Query 011239
Match_columns 490
No_of_seqs 299 out of 1131
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 23:08:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011239.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011239hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4299 PHD Zn-finger protein 99.2 3.3E-12 7.1E-17 138.4 3.5 167 232-436 253-423 (613)
2 KOG1244 Predicted transcriptio 99.2 2E-12 4.2E-17 128.6 0.2 63 219-282 269-331 (336)
3 KOG0825 PHD Zn-finger protein 99.1 2.4E-11 5.2E-16 133.6 0.4 110 169-283 120-267 (1134)
4 PF07496 zf-CW: CW-type Zinc F 99.0 1.7E-10 3.8E-15 88.4 2.1 44 384-442 2-50 (50)
5 KOG1512 PHD Zn-finger protein 98.8 1.4E-09 3E-14 109.2 0.5 61 220-283 303-364 (381)
6 PF00628 PHD: PHD-finger; Int 98.7 5.4E-09 1.2E-13 79.0 1.5 48 234-281 1-50 (51)
7 KOG4443 Putative transcription 98.4 8.6E-08 1.9E-12 105.0 1.7 60 223-283 60-119 (694)
8 smart00249 PHD PHD zinc finger 98.3 5.1E-07 1.1E-11 65.2 3.3 46 234-279 1-47 (47)
9 cd04718 BAH_plant_2 BAH, or Br 98.1 1.9E-06 4.2E-11 80.0 2.9 29 256-284 1-29 (148)
10 KOG1973 Chromatin remodeling p 98.0 2.3E-06 4.9E-11 86.6 1.8 44 234-283 223-269 (274)
11 KOG0383 Predicted helicase [Ge 97.8 9.6E-06 2.1E-10 90.9 3.4 48 233-283 48-95 (696)
12 KOG1245 Chromatin remodeling c 97.7 5.9E-06 1.3E-10 98.8 -0.8 60 225-284 1101-1160(1404)
13 KOG0955 PHD finger protein BR1 97.3 0.00013 2.9E-09 85.0 2.8 51 232-284 219-271 (1051)
14 KOG0957 PHD finger protein [Ge 97.2 0.0001 2.3E-09 79.3 0.8 49 233-281 545-597 (707)
15 KOG4323 Polycomb-like PHD Zn-f 97.1 0.00018 3.9E-09 77.4 1.3 53 234-286 170-228 (464)
16 COG5034 TNG2 Chromatin remodel 96.9 0.00037 8E-09 69.8 1.9 46 233-282 222-270 (271)
17 COG5141 PHD zinc finger-contai 96.6 0.0008 1.7E-08 72.6 1.5 50 232-283 193-244 (669)
18 KOG0954 PHD finger protein [Ge 96.5 0.0011 2.3E-08 74.5 1.4 58 223-282 262-321 (893)
19 PF13831 PHD_2: PHD-finger; PD 96.3 0.0011 2.4E-08 47.9 0.1 34 245-280 2-36 (36)
20 KOG0956 PHD finger protein AF1 96.1 0.0022 4.7E-08 71.7 1.5 50 234-285 7-60 (900)
21 KOG1473 Nucleosome remodeling 95.4 0.0081 1.8E-07 70.2 2.1 48 232-282 344-391 (1414)
22 KOG1246 DNA-binding protein ju 89.1 0.27 5.9E-06 57.6 3.0 51 232-283 155-205 (904)
23 KOG1473 Nucleosome remodeling 88.1 0.12 2.6E-06 60.9 -0.7 50 232-284 428-481 (1414)
24 KOG1245 Chromatin remodeling c 87.2 0.11 2.4E-06 63.4 -1.8 36 326-363 1312-1347(1404)
25 cd05502 Bromo_tif1_like Bromod 87.2 0.094 2E-06 46.0 -1.8 48 313-363 1-49 (109)
26 cd05501 Bromo_SP100C_like Brom 84.3 0.16 3.4E-06 44.8 -1.8 44 316-363 2-46 (102)
27 KOG0956 PHD finger protein AF1 80.2 1.1 2.3E-05 51.0 2.3 51 232-282 117-180 (900)
28 cd05497 Bromo_Brdt_I_like Brom 80.0 0.19 4.2E-06 44.2 -2.9 45 319-363 9-53 (107)
29 PF12861 zf-Apc11: Anaphase-pr 77.3 1 2.2E-05 38.7 0.8 48 233-282 33-80 (85)
30 cd05494 Bromodomain_1 Bromodom 76.3 1.1 2.5E-05 39.9 0.9 34 330-363 18-51 (114)
31 KOG4443 Putative transcription 74.9 0.88 1.9E-05 51.4 -0.3 59 224-283 11-72 (694)
32 KOG4299 PHD Zn-finger protein 73.6 2.9 6.3E-05 47.1 3.3 47 233-282 48-95 (613)
33 cd05505 Bromo_WSTF_like Bromod 73.1 0.37 7.9E-06 41.8 -3.0 32 330-363 15-46 (97)
34 KOG0957 PHD finger protein [Ge 73.1 2.1 4.5E-05 47.3 2.0 50 234-283 121-180 (707)
35 PF14446 Prok-RING_1: Prokaryo 70.4 2.5 5.4E-05 33.5 1.4 32 233-264 6-38 (54)
36 KOG1474 Transcription initiati 70.2 1.2 2.6E-05 50.6 -0.6 51 313-363 219-270 (640)
37 PF15446 zf-PHD-like: PHD/FYVE 70.2 2.3 5E-05 40.9 1.4 49 234-282 1-60 (175)
38 cd05496 Bromo_WDR9_II Bromodom 69.9 0.88 1.9E-05 41.0 -1.4 34 328-363 18-51 (119)
39 PF11793 FANCL_C: FANCL C-term 69.1 0.57 1.2E-05 38.3 -2.5 50 233-282 3-64 (70)
40 PF13639 zf-RING_2: Ring finge 69.0 0.5 1.1E-05 34.6 -2.7 42 234-280 2-44 (44)
41 cd05508 Bromo_RACK7 Bromodomai 66.9 1.3 2.9E-05 38.5 -0.8 32 330-363 17-48 (99)
42 cd05507 Bromo_brd8_like Bromod 65.1 1.4 3E-05 38.5 -1.1 33 329-363 17-49 (104)
43 cd05503 Bromo_BAZ2A_B_like Bro 64.3 0.7 1.5E-05 39.7 -3.1 33 329-363 14-46 (97)
44 KOG0383 Predicted helicase [Ge 61.3 1.6 3.4E-05 50.1 -1.8 64 219-285 492-557 (696)
45 cd05504 Bromo_Acf1_like Bromod 61.0 1.2 2.6E-05 39.7 -2.3 45 317-363 13-58 (115)
46 KOG3612 PHD Zn-finger protein 60.4 14 0.0003 41.4 5.1 49 232-283 60-109 (588)
47 cd05512 Bromo_brd1_like Bromod 59.4 0.92 2E-05 39.4 -3.2 33 329-363 15-47 (98)
48 cd05513 Bromo_brd7_like Bromod 59.2 1 2.2E-05 39.2 -3.0 32 330-363 16-47 (98)
49 cd05500 Bromo_BDF1_2_I Bromodo 58.1 1.7 3.7E-05 37.7 -1.8 36 328-363 17-52 (103)
50 cd05495 Bromo_cbp_like Bromodo 55.9 2.9 6.3E-05 36.8 -0.7 33 331-363 20-52 (108)
51 PF07649 C1_3: C1-like domain; 55.5 5.1 0.00011 27.4 0.6 28 234-261 2-29 (30)
52 cd05510 Bromo_SPT7_like Bromod 52.5 2.9 6.3E-05 37.2 -1.3 31 331-363 24-54 (112)
53 cd05498 Bromo_Brdt_II_like Bro 52.2 2.1 4.4E-05 36.9 -2.3 33 331-363 19-51 (102)
54 PF13901 DUF4206: Domain of un 50.6 11 0.00023 36.9 2.2 43 232-283 152-199 (202)
55 KOG4628 Predicted E3 ubiquitin 48.1 11 0.00023 40.2 1.8 48 233-283 230-277 (348)
56 PF01448 ELM2: ELM2 domain; I 47.7 10 0.00022 29.2 1.2 14 330-343 1-14 (55)
57 cd05520 Bromo_polybromo_III Br 45.7 4.1 8.8E-05 35.7 -1.4 31 331-363 22-52 (103)
58 PF13771 zf-HC5HC2H: PHD-like 45.3 11 0.00024 31.3 1.2 29 233-264 37-68 (90)
59 cd05515 Bromo_polybromo_V Brom 45.2 4.6 0.0001 35.3 -1.2 33 329-363 20-52 (105)
60 KOG1512 PHD Zn-finger protein 44.3 8.3 0.00018 40.1 0.3 48 234-281 260-316 (381)
61 PF13832 zf-HC5HC2H_2: PHD-zin 44.3 11 0.00024 32.5 1.1 30 232-263 55-86 (110)
62 cd05528 Bromo_AAA Bromodomain; 41.1 6 0.00013 35.2 -1.1 32 330-363 18-49 (112)
63 cd05516 Bromo_SNF2L2 Bromodoma 40.7 6.5 0.00014 34.5 -0.9 33 329-363 21-53 (107)
64 cd05518 Bromo_polybromo_IV Bro 40.4 5.9 0.00013 34.7 -1.2 33 329-363 20-52 (103)
65 PF12678 zf-rbx1: RING-H2 zinc 40.4 8.2 0.00018 31.7 -0.3 30 247-280 44-73 (73)
66 cd05511 Bromo_TFIID Bromodomai 40.0 5.5 0.00012 35.3 -1.5 32 330-363 15-46 (112)
67 cd05492 Bromo_ZMYND11 Bromodom 39.3 6.9 0.00015 34.9 -1.0 61 333-395 19-83 (109)
68 cd05506 Bromo_plant1 Bromodoma 38.8 7.8 0.00017 33.1 -0.7 34 330-363 15-48 (99)
69 PF07227 DUF1423: Protein of u 38.8 31 0.00068 37.9 3.6 58 224-283 122-193 (446)
70 cd05525 Bromo_ASH1 Bromodomain 38.5 10 0.00022 33.4 0.0 33 329-363 22-54 (106)
71 cd00162 RING RING-finger (Real 37.9 8.8 0.00019 26.5 -0.5 42 235-281 2-43 (45)
72 cd05509 Bromo_gcn5_like Bromod 37.2 7 0.00015 33.5 -1.2 32 330-363 16-47 (101)
73 cd04718 BAH_plant_2 BAH, or Br 37.2 23 0.0005 33.5 2.1 17 215-231 8-24 (148)
74 cd05499 Bromo_BDF1_2_II Bromod 36.4 9.2 0.0002 33.0 -0.7 33 331-363 19-51 (102)
75 cd05517 Bromo_polybromo_II Bro 34.4 8.1 0.00018 33.8 -1.3 31 331-363 22-52 (103)
76 KOG1244 Predicted transcriptio 32.5 11 0.00023 39.1 -1.0 50 233-282 225-284 (336)
77 cd05529 Bromo_WDR9_I_like Brom 31.7 15 0.00033 33.3 -0.0 34 329-363 41-74 (128)
78 cd05519 Bromo_SNF2 Bromodomain 31.7 11 0.00024 32.6 -0.9 31 331-363 22-52 (103)
79 COG1107 Archaea-specific RecJ- 30.1 49 0.0011 37.8 3.4 38 233-284 69-106 (715)
80 PF00301 Rubredoxin: Rubredoxi 28.6 42 0.00091 25.8 1.9 17 266-283 28-44 (47)
81 KOG0320 Predicted E3 ubiquitin 27.6 27 0.00059 34.1 0.9 35 172-207 128-162 (187)
82 cd05522 Bromo_Rsc1_2_II Bromod 27.4 11 0.00024 32.9 -1.6 32 330-363 22-53 (104)
