Query 009705
Match_columns 528
No_of_seqs 298 out of 913
Neff 4.7
Searched_HMMs 46136
Date Thu Mar 28 16:21:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009705.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009705hhsearch_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 2.9E-12 6.3E-17 140.0 3.8 167 270-474 253-423 (613)
2 KOG1244 Predicted transcriptio 99.1 1.2E-11 2.5E-16 124.3 0.8 63 257-320 269-331 (336)
3 PF07496 zf-CW: CW-type Zinc F 99.0 9.5E-11 2.1E-15 90.7 1.8 44 422-480 2-50 (50)
4 KOG0825 PHD Zn-finger protein 98.9 3E-10 6.6E-15 126.2 0.2 105 215-321 125-267 (1134)
5 KOG1512 PHD Zn-finger protein 98.7 5.1E-09 1.1E-13 106.2 1.2 72 247-321 289-364 (381)
6 PF00628 PHD: PHD-finger; Int 98.6 1.2E-08 2.6E-13 77.9 2.0 48 272-319 1-50 (51)
7 KOG4443 Putative transcription 98.3 2.4E-07 5.3E-12 102.4 2.3 63 259-322 58-120 (694)
8 smart00249 PHD PHD zinc finger 98.2 1E-06 2.2E-11 64.2 3.1 46 272-317 1-47 (47)
9 cd04718 BAH_plant_2 BAH, or Br 98.0 3.2E-06 6.9E-11 79.3 2.5 30 294-323 1-30 (148)
10 KOG1973 Chromatin remodeling p 97.7 2.1E-05 4.5E-10 80.3 2.7 44 272-321 223-269 (274)
11 KOG1245 Chromatin remodeling c 97.6 1.2E-05 2.7E-10 96.9 -0.7 59 264-322 1102-1160(1404)
12 KOG0383 Predicted helicase [Ge 97.5 4.4E-05 9.6E-10 86.5 2.5 55 264-322 42-96 (696)
13 KOG0955 PHD finger protein BR1 97.2 0.00016 3.4E-09 85.1 2.7 52 270-323 219-272 (1051)
14 KOG4323 Polycomb-like PHD Zn-f 97.1 0.00017 3.6E-09 78.4 1.3 54 271-324 169-228 (464)
15 COG5141 PHD zinc finger-contai 96.8 0.00056 1.2E-08 74.4 1.6 51 270-322 193-245 (669)
16 KOG0957 PHD finger protein [Ge 96.7 0.00044 9.6E-09 75.3 0.6 50 270-319 544-597 (707)
17 PF13831 PHD_2: PHD-finger; PD 96.6 0.00071 1.5E-08 49.4 0.8 34 283-318 2-36 (36)
18 KOG0954 PHD finger protein [Ge 96.5 0.001 2.2E-08 75.2 1.5 55 264-320 265-321 (893)
19 KOG0956 PHD finger protein AF1 96.4 0.0014 3E-08 73.8 1.6 49 272-322 7-59 (900)
20 COG5034 TNG2 Chromatin remodel 96.3 0.002 4.4E-08 65.3 2.2 43 275-320 225-270 (271)
21 KOG1473 Nucleosome remodeling 95.6 0.0057 1.2E-07 72.0 2.2 48 270-320 344-391 (1414)
22 cd05502 Bromo_tif1_like Bromod 92.4 0.026 5.6E-07 50.0 -1.0 48 351-401 1-49 (109)
23 cd05501 Bromo_SP100C_like Brom 91.8 0.033 7.1E-07 49.6 -1.1 46 353-402 1-47 (102)
24 KOG1246 DNA-binding protein ju 87.4 0.39 8.3E-06 56.9 2.8 51 270-321 155-205 (904)
25 cd05497 Bromo_Brdt_I_like Brom 85.1 0.12 2.5E-06 46.1 -2.3 48 355-402 7-54 (107)
26 cd05505 Bromo_WSTF_like Bromod 84.0 0.14 3E-06 44.8 -2.3 39 361-401 8-46 (97)
27 cd05496 Bromo_WDR9_II Bromodom 80.9 0.25 5.4E-06 45.0 -1.9 39 361-401 13-51 (119)
28 KOG0957 PHD finger protein [Ge 80.2 2.5 5.5E-05 47.1 5.0 50 272-321 121-180 (707)
29 KOG1473 Nucleosome remodeling 79.6 0.58 1.3E-05 56.0 0.0 50 270-322 428-481 (1414)
30 cd05503 Bromo_BAZ2A_B_like Bro 77.1 0.32 6.8E-06 42.3 -2.4 39 361-401 8-46 (97)
31 cd05494 Bromodomain_1 Bromodom 76.9 1.1 2.5E-05 40.4 1.1 34 368-401 18-51 (114)
32 KOG1474 Transcription initiati 76.4 0.85 1.8E-05 52.2 0.1 52 350-401 218-270 (640)
33 PF13639 zf-RING_2: Ring finge 75.7 0.39 8.5E-06 35.5 -1.9 43 271-318 1-44 (44)
34 cd05508 Bromo_RACK7 Bromodomai 75.4 0.47 1E-05 41.8 -1.8 33 368-402 17-49 (99)
35 PF15446 zf-PHD-like: PHD/FYVE 74.6 1.6 3.4E-05 42.5 1.4 50 272-321 1-61 (175)
36 KOG4443 Putative transcription 74.2 0.95 2.1E-05 51.6 -0.2 59 262-321 11-72 (694)
37 cd05500 Bromo_BDF1_2_I Bromodo 73.4 0.75 1.6E-05 40.4 -1.0 42 361-402 12-53 (103)
38 PF14446 Prok-RING_1: Prokaryo 72.2 2.3 5E-05 34.1 1.5 32 271-302 6-38 (54)
39 PF12861 zf-Apc11: Anaphase-pr 71.6 1.8 4E-05 37.6 1.0 48 272-321 34-81 (85)
40 cd05507 Bromo_brd8_like Bromod 71.6 0.88 1.9E-05 40.1 -1.0 38 362-401 12-49 (104)
41 cd05504 Bromo_Acf1_like Bromod 71.4 0.76 1.6E-05 41.4 -1.5 47 353-401 11-58 (115)
42 cd05512 Bromo_brd1_like Bromod 70.0 0.59 1.3E-05 41.0 -2.5 37 363-401 11-47 (98)
43 cd05513 Bromo_brd7_like Bromod 69.1 0.66 1.4E-05 40.8 -2.3 35 365-401 13-47 (98)
44 cd05498 Bromo_Brdt_II_like Bro 69.0 0.88 1.9E-05 39.6 -1.6 33 369-401 19-51 (102)
45 KOG4299 PHD Zn-finger protein 68.2 2.9 6.3E-05 47.6 1.8 47 271-320 48-95 (613)
46 cd05495 Bromo_cbp_like Bromodo 67.1 0.87 1.9E-05 40.5 -2.0 40 362-401 12-52 (108)
47 PF11793 FANCL_C: FANCL C-term 65.8 0.81 1.8E-05 37.8 -2.3 50 271-320 3-64 (70)
48 KOG0956 PHD finger protein AF1 64.6 2.9 6.2E-05 48.3 0.9 53 270-322 117-182 (900)
49 cd05510 Bromo_SPT7_like Bromod 62.6 1 2.2E-05 40.5 -2.4 40 361-402 15-55 (112)
50 KOG1245 Chromatin remodeling c 62.5 1.1 2.3E-05 55.7 -3.1 39 361-401 1309-1347(1404)
51 KOG0383 Predicted helicase [Ge 59.5 2 4.2E-05 49.8 -1.5 51 270-323 506-557 (696)
52 PF13901 DUF4206: Domain of un 59.4 6.5 0.00014 38.7 2.3 43 270-321 152-199 (202)
53 KOG3612 PHD Zn-finger protein 57.4 31 0.00066 39.2 7.2 48 270-320 60-108 (588)
54 cd05511 Bromo_TFIID Bromodomai 55.5 1.5 3.1E-05 39.4 -2.7 36 365-402 12-47 (112)
55 cd05499 Bromo_BDF1_2_II Bromod 55.5 1.8 3.9E-05 37.8 -2.1 33 369-401 19-51 (102)
56 smart00249 PHD PHD zinc finger 54.4 11 0.00025 26.7 2.3 30 419-461 10-45 (47)
57 PF07649 C1_3: C1-like domain; 52.7 6.8 0.00015 27.1 0.8 28 272-299 2-29 (30)
58 cd05528 Bromo_AAA Bromodomain; 52.6 1.9 4E-05 38.8 -2.5 37 363-401 13-49 (112)
59 cd05506 Bromo_plant1 Bromodoma 52.1 2.2 4.8E-05 36.8 -2.0 37 365-401 12-48 (99)
60 cd05520 Bromo_polybromo_III Br 51.7 3.2 7E-05 36.7 -1.1 33 367-401 20-52 (103)
61 cd05515 Bromo_polybromo_V Brom 51.5 3.6 7.8E-05 36.3 -0.8 33 367-401 20-52 (105)
62 cd05509 Bromo_gcn5_like Bromod 51.4 2 4.4E-05 37.3 -2.4 35 365-401 13-47 (101)
63 KOG4628 Predicted E3 ubiquitin 46.6 11 0.00023 40.7 1.5 47 271-320 230-276 (348)
64 PF13771 zf-HC5HC2H: PHD-like 45.9 11 0.00023 31.6 1.2 30 270-302 36-68 (90)
65 KOG1512 PHD Zn-finger protein 45.8 7.3 0.00016 40.9 0.2 50 271-320 259-317 (381)
66 cd05516 Bromo_SNF2L2 Bromodoma 45.4 5.2 0.00011 35.5 -0.8 33 367-401 21-53 (107)
67 cd05492 Bromo_ZMYND11 Bromodom 45.4 5.6 0.00012 35.9 -0.6 61 371-433 19-83 (109)
68 cd05525 Bromo_ASH1 Bromodomain 45.0 7.9 0.00017 34.5 0.3 33 367-401 22-54 (106)
69 cd05518 Bromo_polybromo_IV Bro 44.5 5.2 0.00011 35.4 -0.9 33 367-401 20-52 (103)
70 PF13832 zf-HC5HC2H_2: PHD-zin 44.5 12 0.00026 32.7 1.3 31 270-302 55-87 (110)
