Aligned_cols=41 Identities=44% Similarity=0.950 Sum_probs=38.6
Q ss_pred ccccccccCC-cCCCCccCcccccCCchhhhhcccccccCCC
Q psy6242 12 LMRCAVCRET-ALHKCSACKEVAYCGKQHQKEHWKLHKPKCK 52 (541)
Q Consensus 12 ~~~C~~C~~~-~~~~Cs~C~~v~YCs~~hQ~~~w~~Hk~~C~ 52 (541)
-+.|..||.+ +.++||.||++.||+++||+.||..||+.|+
T Consensus 319 ~~fCstCG~~ga~KrCs~CKav~YCdqeCQk~hWf~HKK~C~ 360 (396)
T KOG1710|consen 319 CQFCSTCGHPGAKKRCSQCKAVAYCDQECQKFHWFIHKKVCS 360 (396)
T ss_pred cccccccCCCCccchhhhhHHHHHHHHHHHHhhhHHHHHHHH
Confidence 5689999998 7899999999999999999999999999997
No 5
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=98.17 E-value=1.1e-06 Score=75.73 Aligned_cols=40 Identities=18% Similarity=0.388 Sum_probs=32.8
Q ss_pred eEEecccccccCCCCCCceeeeeCC---eEEEEe------cCCeeeeec
Q psy6242 248 QGLYSVICLMEHNCLPNAKHSNMMQ---SKLFVF------RDTHISTMY 287 (541)
Q Consensus 248 ~glYp~~Sl~NHSC~PN~~~~f~~~---~~i~vr------~GeEItisY 287 (541)
..++|.++++||||.||+...+... ..+.++ +|||||++|
T Consensus 68 ~~~~~~~~~iNHsc~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 68 RRKGNIARFINHSCEPNCELLFVEVNGDSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred CccCcHHHeeCCCCCCCEEEEEEEECCCcEEEEEECCCcCCCCEEeecC
Confidence 4478999999999999999987543 135554 999999999
No 6
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=97.72 E-value=3.1e-06 Score=58.12 Aligned_cols=36 Identities=39% Similarity=0.725 Sum_probs=28.9
Q ss_pred cccccCCCCCCCCCCcCCCCCCcc-ccChhhhccccCCCCHhhh
Q psy6242 99 CLGCHKPLNPNLADNARCPRCFWP-ACSARCSGLSDAHTHAPEC 141 (541)
Q Consensus 99 C~~C~~~~~~~~~~~~~C~~C~~~-yCS~~C~~~~~~~~H~~EC 141 (541)
|.+|++.. +.+|++|+.+ |||++|++++| ..|+.+|
T Consensus 1 C~~C~~~~------~~~C~~C~~~~YCs~~Cq~~~w-~~Hk~~C 37 (37)
T PF01753_consen 1 CAVCGKPA------LKRCSRCKSVYYCSEECQRADW-PYHKFEC 37 (37)
T ss_dssp -TTTSSCS------SEEETTTSSSEESSHHHHHHHH-HHHCCTH
T ss_pred CcCCCCCc------CCcCCCCCCEEecCHHHHHHHH-HHHhhhC
Confidence 67788733 3599999998 99999999666 8898887
No 7
>KOG2589|consensus
Probab=96.94 E-value=0.00066 Score=68.56 Aligned_cols=60 Identities=22% Similarity=0.500 Sum_probs=47.3
Q ss_pred EEec-ccccccCCCCCCceeeeeCCeEEEEe------cCCeeeeeccCCCCChHHHHHHHhcCCCeEEeccCCCCCC
Q psy6242 249 GLYS-VICLMEHNCLPNAKHSNMMQSKLFVF------RDTHISTMYTNALWGTQPRREHLAITKYFNCSCERCSDPT 318 (541)
Q Consensus 249 glYp-~~Sl~NHSC~PN~~~~f~~~~~i~vr------~GeEItisY~d~~~~~~~Rr~~L~~~y~F~C~C~rC~~~~ 318 (541)
-|+. -++++||+|.|||.++-.|..++.|| +|||||.=|++.+.+.. .-+|.|.-|....
T Consensus 191 qLwLGPaafINHDCrpnCkFvs~g~~tacvkvlRDIePGeEITcFYgs~fFG~~----------N~~CeC~TCER~g 257 (453)
T KOG2589|consen 191 QLWLGPAAFINHDCRPNCKFVSTGRDTACVKVLRDIEPGEEITCFYGSGFFGEN----------NEECECVTCERRG 257 (453)
T ss_pred hheeccHHhhcCCCCCCceeecCCCceeeeehhhcCCCCceeEEeecccccCCC----------CceeEEeeccccc
Confidence 3443 36789999999999998875466554 99999999999887653 4689999998664
No 8
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=96.17 E-value=0.0015 Score=48.32 Aligned_cols=39 Identities=23% Similarity=0.737 Sum_probs=35.4
Q ss_pred ccccccC----CcCCCCccCcccccCCchhhhhcccccccCCC
Q psy6242 14 RCAVCRE----TALHKCSACKEVAYCGKQHQKEHWKLHKPKCK 52 (541)
Q Consensus 14 ~C~~C~~----~~~~~Cs~C~~v~YCs~~hQ~~~w~~Hk~~C~ 52 (541)
+|.+|+. .....|+.|....|||++|-..|.+.|++.|.
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~~D~e~H~~~c~ 43 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCSEEHWEDDYEEHRQLCE 43 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccCHHHHHHhHHHHHHHHH
Confidence 4888887 57788999999999999999999999999996
No 9
>KOG2061|consensus
Probab=95.98 E-value=0.0052 Score=62.74 Aligned_cols=42 Identities=40% Similarity=0.828 Sum_probs=39.6
Q ss_pred cccccccccCCcCCCCccCcccccCCchhhhhcccc-cccCCC
Q psy6242 11 ELMRCAVCRETALHKCSACKEVAYCGKQHQKEHWKL-HKPKCK 52 (541)
Q Consensus 11 ~~~~C~~C~~~~~~~Cs~C~~v~YCs~~hQ~~~w~~-Hk~~C~ 52 (541)
..+.|..|+..+...|++|+.++|||+.||..||+. |+..|.
T Consensus 135 ~~~~~~~~~~~a~~~~~~~~~a~~~S~~~q~~d~~~~~~~a~a 177 (362)
T KOG2061|consen 135 GADLCGSCGCSAPAACSPCKAAAYCSKKHQSLDWPKGHKDACA 177 (362)
T ss_pred ccchhccCcccCcccccccchhhhcCchhhccccccccccccc
Confidence 468999999999999999999999999999999999 999997
No 10
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=95.84 E-value=0.0056 Score=66.83 Aligned_cols=66 Identities=21% Similarity=0.356 Sum_probs=51.5
Q ss_pred cccccccCCCCCCceeeeeCC-e--EEEE---e---cCCeeeeeccCCCCChHHHHHHHhcCCCeEEeccCCCCC
Q psy6242 252 SVICLMEHNCLPNAKHSNMMQ-S--KLFV---F---RDTHISTMYTNALWGTQPRREHLAITKYFNCSCERCSDP 317 (541)
Q Consensus 252 p~~Sl~NHSC~PN~~~~f~~~-~--~i~v---r---~GeEItisY~d~~~~~~~Rr~~L~~~y~F~C~C~rC~~~ 317 (541)
..+.++||||.||+..+.... + .+.+ | +||||++.|...++....+...+...+...|.+.+|...
T Consensus 404 ~~~r~~nHS~~pN~~~~~~~~~g~~~~~~~~~rDI~~geEl~~dy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 478 (480)
T COG2940 404 DVARFINHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSHT 478 (480)
T ss_pred cccceeecCCCCCcceecccccccceeeecccccchhhhhhccccccccccchhhhhhhhhhhccccCCCccCCC
Confidence 346689999999999997654 2 3332 3 999999999998876555667777778999999999754
No 11
>KOG4442|consensus
Probab=95.52 E-value=0.01 Score=65.01 Aligned_cols=41 Identities=20% Similarity=0.284 Sum_probs=28.0
Q ss_pred cccccCCCCCCceeee---eCCeEE---EEe---cCCeeeeeccCCCCCh
Q psy6242 254 ICLMEHNCLPNAKHSN---MMQSKL---FVF---RDTHISTMYTNALWGT 294 (541)
Q Consensus 254 ~Sl~NHSC~PN~~~~f---~~~~~i---~vr---~GeEItisY~d~~~~~ 294 (541)
+=++||||+|||.+-- .+..+| ..| +|||||.-|--...+.
T Consensus 194 aRFiNHSC~PNa~~~KWtV~~~lRvGiFakk~I~~GEEITFDYqf~rYGr 243 (729)
T KOG4442|consen 194 ARFINHSCDPNAEVQKWTVPDELRVGIFAKKVIKPGEEITFDYQFDRYGR 243 (729)
T ss_pred HHhhcCCCCCCceeeeeeeCCeeEEEEeEecccCCCceeeEecccccccc
Confidence 3478999999998742 232222 223 9999999997665554
No 12
>KOG1080|consensus
Probab=95.51 E-value=0.0095 Score=69.10 Aligned_cols=38 Identities=13% Similarity=0.364 Sum_probs=30.0
Q ss_pred ccccccCCCCCCceeee---eCCeEEEEe------cCCeeeeeccCC
Q psy6242 253 VICLMEHNCLPNAKHSN---MMQSKLFVF------RDTHISTMYTNA 290 (541)
Q Consensus 253 ~~Sl~NHSC~PN~~~~f---~~~~~i~vr------~GeEItisY~d~ 290 (541)
.|.++||||.|||..-. +|..+|+|. +|||||..|--.