83 PF10497 zf-4CXXC_R1: Zinc-fin 27.0 26 0.00056 31.1 0.5 50 232-282 7-70 (105)
84 PF00130 C1_1: Phorbol esters/ 25.8 57 0.0012 24.4 2.2 31 233-263 12-44 (53)
85 cd05521 Bromo_Rsc1_2_I Bromodo 24.4 13 0.00028 32.8 -1.8 18 346-363 36-53 (106)
86 smart00184 RING Ring finger. E 23.4 17 0.00036 24.0 -1.0 28 235-265 1-28 (39)
87 KOG0827 Predicted E3 ubiquitin 22.0 28 0.00061 37.8 -0.2 31 173-207 5-37 (465)
88 PF05191 ADK_lid: Adenylate ki 21.9 65 0.0014 23.4 1.7 28 248-281 2-29 (36)
89 KOG0825 PHD Zn-finger protein 21.8 41 0.00088 39.6 1.0 53 167-231 210-263 (1134)
90 PHA02929 N1R/p28-like protein; 21.8 31 0.00068 34.9 0.1 34 171-207 173-211 (238)
91 cd05524 Bromo_polybromo_I Brom 21.4 16 0.00034 32.5 -1.9 18 346-363 37-54 (113)
92 PF10367 Vps39_2: Vacuolar sor 20.9 64 0.0014 27.1 1.8 31 232-263 78-108 (109)
93 KOG2164 Predicted E3 ubiquitin 20.6 33 0.00072 38.2 -0.0 47 179-243 190-236 (513)
94 PHA02929 N1R/p28-like protein; 20.2 40 0.00086 34.2 0.4 47 233-283 175-226 (238)
95 smart00297 BROMO bromo domain. 20.2 21 0.00046 30.2 -1.3 31 331-363 23-53 (107)
No 1
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.24 E-value=3.3e-12 Score=138.42 Aligned_cols=167 Identities=23% Similarity=0.372 Sum_probs=103.6
Q ss_pred cccccccccccCCCCeEEecCCCCcccccccCCC--cCCCCCCCccccccccccccccc-ccccCCCCcccccccCCCCC
Q 011239 232 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTPR--IKIVPSDEWFCHLCLKKKHKTLK-ATARKSPNIISEKGRGRNAS 308 (490)
Q Consensus 232 ~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~Pp--L~~iP~g~W~C~~C~~~~~~~~k-~~~~k~p~l~~e~~~~r~as 308 (490)
.+||..|++.|.-..++|||+|+++||++|+.|| .+.+|.|.|||+.|..+-..... .+.+..-.+.. .. ....+
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~in~~~~t~~~~~~~~~-i~-t~~~~ 330 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSVINPKMETLSNRGTVVD-IF-TQFVS 330 (613)
T ss_pred HHHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeeecccchhhhhhccchHH-HH-HHHHH
Confidence 4699999999865667999999999999999999 45799999999999876422111 11111000000 00 00111
Q ss_pred CCCCCChhhhhccc-CCCceeeeecCCCccccCCCCCCCCCCCCCCcCCCccCCCCCCCccccccccccCCccCCCceEe
Q 011239 309 AKGEPSPIELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTSECPSLHDLNSYNLSNLSSIGNWLQ 387 (490)
Q Consensus 309 ~~~~mnpie~~L~e-~~~y~~~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~se~~~L~~l~~~~~~k~~s~gnw~q 387 (490)
-....||+.+.+++ +..+|-+|..|.. -.|.++-. ++.|+...+. |......++ +++.|+-+.
T Consensus 331 ~IDs~np~q~~lPe~i~~~~~~v~~g~~------------~~~sd~~~-~~pl~~~~~~-~d~e~~e~g--~~ssg~~~~ 394 (613)
T KOG4299|consen 331 KIDSHNPIQKILPENISESFGGVSRGDD------------GQYSDTQD-EKPLDPPALI-LDGENDENG--IDSSGTELL 394 (613)
T ss_pred hhhccchhhhhCCHHHHhhccccccCCC------------CccccccC-CcCCChhhhc-ccccCCccC--CCccCcchh
Confidence 23567899999999 6777777765531 11211111 2333332221 111112222 345799999
Q ss_pred cccccCCCCCCCCcccCCCccccCcccccCCCCceecccccCCCCCCCC
Q 011239 388 CKQVLEGTGDGVDGTSCGKWRRAPLFEVQTDDWECFCAVQWDPTHADCA 436 (490)
Q Consensus 388 C~~c~~~~~~~~~~i~C~kwrr~p~~~~~~~~w~c~c~~~wdp~h~dC~ 436 (490)
|..|........-+..|. +|+.+| |.||+
T Consensus 395 ~~~c~~~~~~s~~vl~c~-----------------ye~s~~---h~dc~ 423 (613)
T KOG4299|consen 395 CGRCSKTQTESVVVLDCQ-----------------YEQSPE---HPDCK 423 (613)
T ss_pred hcccCcchhhhhhhhccc-----------------cccCCC---Ccccc
Confidence 999988555544555888 999999 99998
No 2
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.21 E-value=2e-12 Score=128.61 Aligned_cols=63 Identities=38% Similarity=0.889 Sum_probs=58.5
Q ss_pred CCCCCCCCCcccccccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCccccccccc
Q 011239 219 NDVDSGTGCSGICSRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKK 282 (490)
Q Consensus 219 e~vp~g~w~cp~c~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 282 (490)
..|..+.|+|.+| ++|.+||..+++++||+||.|+|+|||+||.|||.+.|+|.|.|..|...
T Consensus 269 ~avk~yrwqciec-k~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~~ 331 (336)
T KOG1244|consen 269 AAVKTYRWQCIEC-KYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLEE 331 (336)
T ss_pred HHHHhheeeeeec-ceeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHHH
Confidence 3455778999999 89999999999999999999999999999999999999999999999864
No 3
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.07 E-value=2.4e-11 Score=133.64 Aligned_cols=110 Identities=19% Similarity=0.450 Sum_probs=87.1
Q ss_pred cccCCccCCCCccccccCCcccccccchhhhhhccCcccccCCccccCCC-CCCCC----------C-CC----------
Q 011239 169 VDETGECSSSSAVMLETTGKDLSAKDLCISILRNEGMLERFWPTQIRSSA-NDVDS----------G-TG---------- 226 (490)
Q Consensus 169 ~~d~~eCsss~ic~~e~~ged~s~~D~C~hil~~~gll~~~~p~~~~~~~-e~vp~----------g-~w---------- 226 (490)
..+...| ++|+..+..+.++..-.|.|+||..|+.. |-+.++.|+ ++.-+ + .|
T Consensus 120 ~~~~~~C---P~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s--WsR~aqTCPiDR~EF~~v~V~eS~~~~~~vR~lP~EEs~ 194 (1134)
T KOG0825|consen 120 THVENQC---PNCLKSCNDQLEESEKHTAHYFCEECVGS--WSRCAQTCPVDRGEFGEVKVLESTGIEANVRCLPSEESE 194 (1134)
T ss_pred hhhhhhh---hHHHHHHHHHhhccccccccccHHHHhhh--hhhhcccCchhhhhhheeeeeccccccceeEecchhhhh
Confidence 3455677 99999999999999999999999999887 777666664 11100 0 01
Q ss_pred ---------C-c-----ccccccccccccccCCCCeEEecCCCCc-ccccccCCCcCCCCCCCcccccccccc
Q 011239 227 ---------C-S-----GICSRSCKICGRSETALKLLLCDDCEEA-FHVTCYTPRIKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 227 ---------~-c-----p~c~~~C~VC~~~g~~~~LL~CD~Cdr~-yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 283 (490)
. . ......|.+|+..+.++.||+||.|+.+ ||++||+|+|-++|.++|||+.|.-..
T Consensus 195 ~~~e~~~d~~~d~~~~~~~E~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 195 NILEKGGDEKQDQISGLSQEEVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLLE 267 (1134)
T ss_pred hhhhhccccccccccCcccccccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchhhh
Confidence 0 0 0012469999999999999999999999 999999999999999999999997654
No 4
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=98.99 E-value=1.7e-10 Score=88.40 Aligned_cols=44 Identities=43% Similarity=0.939 Sum_probs=29.1
Q ss_pred ceEecccccCCCCCCCCcccCCCccccCccc-----ccCCCCceecccccCCCCCCCCCCCCCC
Q 011239 384 NWLQCKQVLEGTGDGVDGTSCGKWRRAPLFE-----VQTDDWECFCAVQWDPTHADCAVPQELE 442 (490)
Q Consensus 384 nw~qC~~c~~~~~~~~~~i~C~kwrr~p~~~-----~~~~~w~c~c~~~wdp~h~dC~~P~el~ 442 (490)
+||||. .|+|||++|... .+++.|+|.+|. |+.+++|++|+|++
T Consensus 2 ~WVQCd-------------~C~KWR~lp~~~~~~~~~~~d~W~C~~n~--~~~~~sC~~pee~e 50 (50)
T PF07496_consen 2 YWVQCD-------------SCLKWRRLPEEVDPIREELPDPWYCSMNP--DPPFNSCDAPEEIE 50 (50)
T ss_dssp EEEE-T-------------TT--EEEE-CCHHCTSCCSSTT--GGGSS---CCC-STTS--SS-
T ss_pred eEEECC-------------CCCceeeCChhhCcccccCCCeEEcCCCC--CCCCCCCCCcccCC
Confidence 699999 899999999773 468899999998 78899999999974
No 5
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.77 E-value=1.4e-09 Score=109.23 Aligned_cols=61 Identities=25% Similarity=0.601 Sum_probs=54.9
Q ss_pred CCCCCCCCcccccccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCcccc-cccccc
Q 011239 220 DVDSGTGCSGICSRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCH-LCLKKK 283 (490)
Q Consensus 220 ~vp~g~w~cp~c~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~-~C~~~~ 283 (490)
.+..+.|.|.+| ..|.+|+++..++++++||.|+|+||++|+ +|..+|.|.|.|- .|....