71 PF12678 zf-rbx1: RING-H2 zinc 44.3 7.5 0.00016 32.3 0.0 29 286-318 45-73 (73)
72 PF01448 ELM2: ELM2 domain; I 41.5 17 0.00037 28.3 1.7 14 368-381 1-14 (55)
73 cd05517 Bromo_polybromo_II Bro 41.2 6.2 0.00013 34.9 -1.0 33 367-401 20-52 (103)
74 cd05519 Bromo_SNF2 Bromodomain 38.3 8.3 0.00018 33.8 -0.6 33 367-401 20-52 (103)
75 cd05529 Bromo_WDR9_I_like Brom 37.3 12 0.00026 34.3 0.2 34 367-401 41-74 (128)
76 PF07227 DUF1423: Protein of u 36.8 34 0.00074 38.0 3.6 59 261-321 121-193 (446)
77 cd00162 RING RING-finger (Real 36.3 11 0.00023 26.4 -0.3 42 273-319 2-43 (45)
78 cd05522 Bromo_Rsc1_2_II Bromod 32.4 9.1 0.0002 33.8 -1.3 33 367-401 21-53 (104)
79 cd05521 Bromo_Rsc1_2_I Bromodo 30.8 9.3 0.0002 34.1 -1.6 33 367-401 21-53 (106)
80 cd04718 BAH_plant_2 BAH, or Br 30.2 36 0.00079 32.6 2.2 19 251-269 6-24 (148)
81 KOG1244 Predicted transcriptio 29.0 14 0.00029 38.8 -1.0 50 271-320 225-284 (336)
82 smart00297 BROMO bromo domain. 28.1 8.2 0.00018 33.1 -2.4 33 367-401 21-53 (107)
83 PF00130 C1_1: Phorbol esters/ 27.5 48 0.001 25.1 2.1 31 271-301 12-44 (53)
84 cd05524 Bromo_polybromo_I Brom 26.1 12 0.00027 33.6 -1.7 28 373-402 28-55 (113)
85 KOG1734 Predicted RING-contain 24.4 34 0.00073 36.0 0.9 49 270-322 224-281 (328)
86 KOG0320 Predicted E3 ubiquitin 23.8 38 0.00082 33.5 1.1 34 211-245 129-162 (187)
87 smart00184 RING Ring finger. E 22.9 19 0.00041 24.1 -0.9 28 273-303 1-28 (39)
88 PHA02929 N1R/p28-like protein; 21.9 37 0.0008 34.7 0.6 48 270-321 174-226 (238)
89 PF10497 zf-4CXXC_R1: Zinc-fin 20.3 43 0.00092 30.0 0.6 50 270-320 7-70 (105)
90 PF05191 ADK_lid: Adenylate ki 20.3 68 0.0015 23.5 1.6 28 286-319 2-29 (36)
91 PF10367 Vps39_2: Vacuolar sor 20.3 64 0.0014 27.3 1.7 31 270-301 78-108 (109)
92 PF00301 Rubredoxin: Rubredoxi 20.3 72 0.0016 24.8 1.8 17 304-321 28-44 (47)
No 1
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.25 E-value=2.9e-12 Score=139.99 Aligned_cols=167 Identities=23% Similarity=0.376 Sum_probs=103.8
Q ss_pred ccccccccccccCCceEeccCCCCcccccccCCC--cCCCCCCCccChhccccccccch-hhccCCCCcccccccCCCCC
Q 009705 270 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTPR--IKIVPSDEWFCHLCLKKKHKTLK-ATARKSPNIISEKGRGRNAS 346 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~Pp--L~~iP~g~W~C~~C~~~~~~~~~-et~~ksp~i~~e~~~~r~a~ 346 (528)
+++|..|++.|.-..++|||.|+++||++|+.|| .+.+|.|.|||+.|..+-..-.. ++.+..-.+. +.. .....
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 EDFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSVINPKMETLSNRGTVV-DIF-TQFVS 330 (613)
T ss_pred HHHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeeecccchhhhhhccchH-HHH-HHHHH
Confidence 5799999999966677999999999999999999 55799999999999876432111 1111000000 000 00011
Q ss_pred CCCCCChhhhhccc-CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCCCCCccccccccccCCccCCCCeEe
Q 009705 347 AKGEPSPIELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTSECPSLHDLNSYNLSNLSSIGNWLQ 425 (528)
Q Consensus 347 ~~~gm~Pie~~l~e-lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~se~~~L~~l~~~~~~k~ds~gnw~q 425 (528)
.....+|+.+.+++ +..+|-++..|. ...|.+.-. ++.|+...+. |......+. +++.|+-+.
T Consensus 331 ~IDs~np~q~~lPe~i~~~~~~v~~g~------------~~~~sd~~~-~~pl~~~~~~-~d~e~~e~g--~~ssg~~~~ 394 (613)
T KOG4299|consen 331 KIDSHNPIQKILPENISESFGGVSRGD------------DGQYSDTQD-EKPLDPPALI-LDGENDENG--IDSSGTELL 394 (613)
T ss_pred hhhccchhhhhCCHHHHhhccccccCC------------CCccccccC-CcCCChhhhc-ccccCCccC--CCccCcchh
Confidence 23457788999998 777776766542 111211111 2233332221 111111121 234799999
Q ss_pred cccccCCCCCCCCcccCCCccccCcccccCCCCceeeccccCCCCCCCC
Q 009705 426 CKQVLEGTGDGVDGTSCGKWRRAPLFEVQTDDWECFCAVQWDPTHADCA 474 (528)
Q Consensus 426 C~~c~~~~g~~~~~i~C~kwrr~p~~~~~~~~w~c~c~~~Wdp~h~dC~ 474 (528)
|..|........-+..|. +|+.+| |.||+
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 999998666655666898 999999 99998
No 2
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.12 E-value=1.2e-11 Score=124.26 Aligned_cols=63 Identities=38% Similarity=0.889 Sum_probs=58.1
Q ss_pred CCCCCCCCCccccccccccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccChhcccc
Q 009705 257 NDVDSGTGCSGICSRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKK 320 (528)
Q Consensus 257 e~v~~g~~~cp~c~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 320 (528)
-.|...-|.|.+| .+|.+||...+.++||+||.|+|+|||||+.||+.+.|+|.|.|..|...
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 3455678999998 99999999999999999999999999999999999999999999999864
No 3
>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=99.02 E-value=9.5e-11 Score=90.72 Aligned_cols=44 Identities=43% Similarity=0.939 Sum_probs=29.3
Q ss_pred CeEecccccCCCCCCCCcccCCCccccCccc-----ccCCCCceeeccccCCCCCCCCCCCCCC
Q 009705 422 NWLQCKQVLEGTGDGVDGTSCGKWRRAPLFE-----VQTDDWECFCAVQWDPTHADCAVPQELE 480 (528)
Q Consensus 422 nw~qC~~c~~~~g~~~~~i~C~kwrr~p~~~-----~~~~~w~c~c~~~Wdp~h~dC~~P~el~ 480 (528)
+||||. .|+|||++|... .+++.|+|++|. |+.+++|++|+|++
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 999999999774 468899999999 78899999999974
No 4
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.88 E-value=3e-10 Score=126.20 Aligned_cols=105 Identities=20% Similarity=0.461 Sum_probs=80.5
Q ss_pred CCcccccccCCcccccccccchhhhccCcccccCCCCCCCCC-CCCCCC-----------------------------CC
Q 009705 215 SSSAVMLETTGKDLSAKDLCISILRNEGMLERFWPTQIRSSA-NDVDSG-----------------------------TG 264 (528)
Q Consensus 215 ss~I~~~e~~~ed~s~~D~C~sil~~~gl~~~~~~~~~~~~~-e~v~~g-----------------------------~~ 264 (528)
.|.+|+..+..+++++.-.|.|+||.+|+.. |......++ ++.-++ .+
T Consensus 125 ~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s--WsR~aqTCPiDR~EF~~v~V~eS~~~~~~vR~lP~EEs~~~~e~~~d 202 (1134)
T KOG0825|consen 125 QCPNCLKSCNDQLEESEKHTAHYFCEECVGS--WSRCAQTCPVDRGEFGEVKVLESTGIEANVRCLPSEESENILEKGGD 202 (1134)
T ss_pred hhhHHHHHHHHHhhccccccccccHHHHhhh--hhhhcccCchhhhhhheeeeeccccccceeEecchhhhhhhhhhccc
Confidence 5677888899999999999999999999876 444443332 111110 00
Q ss_pred Cc-------cccccccccccccccCCceEeccCCCCc-ccccccCCCcCCCCCCCccChhccccc
Q 009705 265 CS-------GICSRSCKICGRSETALKLLLCDDCEEA-FHVTCYTPRIKIVPSDEWFCHLCLKKK 321 (528)
Q Consensus 265 ~c-------p~c~d~C~VC~~~g~~~~LL~CD~C~r~-yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 321 (528)
.- ..-...|.+|+..+.++.||+||.|+.+ ||+|||+|+|.++|.++|||+.|....