T Consensus 939 iAr~InHsC~PNCyakvi~V~g~~~IvIyakr~I~~~EElTYDYkF~ 985 (1005)
T KOG1080|consen 939 IARFINHSCNPNCYAKVITVEGDKRIVIYSKRDIAAGEELTYDYKFP 985 (1005)
T ss_pred hhheeecccCCCceeeEEEecCeeEEEEEEecccccCceeeeecccc
Confidence 46789999999998754 555677764 999999999543
No 13
>KOG3612|consensus
Probab=95.37 E-value=0.0029 Score=67.17 Aligned_cols=39 Identities=31% Similarity=0.858 Sum_probs=35.1
Q ss_pred ccccccccCCcCCCCccCcccccCCchhhhhcccccccCCC
Q psy6242 12 LMRCAVCRETALHKCSACKEVAYCGKQHQKEHWKLHKPKCK 52 (541)
Q Consensus 12 ~~~C~~C~~~~~~~Cs~C~~v~YCs~~hQ~~~w~~Hk~~C~ 52 (541)
..=|+.|...+..-| |-.++|||.+||+.||+.|+..|+
T Consensus 527 KQWC~nC~~EAiy~C--CWNTSYCsveCQQ~HW~~H~ksCr 565 (588)
T KOG3612|consen 527 KQWCYNCLDEAIYHC--CWNTSYCSVECQQGHWPEHRKSCR 565 (588)
T ss_pred HHHHHhhhHHHHHHh--hccccccCcchhhccchhHhhhhc
Confidence 445888888888888 999999999999999999999996
No 14
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=93.33 E-value=0.044 Score=40.67 Aligned_cols=47 Identities=32% Similarity=0.538 Sum_probs=33.5
Q ss_pred cccccCCCCCCCCCCcCCCCCCcc-ccChhhhccccCCCCHhhhhhhhhcc
Q psy6242 99 CLGCHKPLNPNLADNARCPRCFWP-ACSARCSGLSDAHTHAPECAILKLGC 148 (541)
Q Consensus 99 C~~C~~~~~~~~~~~~~C~~C~~~-yCS~~C~~~~~~~~H~~EC~~l~~~~ 148 (541)
|.+|...... ...+.|+.||++ |||++=.. .+...|+.-|..|+...
T Consensus 2 Cpv~~~~~~~--~v~~~Cp~cGipthcS~ehw~-~D~e~H~~~c~~LRqvN 49 (55)
T PF13824_consen 2 CPVCKKDLPA--HVNFECPDCGIPTHCSEEHWE-DDYEEHRQLCERLRQVN 49 (55)
T ss_pred CCCCcccccc--ccCCcCCCCCCcCccCHHHHH-HhHHHHHHHHHHHHHhc
Confidence 6666664332 235899999999 99987665 33468888999988753
No 15
>KOG1710|consensus
Probab=93.25 E-value=0.02 Score=56.56 Aligned_cols=42 Identities=26% Similarity=0.624 Sum_probs=36.1
Q ss_pred cccccccCCCCCCCCCCcCCCCCCcc-ccChhhhccccCCCCHhhhhhh
Q psy6242 97 PICLGCHKPLNPNLADNARCPRCFWP-ACSARCSGLSDAHTHAPECAIL 144 (541)
Q Consensus 97 ~~C~~C~~~~~~~~~~~~~C~~C~~~-yCS~~C~~~~~~~~H~~EC~~l 144 (541)
.+|..|..+-. ..+|+.|+.+ ||+++||+ -.|..|+-.|..+
T Consensus 320 ~fCstCG~~ga-----~KrCs~CKav~YCdqeCQk-~hWf~HKK~C~~L 362 (396)
T KOG1710|consen 320 QFCSTCGHPGA-----KKRCSQCKAVAYCDQECQK-FHWFIHKKVCSFL 362 (396)
T ss_pred ccccccCCCCc-----cchhhhhHHHHHHHHHHHH-hhhHHHHHHHHHH
Confidence 78899987765 4799999987 99999999 5688999999876
No 16
>KOG1337|consensus
Probab=90.11 E-value=0.35 Score=52.77 Aligned_cols=79 Identities=13% Similarity=0.120 Sum_probs=57.7
Q ss_pred CCHHHHHHHHhhhhcccccc--C--------CceeEEecccccccCCCCCCceeeeeCC--eEEEEe----cCCeeeeec
Q psy6242 224 TSAKCLHWICGVIEVNGVDI--G--------RYTQGLYSVICLMEHNCLPNAKHSNMMQ--SKLFVF----RDTHISTMY 287 (541)
Q Consensus 224 ~~~~~i~~i~~~l~~Naf~i--~--------~~g~glYp~~Sl~NHSC~PN~~~~f~~~--~~i~vr----~GeEItisY 287 (541)
++.+.+.-.+..+.+.+|.+ . ..-.++.|..-++||++.+....++..+ ..+++. +||||+|+|
T Consensus 197 ~~~~~~~w~~~~~~sr~~~~~~~~~~~~~~~~~~~~L~P~~D~~NH~~~~~~~~~~~~d~~~~l~~~~~v~~geevfi~Y 276 (472)
T KOG1337|consen 197 FTFSAFKWAYSIVNSRAFYLPSLQRLTAGDPDDNEALAPLIDLLNHSPEVIKAGYNQEDEAVELVAERDVSAGEEVFINY 276 (472)
T ss_pred cchHHHHHHHHHHhhhhhccccccccccCCCCcchhhhhhHHhhccCchhccccccCCCCcEEEEEeeeecCCCeEEEec
Confidence 56777888888889988887 1 1236889999999999999444444333 233332 999999999
Q ss_pred cCCCCChHHHHHHHhcCCCeE
Q psy6242 288 TNALWGTQPRREHLAITKYFN 308 (541)
Q Consensus 288 ~d~~~~~~~Rr~~L~~~y~F~ 308 (541)
++.. ...|...|||.
T Consensus 277 G~~~------N~eLL~~YGFv 291 (472)
T KOG1337|consen 277 GPKS------NAELLLHYGFV 291 (472)
T ss_pred CCCc------hHHHHHhcCCC
Confidence 9843 23466779998
No 17
>KOG1141|consensus
Probab=90.08 E-value=0.21 Score=55.83 Aligned_cols=51 Identities=22% Similarity=0.346 Sum_probs=33.6
Q ss_pred cccccCCCCCCceee--eeCC--eE---E------EEecCCeeeeeccCCCCChHHHHHHHhcCCCeEEecc
Q psy6242 254 ICLMEHNCLPNAKHS--NMMQ--SK---L------FVFRDTHISTMYTNALWGTQPRREHLAITKYFNCSCE 312 (541)
Q Consensus 254 ~Sl~NHSC~PN~~~~--f~~~--~~---i------~vr~GeEItisY~d~~~~~~~Rr~~L~~~y~F~C~C~ 312 (541)
+-++||||+||..+. |... .+ + .||+|+|||--|....-.++ ++-..|+|-
T Consensus 1190 GRfLNHSC~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Ye~g~v~--------~keL~C~CG 1253 (1262)
T KOG1141|consen 1190 GRFLNHSCDPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQYEQGQVA--------TKELTCHCG 1253 (1262)
T ss_pred hhhhccCCCccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccccccccc--------cceEEEecC
Confidence 347899999999874 3321 11 1 12299999999987654432 345778875
No 18
>KOG1082|consensus
Probab=89.47 E-value=0.16 Score=53.43 Aligned_cols=37 Identities=16% Similarity=0.261 Sum_probs=27.4
Q ss_pred cccCCCCCCceeeee--CC-----eEEEE---e---cCCeeeeeccCCCC
Q psy6242 256 LMEHNCLPNAKHSNM--MQ-----SKLFV---F---RDTHISTMYTNALW 292 (541)
Q Consensus 256 l~NHSC~PN~~~~f~--~~-----~~i~v---r---~GeEItisY~d~~~ 292 (541)
++||||.||+.+... +. .+|.+ + +|+|||.-|+....
T Consensus 275 finHSC~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p~~ELT~dYg~~~~ 324 (364)
T KOG1082|consen 275 FINHSCSPNLLYQAVFQDEFVLLYLRIGFFALRDISPGEELTLDYGKAYK 324 (364)
T ss_pred cccCCCCccceeeeeeecCCccchheeeeeeccccCCCcccchhhccccc
Confidence 789999999998763 22 12221 2 99999999998765
No 19
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=89.26 E-value=0.13 Score=33.40 Aligned_cols=27 Identities=37% Similarity=0.800 Sum_probs=19.3
Q ss_pred cccccccCCCCCCCCCCcCCCCCCccccChhhh
Q psy6242 97 PICLGCHKPLNPNLADNARCPRCFWPACSARCS 129 (541)
Q Consensus 97 ~~C~~C~~~~~~~~~~~~~C~~C~~~yCS~~C~ 129 (541)
..|..|.. .. .+.|++|+..|||-+|.
T Consensus 3 ~~C~vC~~-~~-----kY~Cp~C~~~~CSl~C~ 29 (30)
T PF04438_consen 3 KLCSVCGN-PA-----KYRCPRCGARYCSLACY 29 (30)
T ss_dssp EEETSSSS-EE-----SEE-TTT--EESSHHHH
T ss_pred CCCccCcC-CC-----EEECCCcCCceeCcEeE
Confidence 57888887 22 58999999999999985
No 20
>PLN03158 methionine aminopeptidase; Provisional
Probab=88.11 E-value=0.19 Score=53.31 Aligned_cols=42 Identities=26% Similarity=0.666 Sum_probs=35.6
Q ss_pred cccccccccccCCcCCCCccCc-------ccccCCchhhhhcccccccC
Q psy6242 9 DEELMRCAVCRETALHKCSACK-------EVAYCGKQHQKEHWKLHKPK 50 (541)
Q Consensus 9 ~~~~~~C~~C~~~~~~~Cs~C~-------~v~YCs~~hQ~~~w~~Hk~~ 50 (541)
+..+..|.-|++++.++|..|. ..++||.+|-+..|+.||..