T Consensus 303 ~~KTY~W~C~~C-~lC~IC~~P~~E~E~~FCD~CDRG~HT~CV--GL~~lP~G~WICD~~C~~~~ 364 (381)
T KOG1512|consen 303 QYKTYFWKCSSC-ELCRICLGPVIESEHLFCDVCDRGPHTLCV--GLQDLPRGEWICDMRCREAT 364 (381)
T ss_pred HHhhcchhhccc-HhhhccCCcccchheeccccccCCCCcccc--ccccccCccchhhhHHHHhc
Confidence 344678999999 799999999999999999999999999999 9999999999999 676543
No 6
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.70 E-value=5.4e-09 Score=79.02 Aligned_cols=48 Identities=33% Similarity=0.949 Sum_probs=42.5
Q ss_pred cccccccccCCCCeEEecCCCCcccccccCCCcC--CCCCCCcccccccc
Q 011239 234 SCKICGRSETALKLLLCDDCEEAFHVTCYTPRIK--IVPSDEWFCHLCLK 281 (490)
Q Consensus 234 ~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~--~iP~g~W~C~~C~~ 281 (490)
+|.+|++.+..+.||.||.|++.||..|+.|++. .++.+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 5889999888889999999999999999999877 55566999999975
No 7
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.40 E-value=8.6e-08 Score=105.01 Aligned_cols=60 Identities=35% Similarity=0.853 Sum_probs=55.5
Q ss_pred CCCCCcccccccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCcccccccccc
Q 011239 223 SGTGCSGICSRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 223 ~g~w~cp~c~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 283 (490)
.+.|.|+.| ..|..|+..+++.++++|+.|+-+||.+|..|+++.+|.|.|+|..|...+
T Consensus 60 ~~gWrC~~c-rvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c~ 119 (694)
T KOG4443|consen 60 SGGWRCPSC-RVCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTRCR 119 (694)
T ss_pred cCCcccCCc-eeeeeccccCCcccccccccccccccccccCCccccccCcccccHHHHhhh
Confidence 455999999 799999999999999999999999999999999999999999999886554
No 8
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=98.08 E-value=1.9e-06 Score=79.97 Aligned_cols=29 Identities=38% Similarity=1.021 Sum_probs=26.9
Q ss_pred cccccccCCCcCCCCCCCccccccccccc
Q 011239 256 AFHVTCYTPRIKIVPSDEWFCHLCLKKKH 284 (490)
Q Consensus 256 ~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~ 284 (490)
+||++||+|||+.+|+|+|+|+.|..+..
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~ 29 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKS 29 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCC
Confidence 69999999999999999999999997653
No 10
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.00 E-value=2.3e-06 Score=86.57 Aligned_cols=44 Identities=34% Similarity=0.847 Sum_probs=38.7
Q ss_pred cccccccccCCCCeEEecC--CC-CcccccccCCCcCCCCCCCcccccccccc
Q 011239 234 SCKICGRSETALKLLLCDD--CE-EAFHVTCYTPRIKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 234 ~C~VC~~~g~~~~LL~CD~--Cd-r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 283 (490)
+|. |...| +|+-||. |+ .+||+.|+ .|+..|.|.|||+.|....
T Consensus 223 ~Cn-qvsyg---~Mi~CDn~~C~~eWFH~~CV--GL~~~PkgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 223 ICN-QVSYG---KMIGCDNPGCPIEWFHFTCV--GLKTKPKGKWYCPRCKAEN 269 (274)
T ss_pred Eec-ccccc---cccccCCCCCCcceEEEecc--ccccCCCCcccchhhhhhh
Confidence 455 66666 8999998 99 99999999 9999999999999998754
No 11
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.84 E-value=9.6e-06 Score=90.94 Aligned_cols=48 Identities=35% Similarity=0.948 Sum_probs=44.4
Q ss_pred ccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCcccccccccc
Q 011239 233 RSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 233 ~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 283 (490)
..|.+|+++| .+|+||.|+.+||.+|+.||+...|.++|.|+.|....
T Consensus 48 e~c~ic~~~g---~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~ 95 (696)
T KOG0383|consen 48 EACRICADGG---ELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCPK 95 (696)
T ss_pred hhhhhhcCCC---cEEEeccccHHHHHHccCCCCCcCCccceeeeeeccCC
Confidence 6799999999 89999999999999999999999999999999995443
No 12
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=97.72 E-value=5.9e-06 Score=98.81 Aligned_cols=60 Identities=33% Similarity=0.829 Sum_probs=53.9
Q ss_pred CCCcccccccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCccccccccccc
Q 011239 225 TGCSGICSRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKH 284 (490)
Q Consensus 225 ~w~cp~c~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~ 284 (490)
.|.-....-.|.+|...+..+.|+.||.|..+||++|+.|.+..+|.|+|+|+.|+..+.
T Consensus 1101 ~w~~s~~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1101 KWDRSAVNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hhccccchhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 365555567899999999999999999999999999999999999999999999998764
No 13
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.28 E-value=0.00013 Score=84.98 Aligned_cols=51 Identities=33% Similarity=0.886 Sum_probs=45.1
Q ss_pred cccccccccccCC--CCeEEecCCCCcccccccCCCcCCCCCCCccccccccccc
Q 011239 232 SRSCKICGRSETA--LKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKH 284 (490)
Q Consensus 232 ~~~C~VC~~~g~~--~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~ 284 (490)
+.+|.||.++.-. +.+|+||.|+.++|+.|+ .+.-+|+|.|+|..|.....
T Consensus 219 D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cy--gi~~ipeg~WlCr~Cl~s~~ 271 (1051)
T KOG0955|consen 219 DAVCCICLDGECQNSNVIVFCDGCNLAVHQECY--GIPFIPEGQWLCRRCLQSPQ 271 (1051)
T ss_pred CccceeecccccCCCceEEEcCCCcchhhhhcc--CCCCCCCCcEeehhhccCcC
Confidence 5789999988755 799999999999999999 47789999999999987653
No 14
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=97.20 E-value=0.0001 Score=79.31 Aligned_cols=49 Identities=35% Similarity=0.839 Sum_probs=44.6
Q ss_pred ccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCC----Ccccccccc
Q 011239 233 RSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSD----EWFCHLCLK 281 (490)
Q Consensus 233 ~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g----~W~C~~C~~ 281 (490)
-.|.+|.+..+...++.||.|...||+.||.|||+.+|.. -|.|..|-.
T Consensus 545 ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk 597 (707)
T KOG0957|consen 545 YSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDK 597 (707)
T ss_pred eeeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccccc
Confidence 4699999998888999999999999999999999999986 499999943
No 15
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.09 E-value=0.00018 Score=77.42 Aligned_cols=53 Identities=34% Similarity=0.834 Sum_probs=42.4
Q ss_pred ccccccccc--CCCCeEEecCCCCcccccccCCCcCCC----CCCCccccccccccccc
Q 011239 234 SCKICGRSE--TALKLLLCDDCEEAFHVTCYTPRIKIV----PSDEWFCHLCLKKKHKT 286 (490)
Q Consensus 234 ~C~VC~~~g--~~~~LL~CD~Cdr~yH~~Cl~PpL~~i----P~g~W~C~~C~~~~~~~ 286 (490)
.|.||+.++ ..+.||.|+.|...||..|+.|+++.. |..+|||..|.......
T Consensus 170 qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~ 228 (464)
T KOG4323|consen 170 QCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKV 228 (464)
T ss_pred eeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhhc
Confidence 488877544 455999999999999999999987754 56689999998765443
No 16
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.95 E-value=0.00037 Score=69.82 Aligned_cols=46 Identities=30% Similarity=0.865 Sum_probs=35.9
Q ss_pred ccccccccccCCCCeEEecC--CCC-cccccccCCCcCCCCCCCccccccccc
Q 011239 233 RSCKICGRSETALKLLLCDD--CEE-AFHVTCYTPRIKIVPSDEWFCHLCLKK 282 (490)
Q Consensus 233 ~~C~VC~~~g~~~~LL~CD~--Cdr-~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 282 (490)
-+| .|++.. -.+|+-||+ |.+ +||+.|+ +|++.|+|.|||+.|+..
T Consensus 222 lYC-fCqqvS-yGqMVaCDn~nCkrEWFH~~CV--GLk~pPKG~WYC~eCk~~ 270 (271)
T COG5034 222 LYC-FCQQVS-YGQMVACDNANCKREWFHLECV--GLKEPPKGKWYCPECKKA 270 (271)
T ss_pred eEE-Eecccc-cccceecCCCCCchhheecccc--ccCCCCCCcEeCHHhHhc
Confidence 344 466532 128999995 874 5899999 999999999999999863
No 17
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=96.62 E-value=0.0008 Score=72.59 Aligned_cols=50 Identities=28% Similarity=0.861 Sum_probs=43.9
Q ss_pred cccccccccccC--CCCeEEecCCCCcccccccCCCcCCCCCCCcccccccccc
Q 011239 232 SRSCKICGRSET--ALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 232 ~~~C~VC~~~g~--~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 283 (490)
++.|.+|.+.+. .+.+++||+|+-+-|..|. ++..+|+|.|+|..|....
T Consensus 193 d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CY--GI~f~peG~WlCrkCi~~~ 244 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCDGCEICVHQSCY--GIQFLPEGFWLCRKCIYGE 244 (669)
T ss_pred hhhhHhccccccCCcceEEEecCcchhhhhhcc--cceecCcchhhhhhhcccc
Confidence 468999998764 4689999999999999999 8889999999999997654
No 18
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.48 E-value=0.0011 Score=74.48 Aligned_cols=58 Identities=29% Similarity=0.740 Sum_probs=48.2
Q ss_pred CCCCCcccccccccccccccC--CCCeEEecCCCCcccccccCCCcCCCCCCCccccccccc
Q 011239 223 SGTGCSGICSRSCKICGRSET--ALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKK 282 (490)
Q Consensus 223 ~g~w~cp~c~~~C~VC~~~g~--~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 282 (490)
+|-..+-+.+-.|.||..++. .++|++||.|.-..|+.|. +|.++|+|.|.|..|.-.
T Consensus 262 eglgie~dedviCDvCrspD~e~~neMVfCd~Cn~cVHqaCy--GIle~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 262 EGLGIEYDEDVICDVCRSPDSEEANEMVFCDKCNICVHQACY--GILEVPEGPWLCRTCALG 321 (893)
T ss_pred ccceeeccccceeceecCCCccccceeEEeccchhHHHHhhh--ceeecCCCCeeehhcccc
Confidence 344455555678999998743 3599999999999999999 999999999999999754
No 19
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.27 E-value=0.0011 Score=47.88 Aligned_cols=34 Identities=41% Similarity=1.092 Sum_probs=20.7
Q ss_pred CCeEEecCCCCcccccccCCCcCCCCCC-Cccccccc
Q 011239 245 LKLLLCDDCEEAFHVTCYTPRIKIVPSD-EWFCHLCL 280 (490)
Q Consensus 245 ~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g-~W~C~~C~ 280 (490)
+.||.|+.|.-..|..|. ++..+|.+ +|+|..|+
T Consensus 2 n~ll~C~~C~v~VH~~CY--Gv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCY--GVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHH--T-SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhC--CcccCCCCCcEECCcCC
Confidence 479999999999999999 88888887 89999884
No 20
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=96.15 E-value=0.0022 Score=71.65 Aligned_cols=50 Identities=34% Similarity=0.897 Sum_probs=41.3
Q ss_pred ccccccccc--CCCCeEEecC--CCCcccccccCCCcCCCCCCCcccccccccccc
Q 011239 234 SCKICGRSE--TALKLLLCDD--CEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKHK 285 (490)
Q Consensus 234 ~C~VC~~~g--~~~~LL~CD~--Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~~ 285 (490)
-|-||-+.. .++.|+.||+ |.-+.|.-|+ .+.++|.|.|||..|....+.