T Consensus 203 ~~~d~~~~~~~E~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 203 EKQDQISGLSQEEVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLLE 267 (1134)
T ss_pred cccccccCcccccccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchhhh
Confidence 00 0013469999999989999999999999 999999999999999999999997654
No 5
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.68 E-value=5.1e-09 Score=106.18 Aligned_cols=72 Identities=22% Similarity=0.504 Sum_probs=60.8
Q ss_pred cCCCCCCCCC---CCCCCCCCCccccccccccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccCh-hccccc
Q 009705 247 FWPTQIRSSA---NDVDSGTGCSGICSRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCH-LCLKKK 321 (528)
Q Consensus 247 ~~~~~~~~~~---e~v~~g~~~cp~c~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~-~C~~~~ 321 (528)
.+|.+..+.+ ..+....|.|.+| ..|.+|+++..++++++||.|+|+||.+|+ +|..+|.|.|.|. .|....
T Consensus 289 ~HP~Ci~M~~elv~~~KTY~W~C~~C-~lC~IC~~P~~E~E~~FCD~CDRG~HT~CV--GL~~lP~G~WICD~~C~~~~ 364 (381)
T KOG1512|consen 289 PHPYCVAMIPELVGQYKTYFWKCSSC-ELCRICLGPVIESEHLFCDVCDRGPHTLCV--GLQDLPRGEWICDMRCREAT 364 (381)
T ss_pred CCCcchhcCHHHHhHHhhcchhhccc-HhhhccCCcccchheeccccccCCCCcccc--ccccccCccchhhhHHHHhc
Confidence 3555555554 3455788999987 899999999999999999999999999999 9999999999999 676654
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=98.64 E-value=1.2e-08 Score=77.86 Aligned_cols=48 Identities=33% Similarity=0.949 Sum_probs=42.5
Q ss_pred ccccccccccCCceEeccCCCCcccccccCCCcC--CCCCCCccChhccc
Q 009705 272 SCKICGRSETALKLLLCDDCEEAFHVTCYTPRIK--IVPSDEWFCHLCLK 319 (528)
Q Consensus 272 ~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~--~iP~g~W~C~~C~~ 319 (528)
+|.+|++.+..+.||.||.|.+.||..|+.|++. .++.+.|+|+.|..
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 45566999999975
No 7
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.30 E-value=2.4e-07 Score=102.43 Aligned_cols=63 Identities=35% Similarity=0.816 Sum_probs=57.1
Q ss_pred CCCCCCCccccccccccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccChhcccccc
Q 009705 259 VDSGTGCSGICSRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKH 322 (528)
Q Consensus 259 v~~g~~~cp~c~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~ 322 (528)
+..+.|.|+.| ..|.+|+.+|++.++++|+.|+-+||.||..|+++.+|.|.|+|..|...+.
T Consensus 58 ~l~~gWrC~~c-rvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c~q 120 (694)
T KOG4443|consen 58 VLSGGWRCPSC-RVCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTRCRQ 120 (694)
T ss_pred HhcCCcccCCc-eeeeeccccCCcccccccccccccccccccCCccccccCcccccHHHHhhhh
Confidence 34566999987 8999999999999999999999999999999999999999999998876543
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=97.99 E-value=3.2e-06 Score=79.31 Aligned_cols=30 Identities=37% Similarity=0.975 Sum_probs=27.4
Q ss_pred cccccccCCCcCCCCCCCccChhccccccc
Q 009705 294 AFHVTCYTPRIKIVPSDEWFCHLCLKKKHK 323 (528)
Q Consensus 294 ~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~~ 323 (528)
+||++||+|||..+|+|+|+|+.|..+...
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~ 30 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSG 30 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCCC
Confidence 699999999999999999999999987543
No 10
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.68 E-value=2.1e-05 Score=80.35 Aligned_cols=44 Identities=34% Similarity=0.847 Sum_probs=38.7
Q ss_pred ccccccccccCCceEeccC--CC-CcccccccCCCcCCCCCCCccChhccccc
Q 009705 272 SCKICGRSETALKLLLCDD--CE-EAFHVTCYTPRIKIVPSDEWFCHLCLKKK 321 (528)
Q Consensus 272 ~C~VC~~~g~~~~LL~CD~--C~-r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 321 (528)
+|. |...| +|+-||. |+ ..||+.|+ .|...|.|.|||+.|....
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 9999998 99 99999999 9999999999999998754
No 11
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=97.58 E-value=1.2e-05 Score=96.93 Aligned_cols=59 Identities=34% Similarity=0.842 Sum_probs=53.1
Q ss_pred CCccccccccccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccChhcccccc
Q 009705 264 GCSGICSRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKH 322 (528)
Q Consensus 264 ~~cp~c~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~ 322 (528)
|.-....-.|.+|...+..+.|+.|+.|..+||++|+.|.+..+|.|+|+|+.|+..+.
T Consensus 1102 w~~s~~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1102 WDRSAVNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hccccchhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 54444467899999999889999999999999999999999999999999999998775
No 12
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.51 E-value=4.4e-05 Score=86.49 Aligned_cols=55 Identities=31% Similarity=0.782 Sum_probs=47.4
Q ss_pred CCccccccccccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccChhcccccc
Q 009705 264 GCSGICSRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKH 322 (528)
Q Consensus 264 ~~cp~c~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~ 322 (528)
|...+ ...|.+|+++| .+|+||.|+.+||.+|+.|++...|.++|.|+.|.....
T Consensus 42 ~~~~~-~e~c~ic~~~g---~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~~ 96 (696)
T KOG0383|consen 42 WDDAE-QEACRICADGG---ELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCPKN 96 (696)
T ss_pred cchhh-hhhhhhhcCCC---cEEEeccccHHHHHHccCCCCCcCCccceeeeeeccCCC
Confidence 44433 47899999999 999999999999999999999999999999999955443
No 13
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.23 E-value=0.00016 Score=85.12 Aligned_cols=52 Identities=33% Similarity=0.885 Sum_probs=45.4
Q ss_pred ccccccccccccC--CceEeccCCCCcccccccCCCcCCCCCCCccChhccccccc
Q 009705 270 SRSCKICGRSETA--LKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKHK 323 (528)
Q Consensus 270 ~d~C~VC~~~g~~--~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~~ 323 (528)
+.+|.+|.++.-. +.+|+||.|+.++|+.|+. +.-+|+|.|+|..|......
T Consensus 219 D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cyg--i~~ipeg~WlCr~Cl~s~~~ 272 (1051)
T KOG0955|consen 219 DAVCCICLDGECQNSNVIVFCDGCNLAVHQECYG--IPFIPEGQWLCRRCLQSPQR 272 (1051)
T ss_pred CccceeecccccCCCceEEEcCCCcchhhhhccC--CCCCCCCcEeehhhccCcCc
Confidence 5789999998744 7999999999999999994 77899999999999876543
No 14
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.11 E-value=0.00017 Score=78.42 Aligned_cols=54 Identities=33% Similarity=0.805 Sum_probs=43.7
Q ss_pred cccccccccc--cCCceEeccCCCCcccccccCCCcCCC----CCCCccChhcccccccc
Q 009705 271 RSCKICGRSE--TALKLLLCDDCEEAFHVTCYTPRIKIV----PSDEWFCHLCLKKKHKT 324 (528)
Q Consensus 271 d~C~VC~~~g--~~~~LL~CD~C~r~yH~~Cl~PpL~~i----P~g~W~C~~C~~~~~~~ 324 (528)
..|.||+.++ ..++||.|+.|...||+.||.|+++.. |..+|||..|.......