T Consensus 6 ~~~~~~c~~c~~~a~l~Cp~C~k~~~~~~~s~fCsq~CFk~~w~~Hk~~ 54 (396)
T PLN03158 6 TTSPLACARCSKPAHLQCPKCLELKLPREGASFCSQDCFKAAWSSHKSV 54 (396)
T ss_pred CCCcccccCCCCcccccCccchhcCCCCCCceeECHHHHHHHHHHHHHH
Confidence 3556679999999999999993 37899999999999998754
No 21
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=86.62 E-value=0.19 Score=44.91 Aligned_cols=28 Identities=39% Similarity=0.515 Sum_probs=21.3
Q ss_pred chhhccccCCCCCccccccCCeeecccc
Q psy6242 65 GRYLQATLDLHPGDRIARESPLIVGPKL 92 (541)
Q Consensus 65 GR~l~A~~~i~~Ge~I~~e~plv~~p~~ 92 (541)
|||++|+++|++|++|+.+.+++..+..
T Consensus 1 GrGl~At~dI~~Ge~I~~p~~~~~~~~~ 28 (162)
T PF00856_consen 1 GRGLFATRDIKAGEVILIPRPAILTPDE 28 (162)
T ss_dssp SEEEEESS-B-TTEEEEEESEEEEEHHH
T ss_pred CEEEEECccCCCCCEEEEECcceEEehh
Confidence 8999999999999999966677665543
No 22
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=86.61 E-value=0.21 Score=32.43 Aligned_cols=29 Identities=31% Similarity=0.687 Sum_probs=21.6
Q ss_pred ccccccccCCcCCCCccCcccccCCchhhh
Q psy6242 12 LMRCAVCRETALHKCSACKEVAYCGKQHQK 41 (541)
Q Consensus 12 ~~~C~~C~~~~~~~Cs~C~~v~YCs~~hQ~ 41 (541)
..+|.+|+..+.-+|.+|... |||.++-+
T Consensus 2 ~~~C~vC~~~~kY~Cp~C~~~-~CSl~C~k 30 (30)
T PF04438_consen 2 RKLCSVCGNPAKYRCPRCGAR-YCSLACYK 30 (30)
T ss_dssp -EEETSSSSEESEE-TTT--E-ESSHHHHH
T ss_pred cCCCccCcCCCEEECCCcCCc-eeCcEeEC
Confidence 468999999989999999766 99988753
No 23
>KOG2857|consensus
Probab=83.46 E-value=0.44 Score=42.10 Aligned_cols=37 Identities=30% Similarity=0.772 Sum_probs=29.5
Q ss_pred cccccccCCCCCCCCCCcCCCCCCccccChhhhccccCCCCHh--hhhh
Q psy6242 97 PICLGCHKPLNPNLADNARCPRCFWPACSARCSGLSDAHTHAP--ECAI 143 (541)
Q Consensus 97 ~~C~~C~~~~~~~~~~~~~C~~C~~~yCS~~C~~~~~~~~H~~--EC~~ 143 (541)
.+|.-|.+... .++|+.|..+|||--|.+ .|+. +|..
T Consensus 6 ~tC~ic~e~~~-----KYKCpkC~vPYCSl~CfK-----iHk~tPq~~~ 44 (157)
T KOG2857|consen 6 TTCVICLESEI-----KYKCPKCSVPYCSLPCFK-----IHKSTPQCET 44 (157)
T ss_pred eeehhhhcchh-----hccCCCCCCccccchhhh-----hccCCccccc
Confidence 57888987653 589999999999999965 6765 6654
No 24
>KOG4317|consensus
Probab=73.33 E-value=1.5 Score=44.01 Aligned_cols=36 Identities=31% Similarity=0.676 Sum_probs=28.3
Q ss_pred cccccccCCCCCCCCCCcCCCCCCccccChhhhccccCCCCHhhhh
Q psy6242 97 PICLGCHKPLNPNLADNARCPRCFWPACSARCSGLSDAHTHAPECA 142 (541)
Q Consensus 97 ~~C~~C~~~~~~~~~~~~~C~~C~~~yCS~~C~~~~~~~~H~~EC~ 142 (541)
..|..|-.... -+.||+|+.+|||-.|.+ .|+.-|.
T Consensus 8 ~~C~ic~vq~~-----~YtCPRCn~~YCsl~CYr-----~h~~~Cs 43 (383)
T KOG4317|consen 8 LACGICGVQKR-----EYTCPRCNLLYCSLKCYR-----NHKHSCS 43 (383)
T ss_pred eeccccccccc-----cccCCCCCccceeeeeec-----CCCccch
Confidence 67888877654 489999999999999977 4555474
No 25
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=72.39 E-value=2 Score=32.62 Aligned_cols=24 Identities=33% Similarity=0.700 Sum_probs=18.4
Q ss_pred CcccccccCCCCCCCCCCcCCCCCCccccChhhhc
Q psy6242 96 EPICLGCHKPLNPNLADNARCPRCFWPACSARCSG 130 (541)
Q Consensus 96 ~~~C~~C~~~~~~~~~~~~~C~~C~~~yCS~~C~~ 130 (541)
+.+|..|..+.++ ...|||++|++
T Consensus 3 HkHC~~CG~~Ip~-----------~~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPP-----------DESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCc-----------chhhhCHHHHH
Confidence 3688888887764 24599999987
No 26
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=69.86 E-value=2 Score=36.22 Aligned_cols=34 Identities=29% Similarity=0.279 Sum_probs=27.8
Q ss_pred cccCCcccchhhccccCCCCCccccccCCeeecc
Q psy6242 57 EIKSSPLLGRYLQATLDLHPGDRIARESPLIVGP 90 (541)
Q Consensus 57 ~i~~s~~~GR~l~A~~~i~~Ge~I~~e~plv~~p 90 (541)
++..++.+|++++|+++|++|++|+...+.+..+
T Consensus 3 ~~~~~~~~G~gl~a~~~i~~g~~i~~~~g~~~~~ 36 (116)
T smart00317 3 EVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITS 36 (116)
T ss_pred EEEecCCCcEEEEECCccCCCCEEEEEEeEEECH
Confidence 3445578999999999999999998888877653
No 27
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=67.69 E-value=2.5 Score=35.85 Aligned_cols=32 Identities=28% Similarity=0.652 Sum_probs=24.4
Q ss_pred cccccccCCCCCCCCCCcCCCCCCccccChhhhccccCCCCH
Q psy6242 97 PICLGCHKPLNPNLADNARCPRCFWPACSARCSGLSDAHTHA 138 (541)
Q Consensus 97 ~~C~~C~~~~~~~~~~~~~C~~C~~~yCS~~C~~~~~~~~H~ 138 (541)
.-|.+|| ++|+.|+..-|+.+|+....|.|-+
T Consensus 68 ~~C~GC~----------~PC~~C~S~KCG~~CR~nRkw~ye~ 99 (103)
T PF14949_consen 68 EDCPGCH----------YPCPKCGSRKCGPECRCNRKWVYES 99 (103)
T ss_pred CCCCCcc----------ccCCCCCCCccChhhCcCCceeeee
Confidence 5677775 8999999999999998744454443
No 28
>PRK11032 hypothetical protein; Provisional
Probab=65.18 E-value=20 Score=33.01 Aligned_cols=65 Identities=22% Similarity=0.305 Sum_probs=34.8
Q ss_pred ChhHHHHHHHHHHHHhcCCCCccccCCHHHHHhhc----ce----eeccccccCcccccccccccCCCCCCC-CCCCCCC
Q psy6242 406 HYHCYAVKHSLIQLYGTQPGYAYTQLSSSLLERKI----SY----VMSPNLKATDEPICLGCHKPLNPNLAD-NARCPRC 476 (541)
Q Consensus 406 h~~~~~~~~~L~~ly~~~~~~~~~~~~~~~l~rk~----~~----~~~Pg~~~~~~~~c~ec~~~l~~~~~~-~~~C~~C 476 (541)
.+.+..++.+|-+.+..+.+-.- +-...|...+ .| ++|||. .+|-.|...+.....+ -..|++|
T Consensus 76 s~~~~~i~~slw~~L~~ItDrTq--vEw~el~~dl~h~g~Y~sGEvvg~G~-----LvC~~Cg~~~~~~~p~~i~pCp~C 148 (160)
T PRK11032 76 SVFMRVIKESLWQELADITDKTQ--LEWREVFQDLNHHGVYHSGEVVGLGN-----LVCEKCHHHLAFYTPEVLPLCPKC 148 (160)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhH--HHHHHHHHHhhhcCeeecceeeecce-----EEecCCCCEEEecCCCcCCCCCCC
Confidence 56677888888887776533221 1122233333 33 888884 6777776655432211 1346655
Q ss_pred C
Q psy6242 477 F 477 (541)
Q Consensus 477 ~ 477 (541)
|
T Consensus 149 ~ 149 (160)
T PRK11032 149 G 149 (160)
T ss_pred C
Confidence 4
No 29
>KOG1083|consensus
Probab=64.69 E-value=4.9 Score=46.68 Aligned_cols=33 Identities=15% Similarity=0.348 Sum_probs=25.4
Q ss_pred cccCCCCCCceee---eeCCeEEEE---e---cCCeeeeecc
Q psy6242 256 LMEHNCLPNAKHS---NMMQSKLFV---F---RDTHISTMYT 288 (541)
Q Consensus 256 l~NHSC~PN~~~~---f~~~~~i~v---r---~GeEItisY~ 288 (541)
++||||.||+... .+|.++|.| | +|||||.-|-
T Consensus 1253 finhscKPNc~~qkwSVNG~~Rv~L~A~rDi~kGEELtYDYN 1294 (1306)
T KOG1083|consen 1253 FINHSCKPNCEMQKWSVNGEYRVGLFALRDLPKGEELTYDYN 1294 (1306)