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCY--GIvqVPtGpWfCrKCesqera 60 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACY--GIVQVPTGPWFCRKCESQERA 60 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcc--eeEecCCCchhhhhhhhhhhh
Confidence 366887633 3669999995 9999999999 899999999999999875433
No 21
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=95.36 E-value=0.0081 Score=70.22 Aligned_cols=48 Identities=29% Similarity=0.710 Sum_probs=44.9
Q ss_pred cccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCccccccccc
Q 011239 232 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKK 282 (490)
Q Consensus 232 ~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 282 (490)
++.|.+|++.+ .++||..|++.||+.|+.||+.++|+..|-|-.|..-
T Consensus 344 ddhcrf~~d~~---~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~h 391 (1414)
T KOG1473|consen 344 DDHCRFCHDLG---DLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIH 391 (1414)
T ss_pred cccccccCccc---ceeecccCCceEEeeecCCccccCCCccchhhhhhhh
Confidence 57899999999 8999999999999999999999999999999999743
No 22
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=89.12 E-value=0.27 Score=57.60 Aligned_cols=51 Identities=33% Similarity=0.977 Sum_probs=45.2
Q ss_pred cccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCcccccccccc
Q 011239 232 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 232 ~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 283 (490)
...|..|..+..+ .++.|+.|...||.+|..|++..++.|+|.|+.|....
T Consensus 155 ~~~~~~~~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 (904)
T KOG1246|consen 155 YPQCNTCSKGKEE-KLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIPTP 205 (904)
T ss_pred chhhhccccCCCc-cceecccccCcccccccCCCCCcCCcCcccCCcccccc
Confidence 3568999988877 55599999999999999999999999999999998763
No 23
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=88.13 E-value=0.12 Score=60.95 Aligned_cols=50 Identities=22% Similarity=0.359 Sum_probs=40.8
Q ss_pred cccccccccccCCCCeEEecC-CCCcccc-cccCC--CcCCCCCCCccccccccccc
Q 011239 232 SRSCKICGRSETALKLLLCDD-CEEAFHV-TCYTP--RIKIVPSDEWFCHLCLKKKH 284 (490)
Q Consensus 232 ~~~C~VC~~~g~~~~LL~CD~-Cdr~yH~-~Cl~P--pL~~iP~g~W~C~~C~~~~~ 284 (490)
.+.|.+|+..+ .+|+|+. |+..||+ .|++- --..++++-|+|+.|..++.
T Consensus 428 ~rrl~Ie~~de---t~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~rqM 481 (1414)
T KOG1473|consen 428 SRRLRIEGMDE---TLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERREEIIRQM 481 (1414)
T ss_pred eeeeEEecCCC---cEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHHHHHHhc
Confidence 36788888766 8999998 9999998 99973 22358999999999987654
No 24
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=87.20 E-value=0.11 Score=63.39 Aligned_cols=36 Identities=11% Similarity=0.082 Sum_probs=28.4
Q ss_pred ceeeeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 326 YTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 326 y~~~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
-...+.-..+|.++|.. .-++.|++||++||+|.+.
T Consensus 1312 e~~~~~~awPFlepVn~--~~vp~Y~~IIk~Pmdl~ti 1347 (1404)
T KOG1245|consen 1312 ELVVHKAAWPFLEPVNP--KEVPDYYDIIKKPMDLSTI 1347 (1404)
T ss_pred HHHHhhhcchhhccCCh--hhcccHHHHhcChhHHHHH
Confidence 33445677899999964 3678999999999999884
No 25
>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=87.16 E-value=0.094 Score=46.01 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=36.8
Q ss_pred CChhhhhccc-CCCceeeeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 313 PSPIELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 313 mnpie~~L~e-~~~y~~~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
|++.++++|+ +...+.....+.+|..+|+. ..++|+++|.+||+|.+-
T Consensus 1 ~~~~~~~~c~~il~~l~~~~~s~~F~~pv~~---~~p~Y~~iI~~PmdL~tI 49 (109)
T cd05502 1 LSPIDQRKCERLLLELYCHELSLPFHEPVSP---SVPNYYKIIKTPMDLSLI 49 (109)
T ss_pred CCHHHHHHHHHHHHHHHhCCCChhhcCCCCC---CCCCHHHHCCCCccHHHH
Confidence 3566777777 44444556788899999976 578999999999998864
No 26
>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=84.31 E-value=0.16 Score=44.80 Aligned_cols=44 Identities=16% Similarity=0.092 Sum_probs=30.5
Q ss_pred hhhhccc-CCCceeeeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 316 IELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 316 ie~~L~e-~~~y~~~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
.+++.|+ +++.+.....+..|.. .|. ..++|+++|++||||.+-
T Consensus 2 ~~l~~ce~il~~l~~~~~s~~f~~-~p~---~~pdY~~iIk~PMDL~tI 46 (102)
T cd05501 2 EELLKCEFLLLKVYCMSKSGFFIS-KPY---YIRDYCQGIKEPMWLNKV 46 (102)
T ss_pred HHHHHHHHHHHHHHhCcccccccC-CCC---CCCchHHHcCCCCCHHHH
Confidence 4566777 4555555555555544 343 678999999999999884
No 27
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=80.19 E-value=1.1 Score=51.03 Aligned_cols=51 Identities=27% Similarity=0.688 Sum_probs=35.1
Q ss_pred cccccccccccCCCCe-----EEec--CCCCcccccccCC-CcCCCC-----CCCccccccccc
Q 011239 232 SRSCKICGRSETALKL-----LLCD--DCEEAFHVTCYTP-RIKIVP-----SDEWFCHLCLKK 282 (490)
Q Consensus 232 ~~~C~VC~~~g~~~~L-----L~CD--~Cdr~yH~~Cl~P-pL~~iP-----~g~W~C~~C~~~ 282 (490)
++.|-+|...|.+.+. +-|. +|.++||..|-.- .|.-.. +.--||-.|..-
T Consensus 117 nKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~H 180 (900)
T KOG0956|consen 117 NKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYH 180 (900)
T ss_pred cceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHH
Confidence 4779999988876533 5564 6889999999853 233222 234799999754
No 28
>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=80.04 E-value=0.19 Score=44.22 Aligned_cols=45 Identities=13% Similarity=0.098 Sum_probs=31.3
Q ss_pred hcccCCCceeeeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 319 MLTSTVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 319 ~L~e~~~y~~~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
.+..++..+...+.+.+|..+|..--...++|+++|++||||.+-
T Consensus 9 ~~~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI 53 (107)
T cd05497 9 LLKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTI 53 (107)
T ss_pred HHHHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHH
Confidence 333333334456778899999964112367999999999998874
No 29
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=77.33 E-value=1 Score=38.73 Aligned_cols=48 Identities=19% Similarity=0.468 Sum_probs=35.7
Q ss_pred ccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCccccccccc
Q 011239 233 RSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKK 282 (490)
Q Consensus 233 ~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 282 (490)
..|..|.-+|+.-.++++. |...||+.|+.--|.+-. ..=.||-|+..
T Consensus 33 g~Cp~Ck~Pgd~Cplv~g~-C~H~FH~hCI~kWl~~~~-~~~~CPmCR~~ 80 (85)
T PF12861_consen 33 GCCPDCKFPGDDCPLVWGK-CSHNFHMHCILKWLSTQS-SKGQCPMCRQP 80 (85)
T ss_pred cCCCCccCCCCCCceeecc-CccHHHHHHHHHHHcccc-CCCCCCCcCCe
Confidence 3467778787666666555 999999999987777642 24589999864
No 30
>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Probab=76.32 E-value=1.1 Score=39.95 Aligned_cols=34 Identities=9% Similarity=0.006 Sum_probs=26.4
Q ss_pred eecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 330 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 330 Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
...+.+|..+|+.-...+++|+++|++||+|.+-
T Consensus 18 ~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti 51 (114)
T cd05494 18 NEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTK 51 (114)
T ss_pred CCCCCCcCCCCCchhcCCCChhhhcCCCCChHHH
Confidence 3467789999954223568999999999999884
No 31
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=74.88 E-value=0.88 Score=51.40 Aligned_cols=59 Identities=31% Similarity=0.654 Sum_probs=42.3
Q ss_pred CCCCccccccccccccccc--CCCCeEEecCCCCcccccccCCCcCCC-CCCCcccccccccc
Q 011239 224 GTGCSGICSRSCKICGRSE--TALKLLLCDDCEEAFHVTCYTPRIKIV-PSDEWFCHLCLKKK 283 (490)
Q Consensus 224 g~w~cp~c~~~C~VC~~~g--~~~~LL~CD~Cdr~yH~~Cl~PpL~~i-P~g~W~C~~C~~~~ 283 (490)
++.++..| ..|.+|+..| .+..|+.|..|...||.+|+.-.+... -.+-|.|+.|+.-.
T Consensus 11 ~~~~~~~~-~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 11 SDKAIIVC-LMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred cchhhhhh-hhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 34444433 5788888755 356799999999999999997544433 23449999998753
No 32
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=73.65 E-value=2.9 Score=47.10 Aligned_cols=47 Identities=36% Similarity=0.808 Sum_probs=39.8
Q ss_pred ccccccccccCCCCeEEecCCCCcccccccCCCcCC-CCCCCccccccccc
Q 011239 233 RSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKI-VPSDEWFCHLCLKK 282 (490)
Q Consensus 233 ~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~-iP~g~W~C~~C~~~ 282 (490)
..|.+|..+| .+++|+.|+.+||..|..+++.. .+.+.|.|..|...
T Consensus 48 ts~~~~~~~g---n~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~~ 95 (613)
T KOG4299|consen 48 TSCGICKSGG---NLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPKG 95 (613)
T ss_pred hhcchhhhcC---CccccccCccccchhccCcccCcccccccccccCCCcc
Confidence 4799999999 79999999999999999998873 33457999988764
No 33
>cd05505 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=73.13 E-value=0.37 Score=41.80 Aligned_cols=32 Identities=16% Similarity=0.297 Sum_probs=25.7
Q ss_pred eecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 330 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 330 Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
.+.+.+|..+|.. ...++|+++|++||+|.+-
T Consensus 15 ~~~s~~F~~pv~~--~~~pdY~~iIk~PmDL~tI 46 (97)
T cd05505 15 YRFSWPFREPVTA--DEAEDYKKVITNPMDLQTM 46 (97)
T ss_pred CCCcccccCCCCh--hhcccHHHHcCCcCCHHHH
Confidence 4567789999863 3568999999999999874
No 34
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=73.06 E-value=2.1 Score=47.29 Aligned_cols=50 Identities=34% Similarity=0.743 Sum_probs=37.5
Q ss_pred ccccccccc--CCCCeEEecCCCCcccccccCCC-cCCCCCC-------Ccccccccccc
Q 011239 234 SCKICGRSE--TALKLLLCDDCEEAFHVTCYTPR-IKIVPSD-------EWFCHLCLKKK 283 (490)
Q Consensus 234 ~C~VC~~~g--~~~~LL~CD~Cdr~yH~~Cl~Pp-L~~iP~g-------~W~C~~C~~~~ 283 (490)
.|-||-+.. +.+++|.||.|+-..|-.|+.-- -.+||.| .|||-.|+..-
T Consensus 121 iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gv 180 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGV 180 (707)
T ss_pred EEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcCC
Confidence 688998643 45689999999999999999421 1234544 69999998764
No 35
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=70.40 E-value=2.5 Score=33.54 Aligned_cols=32 Identities=22% Similarity=0.842 Sum_probs=27.2
Q ss_pred ccccccccccC-CCCeEEecCCCCcccccccCC
Q 011239 233 RSCKICGRSET-ALKLLLCDDCEEAFHVTCYTP 264 (490)
Q Consensus 233 ~~C~VC~~~g~-~~~LL~CD~Cdr~yH~~Cl~P 264 (490)
..|.+|+..-. .+.++.|..|...||-.|+..