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~ 228 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKV 228 (464)
T ss_pred ceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhhc
Confidence 4599988654 455999999999999999999987754 66789999998765443
No 15
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=96.76 E-value=0.00056 Score=74.38 Aligned_cols=51 Identities=27% Similarity=0.830 Sum_probs=44.8
Q ss_pred ccccccccccc--cCCceEeccCCCCcccccccCCCcCCCCCCCccChhcccccc
Q 009705 270 SRSCKICGRSE--TALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKH 322 (528)
Q Consensus 270 ~d~C~VC~~~g--~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~ 322 (528)
++.|.+|.+.. +.+.+++||+|+-+.|+.|+ ++..+|+|.|+|..|.....
T Consensus 193 d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CY--GI~f~peG~WlCrkCi~~~~ 245 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCDGCEICVHQSCY--GIQFLPEGFWLCRKCIYGEY 245 (669)
T ss_pred hhhhHhccccccCCcceEEEecCcchhhhhhcc--cceecCcchhhhhhhccccc
Confidence 57899999876 45689999999999999999 88899999999999986543
No 16
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=96.73 E-value=0.00044 Score=75.28 Aligned_cols=50 Identities=34% Similarity=0.828 Sum_probs=45.1
Q ss_pred ccccccccccccCCceEeccCCCCcccccccCCCcCCCCCC----CccChhccc
Q 009705 270 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSD----EWFCHLCLK 319 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g----~W~C~~C~~ 319 (528)
...|.+|....+...++.||.|...||+-|+.|||+.+|.. -|.|..|-.
T Consensus 544 ~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk 597 (707)
T KOG0957|consen 544 NYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDK 597 (707)
T ss_pred ceeeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccccc
Confidence 46799999988888999999999999999999999999975 499999943
No 17
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.62 E-value=0.00071 Score=49.38 Aligned_cols=34 Identities=41% Similarity=1.092 Sum_probs=20.8
Q ss_pred CceEeccCCCCcccccccCCCcCCCCCC-CccChhcc
Q 009705 283 LKLLLCDDCEEAFHVTCYTPRIKIVPSD-EWFCHLCL 318 (528)
Q Consensus 283 ~~LL~CD~C~r~yH~~Cl~PpL~~iP~g-~W~C~~C~ 318 (528)
+.||.|+.|.-..|..|+ ++..+|.+ +|+|..|+
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 18
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.50 E-value=0.001 Score=75.25 Aligned_cols=55 Identities=29% Similarity=0.738 Sum_probs=46.4
Q ss_pred CCccccccccccccccc--cCCceEeccCCCCcccccccCCCcCCCCCCCccChhcccc
Q 009705 264 GCSGICSRSCKICGRSE--TALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKK 320 (528)
Q Consensus 264 ~~cp~c~d~C~VC~~~g--~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 320 (528)
..+-.++..|.||..++ ..++|++||.|.-..|+.|+ +|.++|.|.|.|..|.-.
T Consensus 265 gie~dedviCDvCrspD~e~~neMVfCd~Cn~cVHqaCy--GIle~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 265 GIEYDEDVICDVCRSPDSEEANEMVFCDKCNICVHQACY--GILEVPEGPWLCRTCALG 321 (893)
T ss_pred eeeccccceeceecCCCccccceeEEeccchhHHHHhhh--ceeecCCCCeeehhcccc
Confidence 33333467899999874 45699999999999999999 999999999999999754
No 19
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=96.38 E-value=0.0014 Score=73.75 Aligned_cols=49 Identities=35% Similarity=0.932 Sum_probs=41.5
Q ss_pred ccccccccc--cCCceEecc--CCCCcccccccCCCcCCCCCCCccChhcccccc
Q 009705 272 SCKICGRSE--TALKLLLCD--DCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKKH 322 (528)
Q Consensus 272 ~C~VC~~~g--~~~~LL~CD--~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~~ 322 (528)
-|-||.+.. .++.|+.|| .|.-+.|+-|+ .+-++|.|.|||..|....+
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCY--GIvqVPtGpWfCrKCesqer 59 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACY--GIVQVPTGPWFCRKCESQER 59 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcc--eeEecCCCchhhhhhhhhhh
Confidence 477888643 466899999 59999999999 99999999999999987543
No 20
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.31 E-value=0.002 Score=65.30 Aligned_cols=43 Identities=30% Similarity=0.869 Sum_probs=34.6
Q ss_pred cccccccCCceEecc--CCCC-cccccccCCCcCCCCCCCccChhcccc
Q 009705 275 ICGRSETALKLLLCD--DCEE-AFHVTCYTPRIKIVPSDEWFCHLCLKK 320 (528)
Q Consensus 275 VC~~~g~~~~LL~CD--~C~r-~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 320 (528)
.|++.. -++|+-|| .|.+ .||+.|+ +|+..|.|.|||+.|+..
T Consensus 225 fCqqvS-yGqMVaCDn~nCkrEWFH~~CV--GLk~pPKG~WYC~eCk~~ 270 (271)
T COG5034 225 FCQQVS-YGQMVACDNANCKREWFHLECV--GLKEPPKGKWYCPECKKA 270 (271)
T ss_pred Eecccc-cccceecCCCCCchhheecccc--ccCCCCCCcEeCHHhHhc
Confidence 455532 23899999 5875 4899999 999999999999999863
No 21
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=95.65 E-value=0.0057 Score=72.02 Aligned_cols=48 Identities=29% Similarity=0.710 Sum_probs=45.2
Q ss_pred ccccccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccChhcccc
Q 009705 270 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKK 320 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 320 (528)
++.|.+|.+.+ .++||..|++.||+.|..||+.++|+..|-|-.|..-
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 67899999999 8999999999999999999999999999999999844
No 22
>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=92.42 E-value=0.026 Score=50.02 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=40.5
Q ss_pred CChhhhhccc-CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 351 PSPIELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 351 m~Pie~~l~e-lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
|++.++++|+ ++..+...+.+.+|..||.. ..++|+++|.+||+|.+-
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 4677888888 67777788899999999987 678999999999998764
No 23
>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=91.83 E-value=0.033 Score=49.60 Aligned_cols=46 Identities=17% Similarity=0.151 Sum_probs=36.6
Q ss_pred hhhhhccc-CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCCC
Q 009705 353 PIELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTSE 402 (528)
Q Consensus 353 Pie~~l~e-lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~se 402 (528)
|.++++|+ +++.+++.+.+..|.. .|. ..++|+++|++||||++-+
T Consensus 1 ~~~l~~ce~il~~l~~~~~s~~f~~-~p~---~~pdY~~iIk~PMDL~tI~ 47 (102)
T cd05501 1 PEELLKCEFLLLKVYCMSKSGFFIS-KPY---YIRDYCQGIKEPMWLNKVK 47 (102)
T ss_pred CHHHHHHHHHHHHHHhCcccccccC-CCC---CCCchHHHcCCCCCHHHHH
Confidence 35678899 8888999998866754 344 6789999999999998753
No 24
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=87.44 E-value=0.39 Score=56.87 Aligned_cols=51 Identities=33% Similarity=0.977 Sum_probs=45.2
Q ss_pred ccccccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccChhccccc
Q 009705 270 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 321 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 321 (528)
...|..|..+..+ .++.|+.|...||.+|..|++..++.|+|.|+.|....