T ss_pred ccccccCCCCccccccccceeeeeeeecCCCCCCceEEEecc
Confidence 6799999999865 345556654 3 9999999984
No 30
>KOG3362|consensus
Probab=59.78 E-value=4 Score=36.39 Aligned_cols=32 Identities=25% Similarity=0.489 Sum_probs=26.0
Q ss_pred CCCCcccccccCCCCCCCCCCcCCCCCCccccChhhhc
Q psy6242 93 ALAEPICLGCHKPLNPNLADNARCPRCFWPACSARCSG 130 (541)
Q Consensus 93 ~~~~~~C~~C~~~~~~~~~~~~~C~~C~~~yCS~~C~~ 130 (541)
...+..|..|.-. +.+.|.+||.-|||..|.+
T Consensus 115 KP~r~fCaVCG~~------S~ysC~~CG~kyCsv~C~~ 146 (156)
T KOG3362|consen 115 KPLRKFCAVCGYD------SKYSCVNCGTKYCSVRCLK 146 (156)
T ss_pred CCcchhhhhcCCC------chhHHHhcCCceeechhhh
Confidence 3446899999822 2689999999999999987
No 31
>KOG1338|consensus
Probab=52.59 E-value=35 Score=35.88 Aligned_cols=69 Identities=9% Similarity=0.049 Sum_probs=54.6
Q ss_pred CcCCHHHHHHHHhhhhcccccc---------------CCceeEEecccccccCCCC-CCceeeeeCC-eEEEE-e---cC
Q psy6242 222 DDTSAKCLHWICGVIEVNGVDI---------------GRYTQGLYSVICLMEHNCL-PNAKHSNMMQ-SKLFV-F---RD 280 (541)
Q Consensus 222 ~~~~~~~i~~i~~~l~~Naf~i---------------~~~g~glYp~~Sl~NHSC~-PN~~~~f~~~-~~i~v-r---~G 280 (541)
+.++.+.++.+.+.+..=+|.| +..|-..-|.+-++||.=. -|+...++.+ .+|++ | +|
T Consensus 172 s~~slEdF~y~~Al~laysfdve~~~s~~~~eee~e~e~ngk~m~p~ad~lNhd~~k~nanl~y~~NcL~mva~r~iekg 251 (466)
T KOG1338|consen 172 SRPSLEDFMYAYALGLAYSFDVEFLLSLDNLEEESEIECNGKLMTPIADFLNHDGLKANANLRYEDNCLEMVADRNIEKG 251 (466)
T ss_pred cccCHHHHHHHHHHHHHHheeeehhcchhhhhhhhccccCcccccchhhhhccchhhcccceeccCcceeeeecCCCCCc
Confidence 4578899999999998888888 1457888899999999876 6777777665 45555 4 99
Q ss_pred CeeeeeccCC
Q psy6242 281 THISTMYTNA 290 (541)
Q Consensus 281 eEItisY~d~ 290 (541)
+|+..+|+-.
T Consensus 252 dev~n~dg~~ 261 (466)
T KOG1338|consen 252 DEVDNSDGLK 261 (466)
T ss_pred cccccccccC
Confidence 9999999743
No 32
>KOG3612|consensus
Probab=52.23 E-value=3.2 Score=44.78 Aligned_cols=41 Identities=24% Similarity=0.580 Sum_probs=30.7
Q ss_pred cccccccCCCCCCCCCCcCCCCCCc-c-ccChhhhccccCCCCHhhhhhhhhc
Q psy6242 97 PICLGCHKPLNPNLADNARCPRCFW-P-ACSARCSGLSDAHTHAPECAILKLG 147 (541)
Q Consensus 97 ~~C~~C~~~~~~~~~~~~~C~~C~~-~-yCS~~C~~~~~~~~H~~EC~~l~~~ 147 (541)
.=|++|..... +. |-| . |||-+||+ ..|..|+.-|..-...
T Consensus 528 QWC~nC~~EAi------y~---CCWNTSYCsveCQQ-~HW~~H~ksCrrk~~~ 570 (588)
T KOG3612|consen 528 QWCYNCLDEAI------YH---CCWNTSYCSVECQQ-GHWPEHRKSCRRKKTN 570 (588)
T ss_pred HHHHhhhHHHH------HH---hhccccccCcchhh-ccchhHhhhhcccCCC
Confidence 67999987653 33 456 4 99999999 6677999999875443
No 33
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=51.91 E-value=6.6 Score=27.78 Aligned_cols=34 Identities=15% Similarity=0.219 Sum_probs=25.5
Q ss_pred ccccccccccCCcCCCCccCcccccCCchhhhhcccc
Q psy6242 10 EELMRCAVCRETALHKCSACKEVAYCGKQHQKEHWKL 46 (541)
Q Consensus 10 ~~~~~C~~C~~~~~~~Cs~C~~v~YCs~~hQ~~~w~~ 46 (541)
..++-|-+|++.-.. .-....|||++|+..|+..
T Consensus 4 ~F~~yC~~Cdk~~~~---~~~~~lYCSe~Cr~~D~~~ 37 (43)
T PF12855_consen 4 AFNDYCIVCDKQIDP---PDDGSLYCSEECRLKDQEK 37 (43)
T ss_pred hhhhHHHHhhccccC---CCCCccccCHHHHhHhhhc
Confidence 457889999875211 3456789999999999875
No 34
>KOG1085|consensus
Probab=51.77 E-value=10 Score=37.85 Aligned_cols=39 Identities=15% Similarity=0.053 Sum_probs=29.1
Q ss_pred cccccCCCCCCceeee---eCCeEEEE--e----cCCeeeeeccCCCC
Q psy6242 254 ICLMEHNCLPNAKHSN---MMQSKLFV--F----RDTHISTMYTNALW 292 (541)
Q Consensus 254 ~Sl~NHSC~PN~~~~f---~~~~~i~v--r----~GeEItisY~d~~~ 292 (541)
.-|+|||=.+|+..-. ++..++++ + +||||+.-|+|-..
T Consensus 334 GRLINHS~~gNl~TKvv~Idg~pHLiLvA~rdIa~GEELlYDYGDRSk 381 (392)
T KOG1085|consen 334 GRLINHSVRGNLKTKVVEIDGSPHLILVARRDIAQGEELLYDYGDRSK 381 (392)
T ss_pred hhhhcccccCcceeeEEEecCCceEEEEeccccccchhhhhhccccch
Confidence 4589999999997643 44444444 3 99999999998654
No 35
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=48.23 E-value=77 Score=28.77 Aligned_cols=54 Identities=17% Similarity=0.244 Sum_probs=27.8
Q ss_pred hhHHHHHHHHHHHHhcCCCCccccCCH--HHHHhhcce----eeccccccCcccccccccccCCC
Q psy6242 407 YHCYAVKHSLIQLYGTQPGYAYTQLSS--SLLERKISY----VMSPNLKATDEPICLGCHKPLNP 465 (541)
Q Consensus 407 ~~~~~~~~~L~~ly~~~~~~~~~~~~~--~~l~rk~~~----~~~Pg~~~~~~~~c~ec~~~l~~ 465 (541)
+.+..+..+|-+.+..+.+-.--++.+ +.+++.-.| ++|||. .+|-.|...+..
T Consensus 65 ~~~~lie~slw~~L~~ItDkTqvEw~el~~d~~h~g~Y~sGE~~g~G~-----l~C~~Cg~~~~~ 124 (146)
T PF07295_consen 65 PDLQLIEESLWDELSSITDKTQVEWAELAQDLEHHGVYHSGEVVGPGT-----LVCENCGHEVEL 124 (146)
T ss_pred ccHHHHHHHHHHHHHhhhchhHHHHHHHHHHHHhcCCeecCcEecCce-----EecccCCCEEEe
Confidence 445566777777666543332111111 223333334 788873 577777665443
No 36
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=48.23 E-value=25 Score=34.11 Aligned_cols=76 Identities=14% Similarity=0.232 Sum_probs=43.8
Q ss_pred CCCcccCcCcCccCHHHHHHHHHH----HHHHHHHHHh--cCCCHHHHHHHHHHh------hcccCCCChhHHHHHHHHH
Q psy6242 350 DSDWTCGSCSARLNARDVHLVTSQ----LGEQVDKLVQ--ENPNVKSLEEMLTKL------EAMFHPHHYHCYAVKHSLI 417 (541)
Q Consensus 350 ~~~w~C~~C~~~~~~~~v~~~l~~----~~~~~~~~~~--~~~~~~~le~~l~~~------~~~Lhp~h~~~~~~~~~L~ 417 (541)
-..|.|.+||..........+-.. +.+.+...-. +-.....++..++.| ..+....+..++.+...||
T Consensus 46 Y~V~vCP~CgyA~~~~~F~~l~~~~~~~i~~~i~~~~~~~~~~~~Rt~~~ai~~YkLAll~~~~~~~~~s~~A~l~LrlA 125 (214)
T PF09986_consen 46 YEVWVCPHCGYAAFEEDFEKLSPEQKEKIKENISSRWKPRDFSGERTLEEAIESYKLALLCAQIKKEKPSKKAGLCLRLA 125 (214)
T ss_pred eeEEECCCCCCcccccccccCCHHHHHHHHHHHHhhcccCCCCCCCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 357999999988665544333222 2222222100 112222333333333 2456678889999999999
Q ss_pred HHHhcCCC
Q psy6242 418 QLYGTQPG 425 (541)
Q Consensus 418 ~ly~~~~~ 425 (541)
++|+..++
T Consensus 126 WlyR~~~~ 133 (214)
T PF09986_consen 126 WLYRDLGD 133 (214)
T ss_pred HHhhccCC
Confidence 99998655
No 37
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=46.49 E-value=6.7 Score=27.17 Aligned_cols=30 Identities=20% Similarity=0.763 Sum_probs=16.5
Q ss_pred ccccccCCCCCceeeecCCCCCC-CCCcccCcCcCc
Q psy6242 327 MKCLNEHKDQGDCWILPVNPLDN-DSDWTCGSCSAR 361 (541)
Q Consensus 327 ~~C~~~~~~~C~g~~lp~~~~~~-~~~w~C~~C~~~ 361 (541)
++|.+ |++++-|--..+. ...|.|.-|+..