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 46999998653 668999999999999999954
No 36
>KOG1474 consensus Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins [Transcription]
Probab=70.24 E-value=1.2 Score=50.64 Aligned_cols=51 Identities=10% Similarity=-0.046 Sum_probs=36.6
Q ss_pred CChhhhhccc-CCCceeeeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 313 PSPIELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 313 mnpie~~L~e-~~~y~~~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
+..-.++.|. ++.-+..++-+.+|+++|-.-.-.+.+|+.||++||||.|-
T Consensus 219 ~~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTI 270 (640)
T KOG1474|consen 219 LTVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTI 270 (640)
T ss_pred ccHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHH
Confidence 3344444444 45566667778999999954334567999999999999985
No 37
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=70.20 E-value=2.3 Score=40.93 Aligned_cols=49 Identities=29% Similarity=0.765 Sum_probs=33.3
Q ss_pred cccccccc---cCCCCeEEecCCCCcccccccCCCc------CCCCCCC--ccccccccc
Q 011239 234 SCKICGRS---ETALKLLLCDDCEEAFHVTCYTPRI------KIVPSDE--WFCHLCLKK 282 (490)
Q Consensus 234 ~C~VC~~~---g~~~~LL~CD~Cdr~yH~~Cl~PpL------~~iP~g~--W~C~~C~~~ 282 (490)
.|.+|+.. .+-..|+.|-+|-.+||..|+-|.- +.+-.+. -.|..|+..
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~ 60 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGI 60 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcCh
Confidence 37788542 2345899999999999999998732 2333332 457777654
No 38
>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=69.86 E-value=0.88 Score=41.03 Aligned_cols=34 Identities=12% Similarity=0.122 Sum_probs=27.0
Q ss_pred eeeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 328 TSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 328 ~~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
..++.+.+|..+|.. ...++|+++|++||||.+-
T Consensus 18 ~~~~~s~~F~~PVd~--~~~pdY~~iIk~PmDL~tI 51 (119)
T cd05496 18 WDCEDSEPFRQPVDL--LKYPDYRDIIDTPMDLGTV 51 (119)
T ss_pred HhCCccccccCCCCh--hhcCcHHHHhCCcccHHHH
Confidence 345667899999964 2468999999999999874
No 39
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=69.13 E-value=0.57 Score=38.33 Aligned_cols=50 Identities=20% Similarity=0.455 Sum_probs=20.0
Q ss_pred ccccccccccC---CCCeEEec--CCCCcccccccCCCcCCCCC-------CCccccccccc
Q 011239 233 RSCKICGRSET---ALKLLLCD--DCEEAFHVTCYTPRIKIVPS-------DEWFCHLCLKK 282 (490)
Q Consensus 233 ~~C~VC~~~g~---~~~LL~CD--~Cdr~yH~~Cl~PpL~~iP~-------g~W~C~~C~~~ 282 (490)
..|.+|..... ....+.|+ .|...||..||.-.+...+. -.+-||.|...
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCe
Confidence 35888886432 23458898 89999999999753332221 13568888764
No 40
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=68.96 E-value=0.5 Score=34.59 Aligned_cols=42 Identities=26% Similarity=0.540 Sum_probs=28.4
Q ss_pred cccccccccC-CCCeEEecCCCCcccccccCCCcCCCCCCCccccccc
Q 011239 234 SCKICGRSET-ALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCL 280 (490)
Q Consensus 234 ~C~VC~~~g~-~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~ 280 (490)
.|.+|...-. .+.++... |...||..|+..-+..- -.||.|+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~----~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRN----NSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHS----SB-TTTH
T ss_pred CCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhC----CcCCccC
Confidence 5888887553 33455455 99999999997765542 3788875
No 41
>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=66.87 E-value=1.3 Score=38.53 Aligned_cols=32 Identities=13% Similarity=0.061 Sum_probs=25.9
Q ss_pred eecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 330 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 330 Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
...+.+|..+|.. ...++|+++|++||||.+-
T Consensus 17 ~~~s~~F~~PV~~--~~~pdY~~iIk~PmDL~tI 48 (99)
T cd05508 17 QPGAEPFLKPVDL--EQFPDYAQYVFKPMDLSTL 48 (99)
T ss_pred CcCcchhcCCCCh--hhCCCHHHHcCCCCCHHHH
Confidence 3566789999965 3568899999999999884
No 42
>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=65.11 E-value=1.4 Score=38.48 Aligned_cols=33 Identities=18% Similarity=0.194 Sum_probs=26.5
Q ss_pred eeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 329 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 329 ~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
..+.+.+|..+|.. ...++|+++|++||||.+-
T Consensus 17 ~~~~a~~F~~pV~~--~~~p~Y~~iIk~PmDL~tI 49 (104)
T cd05507 17 SHRYASVFLKPVTE--DIAPGYHSVVYRPMDLSTI 49 (104)
T ss_pred cCCCCHhhcCCCCc--cccCCHHHHhCCCcCHHHH
Confidence 45667789999975 3567899999999998874
No 43
>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=64.26 E-value=0.7 Score=39.75 Aligned_cols=33 Identities=9% Similarity=0.085 Sum_probs=25.6
Q ss_pred eeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 329 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 329 ~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
....+..|..+|.. ...++|+++|++||+|.+-
T Consensus 14 ~~~~~~~F~~pv~~--~~~p~Y~~iIk~PmdL~tI 46 (97)
T cd05503 14 AHEDAWPFLEPVNT--KLVPGYRKIIKKPMDFSTI 46 (97)
T ss_pred cCCCchhhcCCCCc--cccCCHHHHhCCCCCHHHH
Confidence 34566789988864 2467899999999998874
No 44
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=61.35 E-value=1.6 Score=50.09 Aligned_cols=64 Identities=20% Similarity=0.145 Sum_probs=51.1
Q ss_pred CCCCCCCCCccc-ccccccccccccCCCCeEEecCCCCcccccccCC-CcCCCCCCCcccccccccccc
Q 011239 219 NDVDSGTGCSGI-CSRSCKICGRSETALKLLLCDDCEEAFHVTCYTP-RIKIVPSDEWFCHLCLKKKHK 285 (490)
Q Consensus 219 e~vp~g~w~cp~-c~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~P-pL~~iP~g~W~C~~C~~~~~~ 285 (490)
+++.+-.|+-.+ -+..|..|.... ..+.|+.|-|.||..|+.| |++..+.|.|-|+.|..+..+
T Consensus 492 ~~~~~~~~f~e~~~d~~~~~~~~~l---~~l~~p~~lrr~k~d~l~~~P~Kte~i~~~~~~~~Q~~~yk 557 (696)
T KOG0383|consen 492 GRFNSLEWFLEEFHDISCEEQIKKL---HLLLCPHMLRRLKLDVLKPMPLKTELIGRVELSPCQKKYYK 557 (696)
T ss_pred ccccchhhhhhhcchhhHHHHHHhh---ccccCchhhhhhhhhhccCCCccceeEEEEecCHHHHHHHH
Confidence 344433454432 256799999988 7999999999999999999 999999999999999876533
No 45
>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=60.99 E-value=1.2 Score=39.69 Aligned_cols=45 Identities=11% Similarity=0.064 Sum_probs=30.7
Q ss_pred hhhccc-CCCceeeeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 317 ELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 317 e~~L~e-~~~y~~~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
+...+. +..-+.....+..|..+|.. ...++|+++|.+||+|.+-
T Consensus 13 ~~~~c~~il~~l~~~~~s~~F~~pvd~--~~~pdY~~vI~~PmDL~tI 58 (115)
T cd05504 13 NLSALEQLLVEIVKHKDSWPFLRPVSK--IEVPDYYDIIKKPMDLGTI 58 (115)
T ss_pred HHHHHHHHHHHHHhCCCchhhcCCCCc--cccccHHHHhcCcccHHHH
Confidence 333333 33333345667789999864 3568999999999998864
No 46
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=60.39 E-value=14 Score=41.43 Aligned_cols=49 Identities=22% Similarity=0.242 Sum_probs=37.5
Q ss_pred cccccccccccCCCCeEEecCCCCcccccccCCCcCC-CCCCCcccccccccc
Q 011239 232 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKI-VPSDEWFCHLCLKKK 283 (490)
Q Consensus 232 ~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~-iP~g~W~C~~C~~~~ 283 (490)
+-+|.-|.-.| ..|.|+.|-|.||..|..|.-.. --+..|.|+.|....