T Consensus 155 ~~~~~~~~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 (904)
T KOG1246|consen 155 YPQCNTCSKGKEE-KLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIPTP 205 (904)
T ss_pred chhhhccccCCCc-cceecccccCcccccccCCCCCcCCcCcccCCcccccc
Confidence 3579999988877 55599999999999999999999999999999998763
No 25
>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=85.14 E-value=0.12 Score=46.07 Aligned_cols=48 Identities=13% Similarity=0.112 Sum_probs=34.4
Q ss_pred hhhcccCCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCCC
Q 009705 355 ELMLTSTVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTSE 402 (528)
Q Consensus 355 e~~l~elllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~se 402 (528)
.+.+..++..+...+.+.+|..||..-....++|+++|++||||.+-+
T Consensus 7 ~~~~~~il~~l~~~~~s~~F~~PVd~~~~~~pdY~~iIk~PmDL~tI~ 54 (107)
T cd05497 7 QYLLKVVLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIK 54 (107)
T ss_pred HHHHHHHHHHHHhCCcCccccCCCCcccccCCcHHHHHcCcccHHHHH
Confidence 344444455566778888999999642223689999999999987643
No 26
>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=84.02 E-value=0.14 Score=44.84 Aligned_cols=39 Identities=13% Similarity=0.225 Sum_probs=29.7
Q ss_pred CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 361 TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 361 lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
++..+...+.+.+|..+|.. ...++|+++|++||||.+-
T Consensus 8 il~~l~~~~~s~~F~~pv~~--~~~pdY~~iIk~PmDL~tI 46 (97)
T cd05505 8 ILSKILKYRFSWPFREPVTA--DEAEDYKKVITNPMDLQTM 46 (97)
T ss_pred HHHHHHhCCCcccccCCCCh--hhcccHHHHcCCcCCHHHH
Confidence 33344456678899999964 3578999999999999864
No 27
>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=80.89 E-value=0.25 Score=44.98 Aligned_cols=39 Identities=13% Similarity=0.112 Sum_probs=31.0
Q ss_pred CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 361 TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 361 lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
++..+..++.+.+|..||.. ...++|+++|.+||||++-
T Consensus 13 il~~l~~~~~s~~F~~PVd~--~~~pdY~~iIk~PmDL~tI 51 (119)
T cd05496 13 LVNLMWDCEDSEPFRQPVDL--LKYPDYRDIIDTPMDLGTV 51 (119)
T ss_pred HHHHHHhCCccccccCCCCh--hhcCcHHHHhCCcccHHHH
Confidence 45555567788899999965 2578999999999999874
No 28
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=80.17 E-value=2.5 Score=47.11 Aligned_cols=50 Identities=34% Similarity=0.743 Sum_probs=38.1
Q ss_pred ccccccccc--cCCceEeccCCCCcccccccCCC-cCCCCCC-------CccChhccccc
Q 009705 272 SCKICGRSE--TALKLLLCDDCEEAFHVTCYTPR-IKIVPSD-------EWFCHLCLKKK 321 (528)
Q Consensus 272 ~C~VC~~~g--~~~~LL~CD~C~r~yH~~Cl~Pp-L~~iP~g-------~W~C~~C~~~~ 321 (528)
.|.||-+.. +.+++|.||.|+-..|-.|+.-- -.+||.| .|||-.|+..-
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 799998654 55699999999999999999432 1134543 69999998764
No 29
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=79.62 E-value=0.58 Score=56.03 Aligned_cols=50 Identities=22% Similarity=0.359 Sum_probs=41.6
Q ss_pred ccccccccccccCCceEeccC-CCCcccc-cccCC--CcCCCCCCCccChhcccccc
Q 009705 270 SRSCKICGRSETALKLLLCDD-CEEAFHV-TCYTP--RIKIVPSDEWFCHLCLKKKH 322 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~CD~-C~r~yH~-~Cl~P--pL~~iP~g~W~C~~C~~~~~ 322 (528)
.+.|.+|+..+ .+|+|+. |+..||+ .|++- --..++++-|+|+.|...+.
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 57799999776 8999998 9999998 99973 33458999999999987654
No 30
>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=77.08 E-value=0.32 Score=42.31 Aligned_cols=39 Identities=8% Similarity=0.048 Sum_probs=29.7
Q ss_pred CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 361 TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 361 lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
++..+.....+..|..+|.. ...++|+++|++||||.+-
T Consensus 8 il~~l~~~~~~~~F~~pv~~--~~~p~Y~~iIk~PmdL~tI 46 (97)
T cd05503 8 ILDEMEAHEDAWPFLEPVNT--KLVPGYRKIIKKPMDFSTI 46 (97)
T ss_pred HHHHHHcCCCchhhcCCCCc--cccCCHHHHhCCCCCHHHH
Confidence 44445556677789999965 3568999999999998764
No 31
>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=76.93 E-value=1.1 Score=40.35 Aligned_cols=34 Identities=9% Similarity=0.006 Sum_probs=26.6
Q ss_pred cccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 368 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 368 VR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
...+.+|..||..-...+++|+++|++||+|.+-
T Consensus 18 ~~~~~pF~~PVd~~~~~~pdY~~iIK~PMDL~ti 51 (114)
T cd05494 18 NEDAWPFLEPVNPPRRGAPDYRDVIKRPMSFGTK 51 (114)
T ss_pred CCCCCCcCCCCCchhcCCCChhhhcCCCCChHHH
Confidence 4467799999954223678999999999999875
No 32
>KOG1474 consensus Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins [Transcription]
Probab=76.44 E-value=0.85 Score=52.25 Aligned_cols=52 Identities=10% Similarity=-0.037 Sum_probs=39.3
Q ss_pred CCChhhhhccc-CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 350 EPSPIELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 350 gm~Pie~~l~e-lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+...-.++-|. ++..+..++-+.+|++||-.-.-.+.+|+++|++||||.|-
T Consensus 218 ~~~~~~lk~C~~iLk~l~~~k~awpF~~PVD~v~LgLpDY~~IIK~PMDLgTI 270 (640)
T KOG1474|consen 218 KLTVELLKQCLSILKRLMKHKHAWPFNEPVDVVKLGLPDYHDIIKHPMDLGTI 270 (640)
T ss_pred cccHHHHHHHHHHHHHHHhccCCCCcCCCcCHHhcCCcchhhhcCCCccHHHH
Confidence 34444455555 66677778888999999954444678999999999999885
No 33
>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=75.71 E-value=0.39 Score=35.53 Aligned_cols=43 Identities=26% Similarity=0.526 Sum_probs=29.1
Q ss_pred ccccccccccc-CCceEeccCCCCcccccccCCCcCCCCCCCccChhcc
Q 009705 271 RSCKICGRSET-ALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCL 318 (528)
Q Consensus 271 d~C~VC~~~g~-~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~ 318 (528)
+.|.+|...-. .+.++... |...||..|+..-+... -.||.|+
T Consensus 1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~----~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRN----NSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHS----SB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhC----CcCCccC
Confidence 35888887653 33444444 99999999998766553 2788885
No 34
>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=75.35 E-value=0.47 Score=41.81 Aligned_cols=33 Identities=15% Similarity=0.095 Sum_probs=27.1
Q ss_pred cccCCCccccCCCCCCCCCCCCCCCCCCccCCCCC
Q 009705 368 VRVGKGFQADIPDWLAPTNNDGYALGEPLELDTSE 402 (528)
Q Consensus 368 VR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~se 402 (528)
.+.+.+|..||.. ...++|+++|++||||.+-+
T Consensus 17 ~~~s~~F~~PV~~--~~~pdY~~iIk~PmDL~tI~ 49 (99)
T cd05508 17 QPGAEPFLKPVDL--EQFPDYAQYVFKPMDLSTLE 49 (99)
T ss_pred CcCcchhcCCCCh--hhCCCHHHHcCCCCCHHHHH
Confidence 4567799999975 36789999999999998753
No 35
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=74.61 E-value=1.6 Score=42.48 Aligned_cols=50 Identities=28% Similarity=0.749 Sum_probs=35.0
Q ss_pred ccccccc---cccCCceEeccCCCCcccccccCCCc------CCCCCCC--ccChhccccc
Q 009705 272 SCKICGR---SETALKLLLCDDCEEAFHVTCYTPRI------KIVPSDE--WFCHLCLKKK 321 (528)
Q Consensus 272 ~C~VC~~---~g~~~~LL~CD~C~r~yH~~Cl~PpL------~~iP~g~--W~C~~C~~~~ 321 (528)
.|.+|+. ..+-+.|+.|-+|..+||..|+.|.- +.+-.+. -.|.+|+...
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~ 61 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIA 61 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChh
Confidence 3788854 23455999999999999999998842 2343343 4678887543
No 36
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=74.15 E-value=0.95 Score=51.61 Aligned_cols=59 Identities=29% Similarity=0.590 Sum_probs=42.5
Q ss_pred CCCCccccccccccccccc--cCCceEeccCCCCcccccccCCCcCCC-CCCCccChhccccc
Q 009705 262 GTGCSGICSRSCKICGRSE--TALKLLLCDDCEEAFHVTCYTPRIKIV-PSDEWFCHLCLKKK 321 (528)
Q Consensus 262 g~~~cp~c~d~C~VC~~~g--~~~~LL~CD~C~r~yH~~Cl~PpL~~i-P~g~W~C~~C~~~~ 321 (528)
++.++.. ...|-+|+..| .+..|+.|..|...||.+|+.--+... -.+-|.|+.|+...
T Consensus 11 ~~~~~~~-~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 11 SDKAIIV-CLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred cchhhhh-hhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 3344433 36788888765 466899999999999999997544433 23449999998753
No 37
>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=73.43 E-value=0.75 Score=40.35 Aligned_cols=42 Identities=12% Similarity=0.163 Sum_probs=30.7
Q ss_pred CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCCC
Q 009705 361 TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTSE 402 (528)
Q Consensus 361 lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~se 402 (528)
+...+..++.+.+|..||.+-....++|+++|.+||+|.+-+
T Consensus 12 ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~I~~P~dL~tI~ 53 (103)
T cd05500 12 SIRSLKRLKDARPFLVPVDPVKLNIPHYPTIIKKPMDLGTIE 53 (103)
T ss_pred HHHHHHcCCCChhhcCCCCcccccCCCHHHHhcCCCCHHHHH
Confidence 444455667788999999531245679999999999987643
No 38
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=72.18 E-value=2.3 Score=34.14 Aligned_cols=32 Identities=22% Similarity=0.841 Sum_probs=27.5
Q ss_pred cccccccccc-cCCceEeccCCCCcccccccCC
Q 009705 271 RSCKICGRSE-TALKLLLCDDCEEAFHVTCYTP 302 (528)
Q Consensus 271 d~C~VC~~~g-~~~~LL~CD~C~r~yH~~Cl~P 302 (528)
..|.+|+..- +.++++.|..|...||-.|+..