T Consensus 3 ~rC~~-----C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRR-----CRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TT-----T--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccCC-----CCCEECCcceEcCCCCEEECcCCCCc
Confidence 57887 9888766544332 468999999975
No 38
>PLN03158 methionine aminopeptidase; Provisional
Probab=46.42 E-value=6.1 Score=42.04 Aligned_cols=36 Identities=31% Similarity=0.759 Sum_probs=25.7
Q ss_pred cccccccCCCCCCCCCCcCCCCCCc-------c-ccChhhhccccCCCCHh
Q psy6242 97 PICLGCHKPLNPNLADNARCPRCFW-------P-ACSARCSGLSDAHTHAP 139 (541)
Q Consensus 97 ~~C~~C~~~~~~~~~~~~~C~~C~~-------~-yCS~~C~~~~~~~~H~~ 139 (541)
..|.+|.++. .+.|+.|.. . |||++|.+.+ |..|+.
T Consensus 10 ~~c~~c~~~a------~l~Cp~C~k~~~~~~~s~fCsq~CFk~~-w~~Hk~ 53 (396)
T PLN03158 10 LACARCSKPA------HLQCPKCLELKLPREGASFCSQDCFKAA-WSSHKS 53 (396)
T ss_pred ccccCCCCcc------cccCccchhcCCCCCCceeECHHHHHHH-HHHHHH
Confidence 6799998753 378888752 3 9999999955 455543
No 39
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=46.40 E-value=13 Score=22.78 Aligned_cols=21 Identities=33% Similarity=0.842 Sum_probs=11.8
Q ss_pred cccccCCCCC-CCCCCCCCCCC
Q psy6242 458 GCHKPLNPNL-ADNARCPRCFW 478 (541)
Q Consensus 458 ec~~~l~~~~-~~~~~C~~C~w 478 (541)
-|..+|.+.. ...+.|+.||+
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCcccCceEeCCCCCC
Confidence 3444444432 22378999986
No 40
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=44.59 E-value=16 Score=22.90 Aligned_cols=22 Identities=23% Similarity=0.658 Sum_probs=16.5
Q ss_pred ccccccCCCCCCCCCCcCCCCCCcc
Q psy6242 98 ICLGCHKPLNPNLADNARCPRCFWP 122 (541)
Q Consensus 98 ~C~~C~~~~~~~~~~~~~C~~C~~~ 122 (541)
.|..|.+..+. ....|+.||+.
T Consensus 2 ~CP~C~~~V~~---~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPE---SAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchh---hcCcCCCCCCC
Confidence 57888888763 46789999874
No 41
>KOG0856|consensus
Probab=39.80 E-value=17 Score=32.42 Aligned_cols=27 Identities=33% Similarity=0.695 Sum_probs=21.1
Q ss_pred cccccccccCCCCCCCCCCCCCCCCCccc
Q psy6242 454 PICLGCHKPLNPNLADNARCPRCFWPACS 482 (541)
Q Consensus 454 ~~c~ec~~~l~~~~~~~~~C~~C~wplC~ 482 (541)
-.|.+|..||=... .-..++||||.=.
T Consensus 55 Y~C~~C~~pLykS~--tKfdsgcGWPAF~ 81 (146)
T KOG0856|consen 55 YVCAGCGTPLYKST--TKFDSGCGWPAFF 81 (146)
T ss_pred EEEeecCCcccccc--ccccCCCCCchhh
Confidence 47999999987643 3579999999764
No 42
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=38.70 E-value=14 Score=27.69 Aligned_cols=24 Identities=29% Similarity=0.649 Sum_probs=17.9
Q ss_pred CcccccccCCCCCCCCCCcCCCCCCccccChhhhc
Q psy6242 96 EPICLGCHKPLNPNLADNARCPRCFWPACSARCSG 130 (541)
Q Consensus 96 ~~~C~~C~~~~~~~~~~~~~C~~C~~~yCS~~C~~ 130 (541)
+.+|..|.+..+. +..+||++|+.
T Consensus 8 H~HC~VCg~aIp~-----------de~~CSe~C~e 31 (64)
T COG4068 8 HRHCVVCGKAIPP-----------DEQVCSEECGE 31 (64)
T ss_pred CccccccCCcCCC-----------ccchHHHHHHH
Confidence 3788888888775 23489999975
No 43
>PF04181 RPAP2_Rtr1: Rtr1/RPAP2 family; InterPro: IPR007308 This entry represents a domain found in PAP2 (RNAP II associated polypeptide) protein and the yeast Rtr1 proteins. Its function is not known however it is thought to be a zinc finger.
Probab=38.67 E-value=16 Score=29.40 Aligned_cols=13 Identities=31% Similarity=0.547 Sum_probs=10.5
Q ss_pred CCCCCCCCccccc
Q psy6242 472 RCPRCFWPACSAR 484 (541)
Q Consensus 472 ~C~~C~wplC~~~ 484 (541)
...+||||+|+..
T Consensus 19 ~~~~CGYplC~~~ 31 (79)
T PF04181_consen 19 INGLCGYPLCSNP 31 (79)
T ss_pred hCCCCCCccCCCC
Confidence 5789999999653
No 44
>KOG4442|consensus
Probab=38.42 E-value=17 Score=40.76 Aligned_cols=45 Identities=20% Similarity=0.258 Sum_probs=34.4
Q ss_pred CCchhhhhcccccccCCCCCCccccCCcccchhhccccCCCCCcccccc
Q psy6242 35 CGKQHQKEHWKLHKPKCKKLPYEIKSSPLLGRYLQATLDLHPGDRIARE 83 (541)
Q Consensus 35 Cs~~hQ~~~w~~Hk~~C~~~~~~i~~s~~~GR~l~A~~~i~~Ge~I~~e 83 (541)
|+..||.+-.+.|+ +. .+++..++.+|.||.|..+|++|+.|+.-
T Consensus 105 cg~~C~NQRFQkkq--yA--~vevF~Te~KG~GLRA~~dI~~g~FI~EY 149 (729)
T KOG4442|consen 105 CGVYCKNQRFQKKQ--YA--KVEVFLTEKKGCGLRAEEDIPKGQFILEY 149 (729)
T ss_pred ccccccchhhhhhc--cC--ceeEEEecCcccceeeccccCCCcEEeee
Confidence 55666666555433 34 68888899999999999999999988653
No 45
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=37.08 E-value=15 Score=27.75 Aligned_cols=9 Identities=56% Similarity=1.143 Sum_probs=7.9
Q ss_pred cccChhhhc
Q psy6242 122 PACSARCSG 130 (541)
Q Consensus 122 ~yCS~~C~~ 130 (541)
+|||+.|+.
T Consensus 22 PFCS~RCk~ 30 (57)
T PF03884_consen 22 PFCSERCKL 30 (57)
T ss_dssp SSSSHHHHH
T ss_pred CcccHhhcc
Confidence 499999986
No 46
>KOG1079|consensus
Probab=36.93 E-value=31 Score=38.52 Aligned_cols=38 Identities=16% Similarity=0.187 Sum_probs=27.2
Q ss_pred ccccccCCCCCCceeee---eCCeEEEEe------cCCeeeeeccCC
Q psy6242 253 VICLMEHNCLPNAKHSN---MMQSKLFVF------RDTHISTMYTNA 290 (541)
Q Consensus 253 ~~Sl~NHSC~PN~~~~f---~~~~~i~vr------~GeEItisY~d~ 290 (541)
.+=+.|||=.||+.... .|+.+|-++ +|||||..|...
T Consensus 665 k~rFANHS~nPNCYAkvm~V~GdhRIGifAkRaIeagEELffDYrYs 711 (739)
T KOG1079|consen 665 KIRFANHSFNPNCYAKVMMVAGDHRIGIFAKRAIEAGEELFFDYRYS 711 (739)
T ss_pred hhhhccCCCCCCcEEEEEEecCCcceeeeehhhcccCceeeeeeccC
Confidence 34467999999997642 344455443 999999999654
No 47
>PF08189 Meleagrin: Meleagrin/Cygnin family; InterPro: IPR012573 This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown [].
Probab=36.69 E-value=13 Score=25.08 Aligned_cols=19 Identities=26% Similarity=0.335 Sum_probs=14.0
Q ss_pred CCcc-ccChhhhccccCCCC
Q psy6242 119 CFWP-ACSARCSGLSDAHTH 137 (541)
Q Consensus 119 C~~~-yCS~~C~~~~~~~~H 137 (541)
|..+ |||..|.+..-|.+|
T Consensus 6 cpkiGYCS~~CsKt~vWa~s 25 (39)
T PF08189_consen 6 CPKIGYCSSKCSKTDVWAFS 25 (39)
T ss_pred Ccccceecccccccceeeec
Confidence 5556 999999986555555
No 48
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.68 E-value=17 Score=27.82 Aligned_cols=9 Identities=56% Similarity=1.128 Sum_probs=7.7
Q ss_pred cccChhhhc
Q psy6242 122 PACSARCSG 130 (541)
Q Consensus 122 ~yCS~~C~~ 130 (541)
+|||+.|+.