T Consensus 60 d~~cfechlpg---~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~k 109 (588)
T KOG3612|consen 60 DPFCFECHLPG---AVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQPYSFK 109 (588)
T ss_pred CcccccccCCc---ceeeeehhhccccccccCcchhhccccccccCCcccccC
Confidence 45688899888 89999999999999999874221 122369999887543
No 47
>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=59.38 E-value=0.92 Score=39.36 Aligned_cols=33 Identities=9% Similarity=0.118 Sum_probs=25.7
Q ss_pred eeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 329 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 329 ~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
....+..|..+|.. ...++|+++|++||+|.+-
T Consensus 15 ~~~~~~~F~~pVd~--~~~pdY~~iIk~PmDL~tI 47 (98)
T cd05512 15 EKDTAEIFSEPVDL--SEVPDYLDHIKQPMDFSTM 47 (98)
T ss_pred hCCCchhhcCCCCc--cccCCHHHHhcCCcCHHHH
Confidence 34567788888864 2467899999999998874
No 48
>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=59.18 E-value=1 Score=39.22 Aligned_cols=32 Identities=13% Similarity=0.097 Sum_probs=24.9
Q ss_pred eecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 330 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 330 Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
...+..|..+|.. ...++|+++|++||+|.+-
T Consensus 16 ~~~~~~F~~PV~~--~~~pdY~~vIk~PmDL~tI 47 (98)
T cd05513 16 KDPHGFFAFPVTD--FIAPGYSSIIKHPMDFSTM 47 (98)
T ss_pred CCccccccCcCCc--cccccHHHHHcCccCHHHH
Confidence 3556688888864 2457899999999999874
No 49
>cd05500 Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=58.05 E-value=1.7 Score=37.67 Aligned_cols=36 Identities=11% Similarity=0.152 Sum_probs=27.0
Q ss_pred eeeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 328 TSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 328 ~~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
...+.+..|..+|..--...++|+++|.+||+|.+-
T Consensus 17 ~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI 52 (103)
T cd05500 17 KRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTI 52 (103)
T ss_pred HcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHH
Confidence 355677899999953113457899999999998864
No 50
>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=55.94 E-value=2.9 Score=36.85 Aligned_cols=33 Identities=15% Similarity=0.102 Sum_probs=24.6
Q ss_pred ecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 331 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 331 r~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
..+..|..+|..--...++|+++|++||+|.+-
T Consensus 20 ~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI 52 (108)
T cd05495 20 PESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTI 52 (108)
T ss_pred cccchhcCCCCccccCCCcHHHHhCCCCCHHHH
Confidence 456689999854112357899999999998874
No 51
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=55.50 E-value=5.1 Score=27.35 Aligned_cols=28 Identities=25% Similarity=0.763 Sum_probs=12.3
Q ss_pred cccccccccCCCCeEEecCCCCcccccc
Q 011239 234 SCKICGRSETALKLLLCDDCEEAFHVTC 261 (490)
Q Consensus 234 ~C~VC~~~g~~~~LL~CD~Cdr~yH~~C 261 (490)
.|.+|+..........|..|+=..|..|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 5889998886657888999999999887
No 52
>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=52.51 E-value=2.9 Score=37.24 Aligned_cols=31 Identities=13% Similarity=0.210 Sum_probs=25.1
Q ss_pred ecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 331 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 331 r~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
+.+..|..+|.. ...++|+++|++||+|.+-
T Consensus 24 ~~s~~F~~pv~~--~~~pdY~~iIk~PmdL~tI 54 (112)
T cd05510 24 EHSTPFLTKVSK--REAPDYYDIIKKPMDLGTM 54 (112)
T ss_pred ccccchhcCCCh--hhcCCHHHHhcCccCHHHH
Confidence 456789999864 3568899999999999874
No 53
>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=52.16 E-value=2.1 Score=36.91 Aligned_cols=33 Identities=12% Similarity=0.063 Sum_probs=23.9
Q ss_pred ecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 331 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 331 r~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
+.+..|..+|..-....++|+++|.+||+|.+-
T Consensus 19 ~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~~I 51 (102)
T cd05498 19 AYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTI 51 (102)
T ss_pred cccCcccCcCCccccCCCcHHHHccCCCcHHHH
Confidence 456688988753122357899999999998763
No 54
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=50.65 E-value=11 Score=36.88 Aligned_cols=43 Identities=23% Similarity=0.714 Sum_probs=32.7
Q ss_pred cccccccccccC-----CCCeEEecCCCCcccccccCCCcCCCCCCCcccccccccc
Q 011239 232 SRSCKICGRSET-----ALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 232 ~~~C~VC~~~g~-----~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 283 (490)
...|++|...+- .+...-|..|...||..|... =.||.|...+
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~---------~~CpkC~R~~ 199 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK---------KSCPKCARRQ 199 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC---------CCCCCcHhHh
Confidence 357999987642 347789999999999999952 2399998654
No 55
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.07 E-value=11 Score=40.23 Aligned_cols=48 Identities=27% Similarity=0.576 Sum_probs=34.8
Q ss_pred ccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCcccccccccc
Q 011239 233 RSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 233 ~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 283 (490)
+.|.+|-..-...+.|-==-|...||..|.+|.|.+-- =+||-|+..-
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r---~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTR---TFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcC---ccCCCCCCcC
Confidence 48999997443333333356888999999999987652 3899998743
No 56
>PF01448 ELM2: ELM2 domain; InterPro: IPR000949 The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex []. The domain is usually found to the N terminus of a myb-like DNA binding domain and a GATA binding domain. ELM2, in some instances, is also found associated with the ARID DNA binding domain IPR001606 from INTERPRO. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.
Probab=47.71 E-value=10 Score=29.24 Aligned_cols=14 Identities=50% Similarity=1.021 Sum_probs=12.4
Q ss_pred eecCCCccccCCCC
Q 011239 330 VRVGKGFQADIPDW 343 (490)
Q Consensus 330 Vr~G~~Fqa~VP~w 343 (490)
+|+|..|||.||++
T Consensus 1 IrVG~~yQA~IP~~ 14 (55)
T PF01448_consen 1 IRVGPEYQAEIPEL 14 (55)
T ss_pred CCcCCccCCcCCCC
Confidence 58999999999984
No 57
>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=45.74 E-value=4.1 Score=35.66 Aligned_cols=31 Identities=10% Similarity=0.056 Sum_probs=22.7
Q ss_pred ecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 331 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 331 r~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
....+|...+.. ...++|+++|++||+|.+-
T Consensus 22 ~~s~pF~~~p~~--~~~PdYy~iI~~PmdL~tI 52 (103)
T cd05520 22 LLAEPFLKLPSK--RKYPDYYQEIKNPISLQQI 52 (103)
T ss_pred CccHhhhcCCCc--ccCCCHHHHcCCCcCHHHH
Confidence 455567777543 2457899999999998864
No 58
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=45.32 E-value=11 Score=31.26 Aligned_cols=29 Identities=31% Similarity=0.839 Sum_probs=24.7
Q ss_pred ccccccccc-cCCCCeEEecC--CCCcccccccCC
Q 011239 233 RSCKICGRS-ETALKLLLCDD--CEEAFHVTCYTP 264 (490)
Q Consensus 233 ~~C~VC~~~-g~~~~LL~CD~--Cdr~yH~~Cl~P 264 (490)
..|.+|+.. | -.+-|.. |.+.||..|..-
T Consensus 37 ~~C~~C~~~~G---a~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 37 LKCSICKKKGG---ACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCcCCCCCCC---eEEEEeCCCCCcEEChHHHcc
Confidence 579999998 7 7888875 999999999853
No 59
>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=45.21 E-value=4.6 Score=35.29 Aligned_cols=33 Identities=9% Similarity=0.090 Sum_probs=23.3
Q ss_pred eeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 329 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 329 ~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
+.+.+..|..++.. ...++|+++|++||+|.+-
T Consensus 20 ~~~~a~~F~~~p~~--~~~pdYy~iIk~PmdL~tI 52 (105)
T cd05515 20 GRRLSLIFMRLPSK--SEYPDYYDVIKKPIDMEKI 52 (105)
T ss_pred CCcccHHhccCCCc--ccCCcHHHHcCCCcCHHHH
Confidence 33455577776543 2457899999999998864
No 60
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=44.29 E-value=8.3 Score=40.14 Aligned_cols=48 Identities=17% Similarity=0.250 Sum_probs=34.7
Q ss_pred cccccccc------cCCCCeEEecCCCCcccccccCCCcC---CCCCCCcccccccc
Q 011239 234 SCKICGRS------ETALKLLLCDDCEEAFHVTCYTPRIK---IVPSDEWFCHLCLK 281 (490)
Q Consensus 234 ~C~VC~~~------g~~~~LL~CD~Cdr~yH~~Cl~PpL~---~iP~g~W~C~~C~~ 281 (490)
.|..|-.+ +..+.+++|..|..+||.+|+.-+.. .+-...|.|..|+-
T Consensus 260 ~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~l 316 (381)
T KOG1512|consen 260 ERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCEL 316 (381)
T ss_pred hhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHh
Confidence 57777643 23568999999999999999964322 22345899998864
No 61
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=44.29 E-value=11 Score=32.52 Aligned_cols=30 Identities=40% Similarity=0.882 Sum_probs=24.6
Q ss_pred cccccccccccCCCCeEEecC--CCCcccccccC
Q 011239 232 SRSCKICGRSETALKLLLCDD--CEEAFHVTCYT 263 (490)
Q Consensus 232 ~~~C~VC~~~g~~~~LL~CD~--Cdr~yH~~Cl~ 263 (490)
...|.+|+..+ ...+-|.. |...||..|..
T Consensus 55 ~~~C~iC~~~~--G~~i~C~~~~C~~~fH~~CA~ 86 (110)
T PF13832_consen 55 KLKCSICGKSG--GACIKCSHPGCSTAFHPTCAR 86 (110)
T ss_pred CCcCcCCCCCC--ceeEEcCCCCCCcCCCHHHHH
Confidence 35799999852 16889998 99999999984
No 62
>cd05528 Bromo_AAA Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver
Probab=41.10 E-value=6 Score=35.18 Aligned_cols=32 Identities=13% Similarity=0.184 Sum_probs=24.6
Q ss_pred eecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 330 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 330 Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
...+..|..+|.. ...++|+++|++||+|.+-
T Consensus 18 ~~~~~~F~~pv~~--~~~pdY~~vI~~PmdL~tI 49 (112)
T cd05528 18 DKRFNAFTKPVDE--EEVPDYYEIIKQPMDLQTI 49 (112)
T ss_pred CCCchhhcCCCCc--cccCcHHHHHcCCCCHHHH
Confidence 3455688888854 2567899999999998864
No 63
>cd05516 Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=40.69 E-value=6.5 Score=34.54 Aligned_cols=33 Identities=6% Similarity=0.018 Sum_probs=23.3
Q ss_pred eeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 329 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 329 ~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
+.....+|..++.. ...++|+++|.+||+|.+-
T Consensus 21 g~~~s~~F~~~p~~--~~~pdYy~iI~~Pmdl~tI 53 (107)
T cd05516 21 GRQLAEVFIQLPSR--KELPEYYELIRKPVDFKKI 53 (107)
T ss_pred CCEeeHHhhcCCCc--ccCCCHHHHcCCCCCHHHH
Confidence 44455677775443 2457899999999998864
No 64
>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=40.42 E-value=5.9 Score=34.70 Aligned_cols=33 Identities=18% Similarity=0.130 Sum_probs=22.9
Q ss_pred eeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 329 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 329 ~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
|.+++..|...+.. ...++|+++|++||+|.+-
T Consensus 20 gr~~~~~F~~~p~~--~~~pdYy~iIk~Pmdl~tI 52 (103)
T cd05518 20 GRRLCDLFMEKPSK--KDYPDYYKIILEPIDLKTI 52 (103)
T ss_pred CCcccHHHhcCCCc--ccCccHHHHcCCCcCHHHH
Confidence 44455566655543 2457899999999998763
No 65
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=40.35 E-value=8.2 Score=31.68 Aligned_cols=30 Identities=27% Similarity=0.602 Sum_probs=20.1
Q ss_pred eEEecCCCCcccccccCCCcCCCCCCCccccccc
Q 011239 247 LLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCL 280 (490)
Q Consensus 247 LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~ 280 (490)
.+.=..|.-.||..|+..-|+.. ..||.|+
T Consensus 44 ~i~~~~C~H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 44 PIVWGPCGHIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp -EEEETTSEEEEHHHHHHHHTTS----SB-TTSS
T ss_pred ceEecccCCCEEHHHHHHHHhcC----CcCCCCC
Confidence 33445699999999997655433 3788885
No 66
>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=40.02 E-value=5.5 Score=35.30 Aligned_cols=32 Identities=13% Similarity=0.164 Sum_probs=24.8
Q ss_pred eecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 330 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 330 Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
++.+..|..+|.. ...++|+++|.+||+|.+-
T Consensus 15 ~~~s~~F~~pv~~--~~~p~Y~~~I~~PmdL~tI 46 (112)
T cd05511 15 LPDSWPFHTPVNK--KKVPDYYKIIKRPMDLQTI 46 (112)
T ss_pred CCCchhhcCCCCh--hhcccHHHHhcCCCCHHHH
Confidence 3556688888864 2467899999999998864
No 67
>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=39.30 E-value=6.9 Score=34.90 Aligned_cols=61 Identities=7% Similarity=-0.047 Sum_probs=32.9
Q ss_pred CCCccccC----CCCCCCCCCCCCCcCCCccCCCCCCCccccccccccCCccCCCceEecccccCCC
Q 011239 333 GKGFQADI----PDWLAPTNNDGYALGEPLELDTSECPSLHDLNSYNLSNLSSIGNWLQCKQVLEGT 395 (490)
Q Consensus 333 G~~Fqa~V----P~ws~~~~~y~~~I~ePMdLd~se~~~L~~l~~~~~~k~~s~gnw~qC~~c~~~~ 395 (490)
..+|+.+| |.|. ..++|+++|++||||.+-+.. |...++.....|.++-+|++-...++++
T Consensus 19 ~~~~~~~v~~~~~~~~-~~pdY~~iIk~PmDL~tI~~k-l~~~~Y~s~~ef~~Dv~LI~~N~~~yNg 83 (109)
T cd05492 19 DTTNRAIVLNKRGKAT-KLPKRRRLIHTHLDVADIQEK-INSEKYTSLEEFKADALLLLHNTAIFHG 83 (109)
T ss_pred cccccccccccCchhc-cCCCHHHHhCCCCcHHHHHHH-HHcCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence 34677777 3321 256899999999999884322 1211121111144555555544444433
No 68
>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=38.79 E-value=7.8 Score=33.06 Aligned_cols=34 Identities=18% Similarity=0.102 Sum_probs=24.2
Q ss_pred eecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 330 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 330 Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
.+.+..|..+|..-....++|+++|.+||+|.+-
T Consensus 15 ~~~~~~F~~pv~~~~~~~p~Y~~~I~~P~dl~tI 48 (99)
T cd05506 15 HKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTV 48 (99)
T ss_pred CCCCccccCCCCccccCCCCHHHHHcCCCCHHHH
Confidence 3456788888842112357899999999998874
No 69
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=38.77 E-value=31 Score=37.88 Aligned_cols=58 Identities=24% Similarity=0.514 Sum_probs=41.5
Q ss_pred CCCCcccccccccccccccC---CCCeEEecCCCCcccccccCCCc--------CC---CCCCCcccccccccc
Q 011239 224 GTGCSGICSRSCKICGRSET---ALKLLLCDDCEEAFHVTCYTPRI--------KI---VPSDEWFCHLCLKKK 283 (490)
Q Consensus 224 g~w~cp~c~~~C~VC~~~g~---~~~LL~CD~Cdr~yH~~Cl~PpL--------~~---iP~g~W~C~~C~~~~ 283 (490)
.+.+|..| .|-+|+..++ +-.-|-||.|..+-|+.|-.-.- .. ..++.++|..|-...