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 4799999865 3668999999999999999965
No 39
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=71.61 E-value=1.8 Score=37.62 Aligned_cols=48 Identities=19% Similarity=0.451 Sum_probs=34.8
Q ss_pred ccccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccChhccccc
Q 009705 272 SCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 321 (528)
Q Consensus 272 ~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 321 (528)
.|..|.-+|+.-.++++. |...||+.|+.--|.+-. ..=.||.||..-
T Consensus 34 ~Cp~Ck~Pgd~Cplv~g~-C~H~FH~hCI~kWl~~~~-~~~~CPmCR~~w 81 (85)
T PF12861_consen 34 CCPDCKFPGDDCPLVWGK-CSHNFHMHCILKWLSTQS-SKGQCPMCRQPW 81 (85)
T ss_pred CCCCccCCCCCCceeecc-CccHHHHHHHHHHHcccc-CCCCCCCcCCee
Confidence 466677777665666555 999999999988777642 244899998653
No 40
>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=71.58 E-value=0.88 Score=40.13 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=29.5
Q ss_pred CCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 362 VPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 362 llyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
...+...+.+.+|..||.. ...++|+++|.+||||.+-
T Consensus 12 l~~l~~~~~a~~F~~pV~~--~~~p~Y~~iIk~PmDL~tI 49 (104)
T cd05507 12 YRTLASHRYASVFLKPVTE--DIAPGYHSVVYRPMDLSTI 49 (104)
T ss_pred HHHHHcCCCCHhhcCCCCc--cccCCHHHHhCCCcCHHHH
Confidence 3344456677799999975 3578999999999998764
No 41
>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=71.40 E-value=0.76 Score=41.41 Aligned_cols=47 Identities=13% Similarity=0.135 Sum_probs=34.4
Q ss_pred hhhhhccc-CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 353 PIELMLTS-TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 353 Pie~~l~e-lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+.+...|. ++..+...+.+..|..+|.. ...++|+++|..||+|.+-
T Consensus 11 ~~~~~~c~~il~~l~~~~~s~~F~~pvd~--~~~pdY~~vI~~PmDL~tI 58 (115)
T cd05504 11 PLNLSALEQLLVEIVKHKDSWPFLRPVSK--IEVPDYYDIIKKPMDLGTI 58 (115)
T ss_pred HHHHHHHHHHHHHHHhCCCchhhcCCCCc--cccccHHHHhcCcccHHHH
Confidence 34444455 55555566778889999974 4578999999999998764
No 42
>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=69.97 E-value=0.59 Score=40.97 Aligned_cols=37 Identities=8% Similarity=0.073 Sum_probs=28.1
Q ss_pred CcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 363 PYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 363 lyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
..+...+.+..|..+|.. ...++|+++|++||+|.+-
T Consensus 11 ~~l~~~~~~~~F~~pVd~--~~~pdY~~iIk~PmDL~tI 47 (98)
T cd05512 11 DQLQEKDTAEIFSEPVDL--SEVPDYLDHIKQPMDFSTM 47 (98)
T ss_pred HHHHhCCCchhhcCCCCc--cccCCHHHHhcCCcCHHHH
Confidence 334445667789999965 3578999999999998764
No 43
>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=69.10 E-value=0.66 Score=40.80 Aligned_cols=35 Identities=11% Similarity=0.075 Sum_probs=26.6
Q ss_pred ccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 365 TTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 365 l~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+...+.+..|..||.. ...++|+++|++||||.+-
T Consensus 13 l~~~~~~~~F~~PV~~--~~~pdY~~vIk~PmDL~tI 47 (98)
T cd05513 13 LQRKDPHGFFAFPVTD--FIAPGYSSIIKHPMDFSTM 47 (98)
T ss_pred HHcCCccccccCcCCc--cccccHHHHHcCccCHHHH
Confidence 3344556689999965 2568999999999998764
No 44
>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=68.97 E-value=0.88 Score=39.59 Aligned_cols=33 Identities=12% Similarity=0.063 Sum_probs=24.6
Q ss_pred ccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 369 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 369 R~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+.+.+|..+|..-....++|+++|.+||+|.+-
T Consensus 19 ~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~~I 51 (102)
T cd05498 19 AYAWPFYKPVDPEALGLHDYHDIIKHPMDLSTI 51 (102)
T ss_pred cccCcccCcCCccccCCCcHHHHccCCCcHHHH
Confidence 556689998854122367899999999998764
No 45
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=68.16 E-value=2.9 Score=47.58 Aligned_cols=47 Identities=36% Similarity=0.808 Sum_probs=39.7
Q ss_pred cccccccccccCCceEeccCCCCcccccccCCCcCC-CCCCCccChhcccc
Q 009705 271 RSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKI-VPSDEWFCHLCLKK 320 (528)
Q Consensus 271 d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~-iP~g~W~C~~C~~~ 320 (528)
..|.+|..+| .+++|+.|+.+||..|..+++.. .+.+.|.|..|...
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 5799999999 89999999999999999998872 23457888888764
No 46
>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=67.13 E-value=0.87 Score=40.53 Aligned_cols=40 Identities=13% Similarity=0.040 Sum_probs=28.9
Q ss_pred CCccccc-ccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 362 VPYTTSV-RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 362 llyl~cV-R~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
...+... +.+..|..||..-....++|+++|++||+|.+-
T Consensus 12 l~~l~~~~~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI 52 (108)
T cd05495 12 LEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTI 52 (108)
T ss_pred HHHHHHcCcccchhcCCCCccccCCCcHHHHhCCCCCHHHH
Confidence 3344455 667789999965222468999999999998764
No 47
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=65.75 E-value=0.81 Score=37.85 Aligned_cols=50 Identities=20% Similarity=0.483 Sum_probs=20.6
Q ss_pred ccccccccccc---CCceEecc--CCCCcccccccCCCcCCCCCC-------CccChhcccc
Q 009705 271 RSCKICGRSET---ALKLLLCD--DCEEAFHVTCYTPRIKIVPSD-------EWFCHLCLKK 320 (528)
Q Consensus 271 d~C~VC~~~g~---~~~LL~CD--~C~r~yH~~Cl~PpL~~iP~g-------~W~C~~C~~~ 320 (528)
..|.+|..... ....+.|+ .|...||..|+.-.+.+.+.+ .+-||.|...
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 46888886432 22458898 999999999997544332221 3568888764
No 48
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=64.56 E-value=2.9 Score=48.26 Aligned_cols=53 Identities=26% Similarity=0.646 Sum_probs=36.3
Q ss_pred ccccccccccccCCce-----Eecc--CCCCcccccccCC-CcCCC-----CCCCccChhcccccc
Q 009705 270 SRSCKICGRSETALKL-----LLCD--DCEEAFHVTCYTP-RIKIV-----PSDEWFCHLCLKKKH 322 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~L-----L~CD--~C~r~yH~~Cl~P-pL~~i-----P~g~W~C~~C~~~~~ 322 (528)
++.|-+|...|++++. +-|. .|.++||..|-.- .|.-. -+..-||.+|.....
T Consensus 117 nKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hfs 182 (900)
T KOG0956|consen 117 NKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFS 182 (900)
T ss_pred cceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHHH
Confidence 5679999988766543 5564 6889999999864 23322 223579999976543
No 49
>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=62.61 E-value=1 Score=40.50 Aligned_cols=40 Identities=10% Similarity=0.119 Sum_probs=29.6
Q ss_pred CCCccccc-ccCCCccccCCCCCCCCCCCCCCCCCCccCCCCC
Q 009705 361 TVPYTTSV-RVGKGFQADIPDWLAPTNNDGYALGEPLELDTSE 402 (528)
Q Consensus 361 lllyl~cV-R~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~se 402 (528)
++..+..+ +.+..|..+|.. ...++|+++|++||+|.+-+
T Consensus 15 il~~l~~~~~~s~~F~~pv~~--~~~pdY~~iIk~PmdL~tI~ 55 (112)
T cd05510 15 VLNELKTYTEHSTPFLTKVSK--REAPDYYDIIKKPMDLGTML 55 (112)
T ss_pred HHHHHHhcCccccchhcCCCh--hhcCCHHHHhcCccCHHHHH
Confidence 34444444 567789999965 35789999999999987643
No 50
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=62.52 E-value=1.1 Score=55.70 Aligned_cols=39 Identities=10% Similarity=0.077 Sum_probs=31.0
Q ss_pred CCCcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 361 TVPYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 361 lllyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
++.-+..+.-..+|.++|-. ..++.|++||++||+|.+.