T Consensus 27 PFCSkRCkl 35 (65)
T COG3024 27 PFCSKRCKL 35 (65)
T ss_pred cchhHhhhh
Confidence 489999986
No 49
>KOG2807|consensus
Probab=35.33 E-value=35 Score=34.79 Aligned_cols=86 Identities=23% Similarity=0.470 Sum_probs=53.6
Q ss_pred cCCCCccCcccccCCchhhhhcccccccCCCCCCccccCCcccchhhccccCCCCCccccccCCeeeccccCC-CCcccc
Q psy6242 22 ALHKCSACKEVAYCGKQHQKEHWKLHKPKCKKLPYEIKSSPLLGRYLQATLDLHPGDRIARESPLIVGPKLAL-AEPICL 100 (541)
Q Consensus 22 ~~~~Cs~C~~v~YCs~~hQ~~~w~~Hk~~C~~~~~~i~~s~~~GR~l~A~~~i~~Ge~I~~e~plv~~p~~~~-~~~~C~ 100 (541)
+---|.+|+.. +||- + ..|....+.+..++...|... -+|+-.||+..|.... ....|+
T Consensus 275 ~Gy~CP~Ckak-vCsL-------P---~eCpiC~ltLVss~hLARSyh---------hL~PL~~F~Eip~~~~~~~~~Cf 334 (378)
T KOG2807|consen 275 GGYFCPQCKAK-VCSL-------P---IECPICSLTLVSSPHLARSYH---------HLFPLKPFVEIPETEYNGSRFCF 334 (378)
T ss_pred CceeCCcccCe-eecC-------C---ccCCccceeEecchHHHHHHH---------hhcCCcchhhccccccCCCccee
Confidence 44569999754 7764 2 224322455555655544322 3555667777776543 236799
Q ss_pred cccCCCCCCCCCCcCCCCCCccccChhhhc
Q psy6242 101 GCHKPLNPNLADNARCPRCFWPACSARCSG 130 (541)
Q Consensus 101 ~C~~~~~~~~~~~~~C~~C~~~yCS~~C~~ 130 (541)
.|+....+ ...++|+.|+..||. +|-.
T Consensus 335 ~C~~~~~~--~~~y~C~~Ck~~FCl-dCDv 361 (378)
T KOG2807|consen 335 ACQGELLS--SGRYRCESCKNVFCL-DCDV 361 (378)
T ss_pred eeccccCC--CCcEEchhccceeec-cchH
Confidence 99665543 346899999999996 5754
No 50
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=35.00 E-value=12 Score=27.43 Aligned_cols=32 Identities=34% Similarity=0.915 Sum_probs=17.1
Q ss_pred ccccccCCCCCCC-----CCCcCCCCCCccccChhhhc
Q psy6242 98 ICLGCHKPLNPNL-----ADNARCPRCFWPACSARCSG 130 (541)
Q Consensus 98 ~C~~C~~~~~~~~-----~~~~~C~~C~~~yCS~~C~~ 130 (541)
.|++|.++++... ...++|++|+..|| -+|-.
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC-~dCD~ 37 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFC-IDCDV 37 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B--HHHHH
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccc-cCcCh
Confidence 4888988887521 12478999999999 45743
No 51
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=34.59 E-value=16 Score=40.94 Aligned_cols=37 Identities=30% Similarity=0.689 Sum_probs=28.9
Q ss_pred ccccc----cCCcCCCCccC---c----ccccCCchhhhhcccccccC
Q psy6242 14 RCAVC----RETALHKCSAC---K----EVAYCGKQHQKEHWKLHKPK 50 (541)
Q Consensus 14 ~C~~C----~~~~~~~Cs~C---~----~v~YCs~~hQ~~~w~~Hk~~ 50 (541)
.+.+| ++++.++|..| + ..++||.+|-+..|+.||..
T Consensus 61 ~~~~c~~h~~~~a~lqCp~C~k~~~~~~~s~fCsq~CFk~~w~~Hk~~ 108 (606)
T PLN03144 61 KVAVCSVHPSEPATLQCVGCVKAKLPVSKSYHCSPKCFSDAWRHHRVL 108 (606)
T ss_pred cceeEeecCCCcccccCccchhcCCCcCcceeeCHHHHHHHHHHHHHH
Confidence 45777 34577889988 2 36899999999999998743
No 52
>KOG2857|consensus
Probab=33.83 E-value=20 Score=31.92 Aligned_cols=29 Identities=31% Similarity=0.778 Sum_probs=21.5
Q ss_pred ccccccccccCCCCCCCCCCCCCCCCCccccccC
Q psy6242 453 EPICLGCHKPLNPNLADNARCPRCFWPACSARCS 486 (541)
Q Consensus 453 ~~~c~ec~~~l~~~~~~~~~C~~C~wplC~~~C~ 486 (541)
..+|.-|.... -+|+|+.|..|-||--|-
T Consensus 5 t~tC~ic~e~~-----~KYKCpkC~vPYCSl~Cf 33 (157)
T KOG2857|consen 5 TTTCVICLESE-----IKYKCPKCSVPYCSLPCF 33 (157)
T ss_pred eeeehhhhcch-----hhccCCCCCCccccchhh
Confidence 45666665532 168999999999998885
No 53
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=33.07 E-value=24 Score=27.06 Aligned_cols=9 Identities=56% Similarity=1.132 Sum_probs=7.9
Q ss_pred cccChhhhc
Q psy6242 122 PACSARCSG 130 (541)
Q Consensus 122 ~yCS~~C~~ 130 (541)
+|||+.|+.
T Consensus 26 PFCS~RCk~ 34 (62)
T PRK00418 26 PFCSKRCQL 34 (62)
T ss_pred CcccHHHHh
Confidence 599999987
No 54
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=32.17 E-value=1.2e+02 Score=27.81 Aligned_cols=30 Identities=10% Similarity=0.173 Sum_probs=18.8
Q ss_pred CCCcccCcCcCccCHHHHHHHHHHHHHHHHHH
Q psy6242 350 DSDWTCGSCSARLNARDVHLVTSQLGEQVDKL 381 (541)
Q Consensus 350 ~~~w~C~~C~~~~~~~~v~~~l~~~~~~~~~~ 381 (541)
...-.|.+||+.++. ....++.+.+.++++
T Consensus 66 ~~PsYC~~CGkpyPW--t~~~L~aa~el~ee~ 95 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPW--TENALEAANELIEED 95 (158)
T ss_pred CCChhHHhCCCCCch--HHHHHHHHHHHHHHh
Confidence 356789999999984 334444544444433
No 55
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=31.50 E-value=33 Score=22.59 Aligned_cols=24 Identities=33% Similarity=0.717 Sum_probs=14.9
Q ss_pred ccccccccCCCCCCCCCCCCCCCC
Q psy6242 455 ICLGCHKPLNPNLADNARCPRCFW 478 (541)
Q Consensus 455 ~c~ec~~~l~~~~~~~~~C~~C~w 478 (541)
+|.+|-+.+.....+..+|+.||.
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 466777666554444579999985
No 56
>KOG2738|consensus
Probab=31.07 E-value=20 Score=36.13 Aligned_cols=41 Identities=27% Similarity=0.653 Sum_probs=33.4
Q ss_pred ccccc--ccccCCcCCCCccC-----cccccCCchhhhhcccccccCC
Q psy6242 11 ELMRC--AVCRETALHKCSAC-----KEVAYCGKQHQKEHWKLHKPKC 51 (541)
Q Consensus 11 ~~~~C--~~C~~~~~~~Cs~C-----~~v~YCs~~hQ~~~w~~Hk~~C 51 (541)
....| .-|++++.+.|+.| +..++|+.++-+.-|..||..=
T Consensus 5 ~~~~c~~~~c~~~a~l~Cp~c~~~~i~~~~fc~q~cf~~~w~~hK~~h 52 (369)
T KOG2738|consen 5 AKISCEGLQCGSEASLQCPTCLKLGIKSAYFCAQECFKNSWLSHKKLH 52 (369)
T ss_pred hhceeeccccCChhhccCchhhhcCCCcccccCchhhhcchhhhhhhc
Confidence 34556 66888888999988 5568999999999999988754
No 57
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=30.78 E-value=33 Score=23.97 Aligned_cols=13 Identities=23% Similarity=0.687 Sum_probs=7.1
Q ss_pred CCcccCcCcCccC
Q psy6242 351 SDWTCGSCSARLN 363 (541)
Q Consensus 351 ~~w~C~~C~~~~~ 363 (541)
....|..||.++.
T Consensus 18 g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 18 GELVCPNCGLVLE 30 (43)
T ss_dssp TEEEETTT-BBEE
T ss_pred CeEECCCCCCEee
Confidence 4556666666554
No 58
>PRK01343 zinc-binding protein; Provisional
Probab=29.94 E-value=41 Score=25.34 Aligned_cols=31 Identities=10% Similarity=0.396 Sum_probs=22.3
Q ss_pred ccccccccccCCcCCCCccCcccccCCchhhhhccc
Q psy6242 10 EELMRCAVCRETALHKCSACKEVAYCGKQHQKEHWK 45 (541)
Q Consensus 10 ~~~~~C~~C~~~~~~~Cs~C~~v~YCs~~hQ~~~w~ 45 (541)
.....|.+||++... ...-|||+.|+..|--
T Consensus 7 ~p~~~CP~C~k~~~~-----~~rPFCS~RC~~iDLg 37 (57)
T PRK01343 7 RPTRPCPECGKPSTR-----EAYPFCSERCRDIDLN 37 (57)
T ss_pred CCCCcCCCCCCcCcC-----CCCcccCHHHhhhhHH
Confidence 345679999987542 3557999999887654
No 59
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=28.18 E-value=30 Score=23.16 Aligned_cols=28 Identities=14% Similarity=0.173 Sum_probs=14.0
Q ss_pred ccccCCCCCceeeecCC-CCCCCCCcccCcCcCc
Q psy6242 329 CLNEHKDQGDCWILPVN-PLDNDSDWTCGSCSAR 361 (541)
Q Consensus 329 C~~~~~~~C~g~~lp~~-~~~~~~~w~C~~C~~~ 361 (541)
|+. |++.+.... +.+....+.|..||.+
T Consensus 3 C~~-----CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQ-----CGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TT-----T--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccc-----ccChhhhhcCCCCCccceECCCCCCE
Confidence 676 886653222 2344568899999975
No 60
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=27.57 E-value=27 Score=23.68 Aligned_cols=32 Identities=19% Similarity=0.467 Sum_probs=20.4
Q ss_pred ccccccCCCCCc-eeeecCCCC-CCCCCcccCcCcCccC
Q psy6242 327 MKCLNEHKDQGD-CWILPVNPL-DNDSDWTCGSCSARLN 363 (541)
Q Consensus 327 ~~C~~~~~~~C~-g~~lp~~~~-~~~~~w~C~~C~~~~~ 363 (541)
+.||+ |. .+-+|.+.+ ......+|.+|+..+.