T Consensus 122 ~~gFC~~C--~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~s 193 (446)
T PF07227_consen 122 EPGFCRRC--MCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTS 193 (446)
T ss_pred CCCccccC--CccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChh
Confidence 35789888 8999998653 33558899999999999975311 10 124479999997653
No 70
>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=38.54 E-value=10 Score=33.37 Aligned_cols=33 Identities=12% Similarity=0.091 Sum_probs=23.7
Q ss_pred eeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 329 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 329 ~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
|.+++.+|...++. ...++|++.|.+||+|.+-
T Consensus 22 g~~~s~~F~~lp~k--~~~pdYy~~I~~P~dL~tI 54 (106)
T cd05525 22 GQSLAIPFINLPSK--KKNPDYYERITDPVDLSTI 54 (106)
T ss_pred CCcccHhhccCCCc--ccCCchhhhCCCCcCHHHH
Confidence 34556677776543 3457899999999998764
No 71
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=37.92 E-value=8.8 Score=26.49 Aligned_cols=42 Identities=24% Similarity=0.487 Sum_probs=27.6
Q ss_pred ccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCcccccccc
Q 011239 235 CKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLK 281 (490)
Q Consensus 235 C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~ 281 (490)
|.+|...- ...+.-..|...||..|+...+.. +...||.|+.
T Consensus 2 C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~---~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS---GKNTCPLCRT 43 (45)
T ss_pred CCcCchhh--hCceEecCCCChhcHHHHHHHHHh---CcCCCCCCCC
Confidence 66776543 233444568888999999755443 4567888864
No 72
>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=37.25 E-value=7 Score=33.53 Aligned_cols=32 Identities=13% Similarity=0.171 Sum_probs=24.3
Q ss_pred eecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 330 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 330 Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
...+..|..+|.. ...++|+++|+.||+|.+-
T Consensus 16 ~~~a~~F~~pv~~--~~~p~Y~~~I~~PmdL~tI 47 (101)
T cd05509 16 HKSAWPFLEPVDK--EEAPDYYDVIKKPMDLSTM 47 (101)
T ss_pred CCCchhhcCCCCh--hhcCCHHHHhcCCCCHHHH
Confidence 3455678888864 2467899999999998864
No 73
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=37.19 E-value=23 Score=33.48 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=14.1
Q ss_pred cCCCCCCCCCCCCcccc
Q 011239 215 RSSANDVDSGTGCSGIC 231 (490)
Q Consensus 215 ~~~~e~vp~g~w~cp~c 231 (490)
+.++..+|+|+|+||.|
T Consensus 8 ~Ppl~~~P~g~W~Cp~C 24 (148)
T cd04718 8 RPPLKEVPEGDWICPFC 24 (148)
T ss_pred CCCCCCCCCCCcCCCCC
Confidence 45679999999999855
No 74
>cd05499 Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=36.38 E-value=9.2 Score=33.00 Aligned_cols=33 Identities=15% Similarity=0.065 Sum_probs=24.4
Q ss_pred ecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 331 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 331 r~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
..+.+|..+|..-....++|+++|.+||+|.+-
T Consensus 19 ~~s~~F~~pvd~~~~~~pdY~~~I~~P~dL~~I 51 (102)
T cd05499 19 AYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTI 51 (102)
T ss_pred cccchhcCCCCccccCCCCHHHHhcCCCCHHHH
Confidence 356689988854222457899999999998864
No 75
>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=34.42 E-value=8.1 Score=33.77 Aligned_cols=31 Identities=19% Similarity=0.148 Sum_probs=20.6
Q ss_pred ecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 331 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 331 r~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
.++..|...++. ...++|+++|++||+|.+-
T Consensus 22 ~~~~~F~~lp~~--~~~pdYy~vI~~PmdL~tI 52 (103)
T cd05517 22 LISELFQKLPSK--VLYPDYYAVIKEPIDLKTI 52 (103)
T ss_pred ChhHHHhcCCCC--CCCCCHHHHcCCCcCHHHH
Confidence 344456654332 2347899999999998764
No 76
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=32.51 E-value=11 Score=39.12 Aligned_cols=50 Identities=26% Similarity=0.547 Sum_probs=37.0
Q ss_pred ccccccccc-------cCCCCeEEecCCCCcccccccCCC---cCCCCCCCccccccccc
Q 011239 233 RSCKICGRS-------ETALKLLLCDDCEEAFHVTCYTPR---IKIVPSDEWFCHLCLKK 282 (490)
Q Consensus 233 ~~C~VC~~~-------g~~~~LL~CD~Cdr~yH~~Cl~Pp---L~~iP~g~W~C~~C~~~ 282 (490)
-+|..|-+. |-+++|+-|..|+|+=|.+||.-- +..+-...|.|..|+.-
T Consensus 225 ~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~c 284 (336)
T KOG1244|consen 225 PYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYC 284 (336)
T ss_pred cccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeeccee
Confidence 367777643 347899999999999999999632 12344568999999764
No 77
>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=31.74 E-value=15 Score=33.29 Aligned_cols=34 Identities=12% Similarity=0.090 Sum_probs=25.6
Q ss_pred eeecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 329 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 329 ~Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
+...+..|..+|+.-. ..++|+++|+.||+|.+-
T Consensus 41 ~~~~~~~F~~pv~~~~-~~p~Y~~iI~~PmdL~tI 74 (128)
T cd05529 41 QLEIAEYFEYPVDLRA-WYPDYWNRVPVPMDLETI 74 (128)
T ss_pred cCcccccccCCCCccc-cCCcHHHHcCCCCCHHHH
Confidence 4456678888887511 457899999999998864
No 78
>cd05519 Bromo_SNF2 Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=31.73 E-value=11 Score=32.64 Aligned_cols=31 Identities=13% Similarity=0.145 Sum_probs=21.3
Q ss_pred ecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 331 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 331 r~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
.+...|..++.. ...++|+++|++||+|.+-
T Consensus 22 ~~~~~F~~~p~~--~~~pdYy~iIk~Pmdl~~I 52 (103)
T cd05519 22 KLSELFLEKPSK--KLYPDYYVIIKRPIALDQI 52 (103)
T ss_pred chhHHhcCCCCC--CCCcCHHHHcCCCcCHHHH
Confidence 334456666443 2346899999999998864
No 79
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=30.10 E-value=49 Score=37.84 Aligned_cols=38 Identities=32% Similarity=0.710 Sum_probs=27.6
Q ss_pred ccccccccccCCCCeEEecCCCCcccccccCCCcCCCCCCCccccccccccc
Q 011239 233 RSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKH 284 (490)
Q Consensus 233 ~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~ 284 (490)
..|..|++.| +.+.|+.|+..++. ..+..|+.|..+..
T Consensus 69 ~~c~~c~G~g---kv~~c~~cG~~~~~-----------~~~~lc~~c~~~~~ 106 (715)
T COG1107 69 DTCPECGGTG---KVLTCDICGDIIVP-----------WEEGLCPECRRKPK 106 (715)
T ss_pred eecccCCCce---eEEeeccccceecC-----------cccccChhHhhCCc
Confidence 5688888888 78888888887652 11237999988754
No 80
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=28.56 E-value=42 Score=25.79 Aligned_cols=17 Identities=29% Similarity=0.917 Sum_probs=9.8
Q ss_pred cCCCCCCCcccccccccc
Q 011239 266 IKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 266 L~~iP~g~W~C~~C~~~~ 283 (490)
...+|+ +|.||.|...+
T Consensus 28 F~~Lp~-~w~CP~C~a~K 44 (47)
T PF00301_consen 28 FEDLPD-DWVCPVCGAPK 44 (47)
T ss_dssp GGGS-T-T-B-TTTSSBG
T ss_pred HHHCCC-CCcCcCCCCcc
Confidence 445664 79999998754
No 81
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.64 E-value=27 Score=34.12 Aligned_cols=35 Identities=6% Similarity=0.051 Sum_probs=26.1
Q ss_pred CCccCCCCccccccCCcccccccchhhhhhccCccc
Q 011239 172 TGECSSSSAVMLETTGKDLSAKDLCISILRNEGMLE 207 (490)
Q Consensus 172 ~~eCsss~ic~~e~~ged~s~~D~C~hil~~~gll~ 207 (490)
...|..|+||+..+..... .--.|+|+||+.||-.