T Consensus 1309 il~e~~~~~~awPFlepVn~--~~vp~Y~~IIk~Pmdl~ti 1347 (1404)
T KOG1245|consen 1309 ILHELVVHKAAWPFLEPVNP--KEVPDYYDIIKKPMDLSTI 1347 (1404)
T ss_pred HHHHHHHhhhcchhhccCCh--hhcccHHHHhcChhHHHHH
Confidence 44445566778899999965 3788999999999999774
No 51
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=59.47 E-value=2 Score=49.85 Aligned_cols=51 Identities=24% Similarity=0.257 Sum_probs=46.5
Q ss_pred ccccccccccccCCceEeccCCCCcccccccCC-CcCCCCCCCccChhccccccc
Q 009705 270 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTP-RIKIVPSDEWFCHLCLKKKHK 323 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~P-pL~~iP~g~W~C~~C~~~~~~ 323 (528)
++.|..|.... ..+.|+.|-|.||..|+.| |++..+.|.|-|+.|..+..+
T Consensus 506 d~~~~~~~~~l---~~l~~p~~lrr~k~d~l~~~P~Kte~i~~~~~~~~Q~~~yk 557 (696)
T KOG0383|consen 506 DISCEEQIKKL---HLLLCPHMLRRLKLDVLKPMPLKTELIGRVELSPCQKKYYK 557 (696)
T ss_pred hhhHHHHHHhh---ccccCchhhhhhhhhhccCCCccceeEEEEecCHHHHHHHH
Confidence 67899999988 8999999999999999999 999999999999999876543
No 52
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=59.36 E-value=6.5 Score=38.74 Aligned_cols=43 Identities=23% Similarity=0.719 Sum_probs=33.0
Q ss_pred ccccccccccc-----cCCceEeccCCCCcccccccCCCcCCCCCCCccChhccccc
Q 009705 270 SRSCKICGRSE-----TALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 321 (528)
Q Consensus 270 ~d~C~VC~~~g-----~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 321 (528)
...|++|.+.+ +.+....|..|...||..|... =.||.|...+
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 35799998765 3447789999999999999952 1399997654
No 53
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=57.41 E-value=31 Score=39.22 Aligned_cols=48 Identities=21% Similarity=0.225 Sum_probs=36.6
Q ss_pred ccccccccccccCCceEeccCCCCcccccccCCCcCC-CCCCCccChhcccc
Q 009705 270 SRSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKI-VPSDEWFCHLCLKK 320 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~-iP~g~W~C~~C~~~ 320 (528)
+-+|.-|.-.| ..|.|+.|-|.||..|..|.-.. --...|.|+.|..-
T Consensus 60 d~~cfechlpg---~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~ 108 (588)
T KOG3612|consen 60 DPFCFECHLPG---AVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQPYSF 108 (588)
T ss_pred CcccccccCCc---ceeeeehhhccccccccCcchhhccccccccCCccccc
Confidence 34677888888 89999999999999999874222 12236999988754
No 54
>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=55.54 E-value=1.5 Score=39.38 Aligned_cols=36 Identities=11% Similarity=0.147 Sum_probs=27.5
Q ss_pred ccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCCC
Q 009705 365 TTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTSE 402 (528)
Q Consensus 365 l~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~se 402 (528)
+..++.+..|..+|.. ...++|+++|..||+|.+-+
T Consensus 12 l~~~~~s~~F~~pv~~--~~~p~Y~~~I~~PmdL~tI~ 47 (112)
T cd05511 12 LKNLPDSWPFHTPVNK--KKVPDYYKIIKRPMDLQTIR 47 (112)
T ss_pred HHhCCCchhhcCCCCh--hhcccHHHHhcCCCCHHHHH
Confidence 3345667789999965 35789999999999987643
No 55
>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=55.53 E-value=1.8 Score=37.75 Aligned_cols=33 Identities=15% Similarity=0.065 Sum_probs=25.0
Q ss_pred ccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 369 RVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 369 R~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
..+.+|..+|..-....++|+++|.+||+|.+-
T Consensus 19 ~~s~~F~~pvd~~~~~~pdY~~~I~~P~dL~~I 51 (102)
T cd05499 19 AYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTI 51 (102)
T ss_pred cccchhcCCCCccccCCCCHHHHhcCCCCHHHH
Confidence 456689999865223567899999999998764
No 56
>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 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=52.74 E-value=6.8 Score=27.09 Aligned_cols=28 Identities=25% Similarity=0.763 Sum_probs=12.3
Q ss_pred ccccccccccCCceEeccCCCCcccccc
Q 009705 272 SCKICGRSETALKLLLCDDCEEAFHVTC 299 (528)
Q Consensus 272 ~C~VC~~~g~~~~LL~CD~C~r~yH~~C 299 (528)
.|.+|+..+.......|..|+-..|..|
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 5889998876557788999999999887
No 58
>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=52.59 E-value=1.9 Score=38.82 Aligned_cols=37 Identities=14% Similarity=0.152 Sum_probs=27.6
Q ss_pred CcccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 363 PYTTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 363 lyl~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
..+...+.+..|..+|.. ...++|+++|.+||+|.+-
T Consensus 13 ~~l~~~~~~~~F~~pv~~--~~~pdY~~vI~~PmdL~tI 49 (112)
T cd05528 13 KRLASDKRFNAFTKPVDE--EEVPDYYEIIKQPMDLQTI 49 (112)
T ss_pred HHHHhCCCchhhcCCCCc--cccCcHHHHHcCCCCHHHH
Confidence 334445566689999965 3578999999999998764
No 59
>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=52.06 E-value=2.2 Score=36.80 Aligned_cols=37 Identities=16% Similarity=0.078 Sum_probs=26.3
Q ss_pred ccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 365 TTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 365 l~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+...+.+..|..+|..-....++|+++|.+||+|.+-
T Consensus 12 l~~~~~~~~F~~pv~~~~~~~p~Y~~~I~~P~dl~tI 48 (99)
T cd05506 12 LMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTV 48 (99)
T ss_pred HHhCCCCccccCCCCccccCCCCHHHHHcCCCCHHHH
Confidence 3345567789988843112357899999999998764
No 60
>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=51.73 E-value=3.2 Score=36.67 Aligned_cols=33 Identities=9% Similarity=0.042 Sum_probs=24.5
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+...+.+|..++.. ...++|+++|++||+|.+-
T Consensus 20 g~~~s~pF~~~p~~--~~~PdYy~iI~~PmdL~tI 52 (103)
T cd05520 20 GQLLAEPFLKLPSK--RKYPDYYQEIKNPISLQQI 52 (103)
T ss_pred CCCccHhhhcCCCc--ccCCCHHHHcCCCcCHHHH
Confidence 44455678887654 3568999999999998764
No 61
>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=51.49 E-value=3.6 Score=36.34 Aligned_cols=33 Identities=9% Similarity=0.090 Sum_probs=24.4
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+.+.+..|..++.. ...++|+++|.+||+|.+-
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 44555678877644 3567999999999998764
No 62
>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=51.38 E-value=2 Score=37.27 Aligned_cols=35 Identities=11% Similarity=0.154 Sum_probs=26.6
Q ss_pred ccccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 365 TTSVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 365 l~cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+..+..+..|..+|.. ...++|+++|..||+|.+-
T Consensus 13 l~~~~~a~~F~~pv~~--~~~p~Y~~~I~~PmdL~tI 47 (101)
T cd05509 13 LKNHKSAWPFLEPVDK--EEAPDYYDVIKKPMDLSTM 47 (101)
T ss_pred HHhCCCchhhcCCCCh--hhcCCHHHHhcCCCCHHHH
Confidence 3345566689999865 2478999999999998764
No 63
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.61 E-value=11 Score=40.66 Aligned_cols=47 Identities=28% Similarity=0.603 Sum_probs=34.6
Q ss_pred cccccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccChhcccc
Q 009705 271 RSCKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKK 320 (528)
Q Consensus 271 d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~ 320 (528)
+.|.+|...-..++.|-==-|...||..|.+|.|..-- =+||.|+..