T Consensus 3 i~CP~-----C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPN-----CQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCC-----CCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 56887 87 444554432 2345778999998753
No 61
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.11 E-value=32 Score=25.04 Aligned_cols=26 Identities=19% Similarity=0.560 Sum_probs=18.3
Q ss_pred ccccccCCCCCc-eeeecCCCCCCCCCcccCcCcCc
Q psy6242 327 MKCLNEHKDQGD-CWILPVNPLDNDSDWTCGSCSAR 361 (541)
Q Consensus 327 ~~C~~~~~~~C~-g~~lp~~~~~~~~~w~C~~C~~~ 361 (541)
-.||+ |+ |.++... ...|.|.+||.+
T Consensus 20 ~~CPr-----CG~gvfmA~H----~dR~~CGkCgyT 46 (51)
T COG1998 20 RFCPR-----CGPGVFMADH----KDRWACGKCGYT 46 (51)
T ss_pred ccCCC-----CCCcchhhhc----CceeEeccccce
Confidence 35888 87 6665433 248999999975
No 62
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 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. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=26.72 E-value=17 Score=24.42 Aligned_cols=29 Identities=14% Similarity=0.359 Sum_probs=18.0
Q ss_pred ccccCCCCCceeeecCCCCCCCCCcccCcCcCccCH
Q psy6242 329 CLNEHKDQGDCWILPVNPLDNDSDWTCGSCSARLNA 364 (541)
Q Consensus 329 C~~~~~~~C~g~~lp~~~~~~~~~w~C~~C~~~~~~ 364 (541)
|+. |++.++|...... .. .|..|+...+.
T Consensus 4 Cp~-----C~nlL~p~~~~~~-~~-~C~~C~Y~~~~ 32 (35)
T PF02150_consen 4 CPE-----CGNLLYPKEDKEK-RV-ACRTCGYEEPI 32 (35)
T ss_dssp ETT-----TTSBEEEEEETTT-TE-EESSSS-EEE-
T ss_pred CCC-----CCccceEcCCCcc-Cc-CCCCCCCccCC
Confidence 777 9888877643221 12 79999987653
No 63
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=26.42 E-value=52 Score=28.26 Aligned_cols=26 Identities=23% Similarity=0.460 Sum_probs=18.6
Q ss_pred cccccccCCCCCCCCCCcCCCCCCcc
Q psy6242 97 PICLGCHKPLNPNLADNARCPRCFWP 122 (541)
Q Consensus 97 ~~C~~C~~~~~~~~~~~~~C~~C~~~ 122 (541)
++|..|.+++-......+.||.|+..
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCc
Confidence 89999998876432346779887763
No 64
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=26.41 E-value=35 Score=28.99 Aligned_cols=7 Identities=43% Similarity=1.583 Sum_probs=3.7
Q ss_pred CCCCCCC
Q psy6242 472 RCPRCFW 478 (541)
Q Consensus 472 ~C~~C~w 478 (541)
.|++|-|
T Consensus 69 ~C~GC~~ 75 (103)
T PF14949_consen 69 DCPGCHY 75 (103)
T ss_pred CCCCccc
Confidence 3555555
No 65
>KOG1081|consensus
Probab=26.35 E-value=20 Score=38.92 Aligned_cols=43 Identities=14% Similarity=0.316 Sum_probs=29.0
Q ss_pred EEecccc-cccCCCCCCceeeeeC---CeEEEE---e---cCCeeeeeccCCC
Q psy6242 249 GLYSVIC-LMEHNCLPNAKHSNMM---QSKLFV---F---RDTHISTMYTNAL 291 (541)
Q Consensus 249 glYp~~S-l~NHSC~PN~~~~f~~---~~~i~v---r---~GeEItisY~d~~ 291 (541)
+-+...| ++||||.||+.-.-.. ...+.+ | .|+|+|.+|.-.-
T Consensus 366 ~~~~n~sr~~nh~~~~~v~~~k~~~~~~t~~~~~a~~~i~~g~e~t~~~n~~~ 418 (463)
T KOG1081|consen 366 GPKGNYSRFLNHSCQPNVETEKWQVIGDTRVGLFAPRQIEAGEELTFNYNGNC 418 (463)
T ss_pred ccccchhhhhcccCCCceeechhheecccccccccccccccchhhhheeeccc
Confidence 4455555 7899999999865322 222222 2 9999999997554
No 66
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.15 E-value=43 Score=20.70 Aligned_cols=24 Identities=25% Similarity=0.675 Sum_probs=16.2
Q ss_pred cccccccccCCCCCCCCCCCCCCCCCc
Q psy6242 454 PICLGCHKPLNPNLADNARCPRCFWPA 480 (541)
Q Consensus 454 ~~c~ec~~~l~~~~~~~~~C~~C~wpl 480 (541)
..|-.|-+.+..+ ...|+.||=||
T Consensus 3 ~~Cp~Cg~~~~~~---~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEIDPD---AKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcCCcc---cccChhhCCCC
Confidence 4567777766553 35799988765
No 67
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=24.69 E-value=38 Score=22.84 Aligned_cols=31 Identities=13% Similarity=0.391 Sum_probs=18.6
Q ss_pred ccccccCCCCCc-eeeecCCCC-CCCCCcccCcCcCcc
Q psy6242 327 MKCLNEHKDQGD-CWILPVNPL-DNDSDWTCGSCSARL 362 (541)
Q Consensus 327 ~~C~~~~~~~C~-g~~lp~~~~-~~~~~w~C~~C~~~~ 362 (541)
+.|++ |. .+-++.+.. ......+|.+|++.+
T Consensus 3 i~Cp~-----C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPN-----CQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCC-----CCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 56776 87 444443322 224567899998864
No 68
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=24.65 E-value=41 Score=24.52 Aligned_cols=27 Identities=26% Similarity=0.545 Sum_probs=17.5
Q ss_pred eccCCCCCCccccccccccccccCCCCCceee
Q psy6242 310 SCERCSDPTELGTYFSAMKCLNEHKDQGDCWI 341 (541)
Q Consensus 310 ~C~rC~~~~e~~~~l~~~~C~~~~~~~C~g~~ 341 (541)
.|.+|...-|+..-...++|+. |+..+
T Consensus 8 ~C~~Cg~~~~~~~~~~~irCp~-----Cg~rI 34 (49)
T COG1996 8 KCARCGREVELDQETRGIRCPY-----CGSRI 34 (49)
T ss_pred EhhhcCCeeehhhccCceeCCC-----CCcEE
Confidence 4777776666555556777777 77443
No 69
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=23.81 E-value=48 Score=24.71 Aligned_cols=32 Identities=28% Similarity=0.505 Sum_probs=22.8
Q ss_pred CcccccccCCCCCCCCCCcCCCCCCccccChhhh
Q psy6242 96 EPICLGCHKPLNPNLADNARCPRCFWPACSARCS 129 (541)
Q Consensus 96 ~~~C~~C~~~~~~~~~~~~~C~~C~~~yCS~~C~ 129 (541)
...|..|..++... .+.+.|+.|+.||= ++|.
T Consensus 5 ~~~C~~Cg~~~~~~-dDiVvCp~CgapyH-R~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG-DDIVVCPECGAPYH-RDCW 36 (54)
T ss_pred CccChhhCCcccCC-CCEEECCCCCCccc-HHHH
Confidence 36899999888532 45789999988753 3454
No 70
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=23.68 E-value=61 Score=24.58 Aligned_cols=47 Identities=15% Similarity=0.277 Sum_probs=26.1
Q ss_pred eccCCCCCCccccccccccccccCCCCCceeeecCCC--CCCCCCcccCcCcCc
Q psy6242 310 SCERCSDPTELGTYFSAMKCLNEHKDQGDCWILPVNP--LDNDSDWTCGSCSAR 361 (541)
Q Consensus 310 ~C~rC~~~~e~~~~l~~~~C~~~~~~~C~g~~lp~~~--~~~~~~w~C~~C~~~ 361 (541)
.|..|-..-..+.....+.||+ |+..++---. -.....++|.+||..
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPn-----CGe~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPN-----CGEVEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eeccCCCEeccCCceeEeeCCC-----CCceeeehhhhHHHcCCceECCCcCcc
Confidence 4667766554455557788887 8733321100 011346678888754
No 71
>KOG1085|consensus
Probab=23.64 E-value=35 Score=34.18 Aligned_cols=35 Identities=17% Similarity=0.104 Sum_probs=29.3
Q ss_pred ccCCCCCCccccCCcccchhhccccCCCCCccccccC
Q psy6242 48 KPKCKKLPYEIKSSPLLGRYLQATLDLHPGDRIARES 84 (541)
Q Consensus 48 k~~C~~~~~~i~~s~~~GR~l~A~~~i~~Ge~I~~e~ 84 (541)
+..|. .+.+..-..+|||++|++.++.||+|..-.