T Consensus 128 ~~~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~ 162 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKD 162 (187)
T ss_pred cccccCCCceecchhhccc-cccccchhHHHHHHHH
Confidence 3455666999988765543 4567999999999766
No 82
>cd05522 Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=27.41 E-value=11 Score=32.87 Aligned_cols=32 Identities=16% Similarity=0.096 Sum_probs=21.4
Q ss_pred eecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 330 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 330 Vr~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
..+...|...+.. ...++|+++|++||+|.+-
T Consensus 22 ~~l~~~F~~~p~~--~~~pdYy~~I~~Pmdl~tI 53 (104)
T cd05522 22 RLLTLHFEKLPDK--AREPEYYQEISNPISLDDI 53 (104)
T ss_pred CcccHHHhcCCCc--cccCcHHHHhCCCcCHHHH
Confidence 3444456655432 2457899999999998864
No 83
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=27.04 E-value=26 Score=31.08 Aligned_cols=50 Identities=22% Similarity=0.683 Sum_probs=29.9
Q ss_pred cccccccccccCCCCeEEe------cCC---CCcccccccCCCc-----CCCCCCCccccccccc
Q 011239 232 SRSCKICGRSETALKLLLC------DDC---EEAFHVTCYTPRI-----KIVPSDEWFCHLCLKK 282 (490)
Q Consensus 232 ~~~C~VC~~~g~~~~LL~C------D~C---dr~yH~~Cl~PpL-----~~iP~g~W~C~~C~~~ 282 (490)
...|..|.....+.. ..| ..| ...|=..||.-.. +.+..++|.||.|+..
T Consensus 7 g~~CHqCrqKt~~~~-~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi 70 (105)
T PF10497_consen 7 GKTCHQCRQKTLDFK-TICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI 70 (105)
T ss_pred CCCchhhcCCCCCCc-eEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence 356777777554333 345 555 6666666665322 2235678999999864
No 84
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=25.80 E-value=57 Score=24.40 Aligned_cols=31 Identities=23% Similarity=0.557 Sum_probs=23.2
Q ss_pred cccccccccc--CCCCeEEecCCCCcccccccC
Q 011239 233 RSCKICGRSE--TALKLLLCDDCEEAFHVTCYT 263 (490)
Q Consensus 233 ~~C~VC~~~g--~~~~LL~CD~Cdr~yH~~Cl~ 263 (490)
.+|.+|+..- .....+.|..|....|..|+.
T Consensus 12 ~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~ 44 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLS 44 (53)
T ss_dssp EB-TTSSSBECSSSSCEEEETTTT-EEETTGGC
T ss_pred CCCcccCcccCCCCCCeEEECCCCChHhhhhhh
Confidence 4688888743 445789999999999999984
No 85
>cd05521 Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=24.37 E-value=13 Score=32.83 Aligned_cols=18 Identities=22% Similarity=0.207 Sum_probs=15.0
Q ss_pred CCCCCCCCcCCCccCCCC
Q 011239 346 PTNNDGYALGEPLELDTS 363 (490)
Q Consensus 346 ~~~~y~~~I~ePMdLd~s 363 (490)
..++|+++|++||+|.+-
T Consensus 36 ~~pdYy~iI~~PmdL~tI 53 (106)
T cd05521 36 DYPDYYKIIKNPLSLNTV 53 (106)
T ss_pred cCccHHHHhcCCCCHHHH
Confidence 446899999999998863
No 86
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=23.37 E-value=17 Score=24.01 Aligned_cols=28 Identities=25% Similarity=0.466 Sum_probs=16.7
Q ss_pred ccccccccCCCCeEEecCCCCcccccccCCC
Q 011239 235 CKICGRSETALKLLLCDDCEEAFHVTCYTPR 265 (490)
Q Consensus 235 C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~Pp 265 (490)
|.+|.... ..+.--.|...||..|+...
T Consensus 1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~ 28 (39)
T smart00184 1 CPICLEEL---KDPVVLPCGHTFCRSCIRKW 28 (39)
T ss_pred CCcCccCC---CCcEEecCCChHHHHHHHHH
Confidence 45666553 23333358888888887543
No 87
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.97 E-value=28 Score=37.76 Aligned_cols=31 Identities=16% Similarity=0.416 Sum_probs=24.9
Q ss_pred CccCCCCccccccC--CcccccccchhhhhhccCccc
Q 011239 173 GECSSSSAVMLETT--GKDLSAKDLCISILRNEGMLE 207 (490)
Q Consensus 173 ~eCsss~ic~~e~~--ged~s~~D~C~hil~~~gll~ 207 (490)
++| .|| .++. .++++....|+|+|+..|++.
T Consensus 5 A~C---~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~q 37 (465)
T KOG0827|consen 5 AEC---HIC-IDGRPNDHELGPIGTCGHIFHTTCLTQ 37 (465)
T ss_pred cee---eEe-ccCCccccccccccchhhHHHHHHHHH
Confidence 467 777 5554 477888999999999999887
No 88
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=21.90 E-value=65 Score=23.35 Aligned_cols=28 Identities=25% Similarity=0.616 Sum_probs=19.6
Q ss_pred EEecCCCCcccccccCCCcCCCCCCCcccccccc
Q 011239 248 LLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLK 281 (490)
Q Consensus 248 L~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~ 281 (490)
..|..|.+.||..=. .|.-+..|..|-.
T Consensus 2 r~C~~Cg~~Yh~~~~------pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFN------PPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--------SSTTBCTTTTE
T ss_pred cCcCCCCCccccccC------CCCCCCccCCCCC
Confidence 468999999996544 3555678888865
No 89
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=21.84 E-value=41 Score=39.59 Aligned_cols=53 Identities=11% Similarity=0.098 Sum_probs=31.0
Q ss_pred CCcccCCccCCCCccccccCCcccccccchhhh-hhccCcccccCCccccCCCCCCCCCCCCcccc
Q 011239 167 TEVDETGECSSSSAVMLETTGKDLSAKDLCISI-LRNEGMLERFWPTQIRSSANDVDSGTGCSGIC 231 (490)
Q Consensus 167 ~~~~d~~eCsss~ic~~e~~ged~s~~D~C~hi-l~~~gll~~~~p~~~~~~~e~vp~g~w~cp~c 231 (490)
....++..| .||...-.-+-+-.+|.|-.. +|..||-- .+-.+|-+.|+|++|
T Consensus 210 ~~~~E~~~C---~IC~~~DpEdVLLLCDsCN~~~YH~YCLDP---------dl~eiP~~eWYC~NC 263 (1134)
T KOG0825|consen 210 GLSQEEVKC---DICTVHDPEDVLLLCDSCNKVYYHVYCLDP---------DLSESPVNEWYCTNC 263 (1134)
T ss_pred Ccccccccc---eeeccCChHHhheeecccccceeeccccCc---------ccccccccceecCcc
Confidence 334455566 787775555555666666544 44333322 124578889999866
No 90
>PHA02929 N1R/p28-like protein; Provisional
Probab=21.79 E-value=31 Score=34.89 Aligned_cols=34 Identities=18% Similarity=0.250 Sum_probs=25.4
Q ss_pred cCCccCCCCccccccCCcc-----cccccchhhhhhccCccc
Q 011239 171 ETGECSSSSAVMLETTGKD-----LSAKDLCISILRNEGMLE 207 (490)
Q Consensus 171 d~~eCsss~ic~~e~~ged-----~s~~D~C~hil~~~gll~ 207 (490)
+..+| .||+.++...+ ++....|.|+||..||..
T Consensus 173 ~~~eC---~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~ 211 (238)
T PHA02929 173 KDKEC---AICMEKVYDKEIKNMYFGILSNCNHVFCIECIDI 211 (238)
T ss_pred CCCCC---ccCCcccccCccccccceecCCCCCcccHHHHHH
Confidence 34677 99998765433 345668999999999877
No 91
>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=21.44 E-value=16 Score=32.51 Aligned_cols=18 Identities=11% Similarity=0.078 Sum_probs=15.1
Q ss_pred CCCCCCCCcCCCccCCCC
Q 011239 346 PTNNDGYALGEPLELDTS 363 (490)
Q Consensus 346 ~~~~y~~~I~ePMdLd~s 363 (490)
..++|+++|.+||+|.+-
T Consensus 37 ~~PdYy~iI~~Pmdl~tI 54 (113)
T cd05524 37 NEPEYYEVVSNPIDLLKI 54 (113)
T ss_pred cCCCHHHHhCCccCHHHH
Confidence 446899999999998874
No 92
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=20.87 E-value=64 Score=27.05 Aligned_cols=31 Identities=23% Similarity=0.615 Sum_probs=20.7
Q ss_pred cccccccccccCCCCeEEecCCCCcccccccC
Q 011239 232 SRSCKICGRSETALKLLLCDDCEEAFHVTCYT 263 (490)
Q Consensus 232 ~~~C~VC~~~g~~~~LL~CD~Cdr~yH~~Cl~ 263 (490)
...|.+|++.-....+ .---|+..||..|..
T Consensus 78 ~~~C~vC~k~l~~~~f-~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVF-VVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceE-EEeCCCeEEeccccc
Confidence 3579999986544333 333455889999973
No 93
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.62 E-value=33 Score=38.24 Aligned_cols=47 Identities=19% Similarity=0.342 Sum_probs=30.7
Q ss_pred CccccccCCcccccccchhhhhhccCcccccCCccccCCCCCCCCCCCCcccccccccccccccC
Q 011239 179 SAVMLETTGKDLSAKDLCISILRNEGMLERFWPTQIRSSANDVDSGTGCSGICSRSCKICGRSET 243 (490)
Q Consensus 179 ~ic~~e~~ged~s~~D~C~hil~~~gll~~~~p~~~~~~~e~vp~g~w~cp~c~~~C~VC~~~g~ 243 (490)
+||+.+.. +...-.|+|+||..||+.= |.. +.|.++ ..|..|...-.
T Consensus 190 PICL~~~~---~p~~t~CGHiFC~~CiLqy-~~~-----------s~~~~~---~~CPiC~s~I~ 236 (513)
T KOG2164|consen 190 PICLEPPS---VPVRTNCGHIFCGPCILQY-WNY-----------SAIKGP---CSCPICRSTIT 236 (513)
T ss_pred CcccCCCC---cccccccCceeeHHHHHHH-Hhh-----------hcccCC---ccCCchhhhcc
Confidence 88887655 4445569999999999982 321 123332 35888886553
No 94
>PHA02929 N1R/p28-like protein; Provisional
Probab=20.20 E-value=40 Score=34.17 Aligned_cols=47 Identities=19% Similarity=0.445 Sum_probs=31.7
Q ss_pred ccccccccccCCCC-----eEEecCCCCcccccccCCCcCCCCCCCcccccccccc
Q 011239 233 RSCKICGRSETALK-----LLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 283 (490)
Q Consensus 233 ~~C~VC~~~g~~~~-----LL~CD~Cdr~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 283 (490)
..|.+|...-.+.. +..=..|...||..|+...+...+ .||.|+..-
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~----tCPlCR~~~ 226 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKN----TCPVCRTPF 226 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCC----CCCCCCCEe
Confidence 57999987532211 223347889999999987665433 799998753
No 95
>smart00297 BROMO bromo domain.
Probab=20.15 E-value=21 Score=30.18 Aligned_cols=31 Identities=16% Similarity=0.217 Sum_probs=23.2
Q ss_pred ecCCCccccCCCCCCCCCCCCCCcCCCccCCCC
Q 011239 331 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 363 (490)
Q Consensus 331 r~G~~Fqa~VP~ws~~~~~y~~~I~ePMdLd~s 363 (490)
+.+..|..+|.. ...++|+++|.+||+|.+-
T Consensus 23 ~~~~~F~~~~~~--~~~p~Y~~~i~~P~dl~~I 53 (107)
T smart00297 23 RLSWPFLKPVDR--KEAPDYYDIIKKPMDLSTI 53 (107)
T ss_pred ccchhhccCCCh--hhccCHHHHhcCCCCHHHH
Confidence 566678887754 2357899999999998764
Done!