T Consensus 252 ~g~~e--gl~~~~~dgKGRGv~a~~~F~rgdFVVEY~ 286 (392)
T KOG1085|consen 252 KGTNE--GLLEVYKDGKGRGVRAKVNFERGDFVVEYR 286 (392)
T ss_pred hcccc--ceeEEeeccccceeEeecccccCceEEEEe
Confidence 45676 777788888999999999999999987653
No 72
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=23.53 E-value=52 Score=23.30 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=7.5
Q ss_pred CcccCcCcCcc
Q psy6242 352 DWTCGSCSARL 362 (541)
Q Consensus 352 ~w~C~~C~~~~ 362 (541)
.+.|..||..+
T Consensus 21 ~~~Cp~CG~~~ 31 (46)
T PRK00398 21 GVRCPYCGYRI 31 (46)
T ss_pred ceECCCCCCeE
Confidence 56777777654
No 73
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=23.48 E-value=35 Score=22.97 Aligned_cols=32 Identities=22% Similarity=0.473 Sum_probs=18.7
Q ss_pred ccccccCCCCCce-eeecCCCCC-CCCCcccCcCcCccC
Q psy6242 327 MKCLNEHKDQGDC-WILPVNPLD-NDSDWTCGSCSARLN 363 (541)
Q Consensus 327 ~~C~~~~~~~C~g-~~lp~~~~~-~~~~w~C~~C~~~~~ 363 (541)
+.|+. |+. +-++.+.+. ......|.+|+..+.
T Consensus 3 ~~CP~-----C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPN-----CKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCC-----CCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 56777 873 334433322 233578999988764
No 74
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=23.07 E-value=50 Score=19.91 Aligned_cols=21 Identities=29% Similarity=0.700 Sum_probs=14.4
Q ss_pred ccccccCCCCCCCCCCcCCCCCCc
Q psy6242 98 ICLGCHKPLNPNLADNARCPRCFW 121 (541)
Q Consensus 98 ~C~~C~~~~~~~~~~~~~C~~C~~ 121 (541)
.|.+|...+.. +...|+.|+.
T Consensus 1 ~Cp~CG~~~~~---~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIED---DAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCC---cCcchhhhCC
Confidence 37788887764 3566887775
No 75
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.05 E-value=78 Score=24.28 Aligned_cols=40 Identities=10% Similarity=0.204 Sum_probs=26.4
Q ss_pred ccccccccccccCCCCCceeeecCCCCCCCCCcccCcCcCccCHHHHH
Q psy6242 321 GTYFSAMKCLNEHKDQGDCWILPVNPLDNDSDWTCGSCSARLNARDVH 368 (541)
Q Consensus 321 ~~~l~~~~C~~~~~~~C~g~~lp~~~~~~~~~w~C~~C~~~~~~~~v~ 368 (541)
+.+.++-.|+. |+..... ......|.|..||...+.+...
T Consensus 23 ~~~~TSq~C~~-----CG~~~~~---~~~~r~~~C~~Cg~~~~rD~na 62 (69)
T PF07282_consen 23 DEAYTSQTCPR-----CGHRNKK---RRSGRVFTCPNCGFEMDRDVNA 62 (69)
T ss_pred CCCCCccCccC-----ccccccc---ccccceEEcCCCCCEECcHHHH
Confidence 34447778887 8644322 1224689999999998866544
No 76
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=22.28 E-value=56 Score=22.46 Aligned_cols=24 Identities=25% Similarity=0.570 Sum_probs=17.0
Q ss_pred cccccCCCCCCCCCCcCCCCCCccccC
Q psy6242 99 CLGCHKPLNPNLADNARCPRCFWPACS 125 (541)
Q Consensus 99 C~~C~~~~~~~~~~~~~C~~C~~~yCS 125 (541)
|+.|-+...- ..+.|..|+..||+
T Consensus 1 C~~C~~~~~l---~~f~C~~C~~~FC~ 24 (39)
T smart00154 1 CHFCRKKVGL---TGFKCRHCGNLFCG 24 (39)
T ss_pred CcccCCcccc---cCeECCccCCcccc
Confidence 5566665432 14789999999997
No 77
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=22.13 E-value=1.1e+02 Score=22.34 Aligned_cols=28 Identities=14% Similarity=0.426 Sum_probs=20.2
Q ss_pred ccCcCcCccCHHHHHHHHHHHHHHHHHH
Q psy6242 354 TCGSCSARLNARDVHLVTSQLGEQVDKL 381 (541)
Q Consensus 354 ~C~~C~~~~~~~~v~~~l~~~~~~~~~~ 381 (541)
.|..|+..++.+.-..++.....++..+
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~~~i~~~ 49 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYKSEIEEL 49 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHhh
Confidence 7999999999888888888888777765
No 78
>KOG4850|consensus
Probab=21.96 E-value=32 Score=31.31 Aligned_cols=19 Identities=21% Similarity=0.537 Sum_probs=16.6
Q ss_pred CcCCCCCCccccChhhhcc
Q psy6242 113 NARCPRCFWPACSARCSGL 131 (541)
Q Consensus 113 ~~~C~~C~~~yCS~~C~~~ 131 (541)
.+.|+.|+..-|+.+|+..
T Consensus 149 ~Y~C~~CGSTkCG~~CR~n 167 (190)
T KOG4850|consen 149 HYPCKQCGSTKCGIGCRQN 167 (190)
T ss_pred eeccccccccccccccccc
Confidence 3789999999999999873
No 79
>KOG4215|consensus
Probab=21.53 E-value=29 Score=36.02 Aligned_cols=37 Identities=27% Similarity=0.510 Sum_probs=29.9
Q ss_pred ccccccccccCCc------CCCCccCcccccCCchhhhhcccccccCCC
Q psy6242 10 EELMRCAVCRETA------LHKCSACKEVAYCGKQHQKEHWKLHKPKCK 52 (541)
Q Consensus 10 ~~~~~C~~C~~~~------~~~Cs~C~~v~YCs~~hQ~~~w~~Hk~~C~ 52 (541)
.....|++||-++ ..+|.+||--+--|. |+.|+..|.
T Consensus 17 ~~~~~CaICGDkaTGKHYGA~SCdGCKGFFRRSV------rk~~~YtCR 59 (432)
T KOG4215|consen 17 GVAEFCAICGDKATGKHYGAISCDGCKGFFRRSV------RKNHQYTCR 59 (432)
T ss_pred cccchhheeCCcccccccceeecCcchHHHHHHH------Hhcceeeee
Confidence 5678999999764 477999988776665 899999995
No 80
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.87 E-value=1e+02 Score=26.64 Aligned_cols=11 Identities=27% Similarity=0.432 Sum_probs=5.7
Q ss_pred cCCCHHHHHHH
Q psy6242 384 ENPNVKSLEEM 394 (541)
Q Consensus 384 ~~~~~~~le~~ 394 (541)
.++++.++++.
T Consensus 48 ~rGnlKe~e~~ 58 (113)
T PF09862_consen 48 NRGNLKEMEKE 58 (113)
T ss_pred hcCCHHHHHHH
Confidence 34566555543
No 81
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.86 E-value=54 Score=22.61 Aligned_cols=9 Identities=33% Similarity=0.959 Sum_probs=5.2
Q ss_pred eccCCCCCC
Q psy6242 310 SCERCSDPT 318 (541)
Q Consensus 310 ~C~rC~~~~ 318 (541)
+|++|..+.
T Consensus 1 ~CP~C~~~l 9 (41)
T PF13453_consen 1 KCPRCGTEL 9 (41)
T ss_pred CcCCCCccc
Confidence 467776543
No 82
>KOG3507|consensus
Probab=20.40 E-value=44 Score=25.18 Aligned_cols=26 Identities=27% Similarity=0.496 Sum_probs=18.6
Q ss_pred ccccccccccCCCCCCCCCCCCCCCC
Q psy6242 453 EPICLGCHKPLNPNLADNARCPRCFW 478 (541)
Q Consensus 453 ~~~c~ec~~~l~~~~~~~~~C~~C~w 478 (541)
--+|-+|++.......+-.+|..||+
T Consensus 20 iYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 20 IYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEEeccccccccccCCCcEehhhcch
Confidence 34788998866654444578998886
No 83
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=20.10 E-value=46 Score=26.45 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=10.9
Q ss_pred cccccccCCCCCCCCCCcCCCCCCc
Q psy6242 97 PICLGCHKPLNPNLADNARCPRCFW 121 (541)
Q Consensus 97 ~~C~~C~~~~~~~~~~~~~C~~C~~ 121 (541)
..|+.||..... ....-|+.|+.
T Consensus 10 lrC~aCf~~t~~--~~k~FCp~CGn 32 (73)
T PF08772_consen 10 LRCHACFKITKD--MTKQFCPKCGN 32 (73)
T ss_dssp EE-SSS--EES---SS--S-SSS--
T ss_pred EEccccccCcCC--CCceeCcccCC
Confidence 689999988764 34677998885
No 84
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=20.04 E-value=66 Score=22.79 Aligned_cols=31 Identities=10% Similarity=0.366 Sum_probs=19.7
Q ss_pred ccccccccccCCCCCcee-eecCCCCCCCCCcccCcCcCc
Q psy6242 323 YFSAMKCLNEHKDQGDCW-ILPVNPLDNDSDWTCGSCSAR 361 (541)
Q Consensus 323 ~l~~~~C~~~~~~~C~g~-~lp~~~~~~~~~w~C~~C~~~ 361 (541)
|-.++.||. |+.. ..... ....|+|..|++.
T Consensus 15 W~~g~~CP~-----Cg~~~~~~~~---~~~~~~C~~C~~q 46 (46)
T PF12760_consen 15 WPDGFVCPH-----CGSTKHYRLK---TRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCC-----CCCeeeEEeC---CCCeEECCCCCCc
Confidence 456788998 8742 22221 1468999999863
Done!