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r---~~CPvCK~d 276 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTR---TFCPVCKRD 276 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcC---ccCCCCCCc
Confidence 58999997543333333356888999999999887652 389999874
No 64
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=45.91 E-value=11 Score=31.64 Aligned_cols=30 Identities=30% Similarity=0.812 Sum_probs=25.2
Q ss_pred cccccccccc-ccCCceEeccC--CCCcccccccCC
Q 009705 270 SRSCKICGRS-ETALKLLLCDD--CEEAFHVTCYTP 302 (528)
Q Consensus 270 ~d~C~VC~~~-g~~~~LL~CD~--C~r~yH~~Cl~P 302 (528)
...|.+|+.. | -.+-|.. |.+.||..|..-
T Consensus 36 ~~~C~~C~~~~G---a~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKKGG---ACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCCCC---eEEEEeCCCCCcEEChHHHcc
Confidence 3579999998 7 7888875 999999999854
No 65
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=45.79 E-value=7.3 Score=40.93 Aligned_cols=50 Identities=16% Similarity=0.224 Sum_probs=37.3
Q ss_pred ccccccccc------ccCCceEeccCCCCcccccccCCCcC---CCCCCCccChhcccc
Q 009705 271 RSCKICGRS------ETALKLLLCDDCEEAFHVTCYTPRIK---IVPSDEWFCHLCLKK 320 (528)
Q Consensus 271 d~C~VC~~~------g~~~~LL~CD~C~r~yH~~Cl~PpL~---~iP~g~W~C~~C~~~ 320 (528)
..|.+|-.+ +..+.+++|..|..+||.+|+.-+.. .+-...|.|..|+--
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC 317 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELC 317 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhh
Confidence 478888754 34568999999999999999975422 234568999988643
No 66
>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=45.44 E-value=5.2 Score=35.53 Aligned_cols=33 Identities=6% Similarity=0.018 Sum_probs=24.1
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+.+.+.+|..++.. ...++|+++|.+||+|.+-
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 44556678876543 2567999999999998764
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=45.36 E-value=5.6 Score=35.87 Aligned_cols=61 Identities=7% Similarity=-0.047 Sum_probs=34.9
Q ss_pred CCCccccC----CCCCCCCCCCCCCCCCCccCCCCCCCccccccccccCCccCCCCeEecccccCCC
Q 009705 371 GKGFQADI----PDWLAPTNNDGYALGEPLELDTSECPSLHDLNSYNLSNLSSIGNWLQCKQVLEGT 433 (528)
Q Consensus 371 G~~Fqa~V----P~Wsg~~~~y~~~IgePMdLd~se~~~L~~l~~~~~~k~ds~gnw~qC~~c~~~~ 433 (528)
..+|+++| |.|. ..++|+++|++||||++-+.. |...+......+.++-+|++-+..++++
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 45788888 3422 367899999999999875322 1111111111245666666666555533
No 68
>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=44.96 E-value=7.9 Score=34.49 Aligned_cols=33 Identities=12% Similarity=0.091 Sum_probs=24.8
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+.+++.+|...++. ...++|++.|.+||+|.+-
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 44556678877554 4568999999999998764
No 69
>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=44.52 E-value=5.2 Score=35.40 Aligned_cols=33 Identities=18% Similarity=0.130 Sum_probs=23.9
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+.+.+..|..++.. ...++|+++|.+||+|.+-
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 44555567766654 3568999999999998763
No 70
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=44.45 E-value=12 Score=32.73 Aligned_cols=31 Identities=39% Similarity=0.847 Sum_probs=25.0
Q ss_pred ccccccccccccCCceEeccC--CCCcccccccCC
Q 009705 270 SRSCKICGRSETALKLLLCDD--CEEAFHVTCYTP 302 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~CD~--C~r~yH~~Cl~P 302 (528)
...|.+|+..+ +..+-|.. |...||..|..-
T Consensus 55 ~~~C~iC~~~~--G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 55 KLKCSICGKSG--GACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred CCcCcCCCCCC--ceeEEcCCCCCCcCCCHHHHHH
Confidence 45799999852 27889988 999999999843
No 71
>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=44.30 E-value=7.5 Score=32.27 Aligned_cols=29 Identities=28% Similarity=0.649 Sum_probs=20.2
Q ss_pred EeccCCCCcccccccCCCcCCCCCCCccChhcc
Q 009705 286 LLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCL 318 (528)
Q Consensus 286 L~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~ 318 (528)
+.=..|+..||..|+..-|... ..||.|+
T Consensus 45 i~~~~C~H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 45 IVWGPCGHIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp EEEETTSEEEEHHHHHHHHTTS----SB-TTSS
T ss_pred eEecccCCCEEHHHHHHHHhcC----CcCCCCC
Confidence 3445799999999997655443 3788885
No 72
>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=41.54 E-value=17 Score=28.29 Aligned_cols=14 Identities=50% Similarity=1.021 Sum_probs=12.5
Q ss_pred cccCCCccccCCCC
Q 009705 368 VRVGKGFQADIPDW 381 (528)
Q Consensus 368 VR~G~~Fqa~VP~W 381 (528)
+|+|..|||.||++
T Consensus 1 IrVG~~yQA~IP~~ 14 (55)
T PF01448_consen 1 IRVGPEYQAEIPEL 14 (55)
T ss_pred CCcCCccCCcCCCC
Confidence 58999999999984
No 73
>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=41.23 E-value=6.2 Score=34.91 Aligned_cols=33 Identities=18% Similarity=0.123 Sum_probs=22.8
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+..++..|...+.. ...++|+++|.+||+|.+-
T Consensus 20 gr~~~~~F~~lp~~--~~~pdYy~vI~~PmdL~tI 52 (103)
T cd05517 20 GRLISELFQKLPSK--VLYPDYYAVIKEPIDLKTI 52 (103)
T ss_pred CCChhHHHhcCCCC--CCCCCHHHHcCCCcCHHHH
Confidence 44445567765433 2457899999999998764
No 74
>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=38.31 E-value=8.3 Score=33.78 Aligned_cols=33 Identities=12% Similarity=0.120 Sum_probs=23.4
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
+..++..|..++.. ...++|+++|.+||+|.+-
T Consensus 20 ~~~~~~~F~~~p~~--~~~pdYy~iIk~Pmdl~~I 52 (103)
T cd05519 20 GRKLSELFLEKPSK--KLYPDYYVIIKRPIALDQI 52 (103)
T ss_pred CCchhHHhcCCCCC--CCCcCHHHHcCCCcCHHHH
Confidence 33445567777654 2467899999999998764
No 75
>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=37.33 E-value=12 Score=34.35 Aligned_cols=34 Identities=12% Similarity=0.090 Sum_probs=26.2
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
....+..|..+|+.-. ..++|+++|..||+|.+-
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 5556778999987611 468999999999998764
No 76
>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=36.85 E-value=34 Score=38.00 Aligned_cols=59 Identities=24% Similarity=0.504 Sum_probs=41.9
Q ss_pred CCCCCccccccccccccccc---cCCceEeccCCCCcccccccCCCcC-------C----CCCCCccChhccccc
Q 009705 261 SGTGCSGICSRSCKICGRSE---TALKLLLCDDCEEAFHVTCYTPRIK-------I----VPSDEWFCHLCLKKK 321 (528)
Q Consensus 261 ~g~~~cp~c~d~C~VC~~~g---~~~~LL~CD~C~r~yH~~Cl~PpL~-------~----iP~g~W~C~~C~~~~ 321 (528)
..+.+|-.| .|-+|+.-+ ++-.-|-||.|...-|+.|-.-.-. . ..++.++|..|-...
T Consensus 121 ~~~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 121 SEPGFCRRC--MCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTS 193 (446)
T ss_pred CCCCccccC--CccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChh
Confidence 345788866 899998754 3445688999999999999764211 0 124479999997653
No 77
>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=36.29 E-value=11 Score=26.36 Aligned_cols=42 Identities=24% Similarity=0.487 Sum_probs=27.4
Q ss_pred cccccccccCCceEeccCCCCcccccccCCCcCCCCCCCccChhccc
Q 009705 273 CKICGRSETALKLLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLK 319 (528)
Q Consensus 273 C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~ 319 (528)
|.+|...- ...+.-..|...||..|+...+.. +...|+.|+.
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 233444568889999999765443 4567888864
No 78
>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=32.38 E-value=9.1 Score=33.79 Aligned_cols=33 Identities=15% Similarity=0.097 Sum_probs=23.1
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
|.+++..|...+.. ...++|+++|.+||+|.+-
T Consensus 21 g~~l~~~F~~~p~~--~~~pdYy~~I~~Pmdl~tI 53 (104)
T cd05522 21 GRLLTLHFEKLPDK--AREPEYYQEISNPISLDDI 53 (104)
T ss_pred CCcccHHHhcCCCc--cccCcHHHHhCCCcCHHHH
Confidence 34555567765542 2567899999999998764
No 79
>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=30.80 E-value=9.3 Score=34.08 Aligned_cols=33 Identities=18% Similarity=0.242 Sum_probs=21.4
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
|...+..|.. .|.. ...++|+++|.+||+|++-
T Consensus 21 g~~~~~~F~~-lp~~-~~~pdYy~iI~~PmdL~tI 53 (106)
T cd05521 21 GIEIHPIFNV-LPLR-KDYPDYYKIIKNPLSLNTV 53 (106)
T ss_pred CCCchHhhhc-CCcc-ccCccHHHHhcCCCCHHHH
Confidence 3344445553 3431 2457899999999998754
No 80
>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=30.20 E-value=36 Score=32.57 Aligned_cols=19 Identities=21% Similarity=0.415 Sum_probs=15.0
Q ss_pred CCCCCCCCCCCCCCCcccc
Q 009705 251 QIRSSANDVDSGTGCSGIC 269 (528)
Q Consensus 251 ~~~~~~e~v~~g~~~cp~c 269 (528)
+-.+++..+|+|+|+||.|
T Consensus 6 CL~Ppl~~~P~g~W~Cp~C 24 (148)
T cd04718 6 CLRPPLKEVPEGDWICPFC 24 (148)
T ss_pred cCCCCCCCCCCCCcCCCCC
Confidence 3457789999999999844
No 81
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=28.95 E-value=14 Score=38.80 Aligned_cols=50 Identities=26% Similarity=0.554 Sum_probs=37.9
Q ss_pred cccccccccc-------cCCceEeccCCCCcccccccCCC---cCCCCCCCccChhcccc
Q 009705 271 RSCKICGRSE-------TALKLLLCDDCEEAFHVTCYTPR---IKIVPSDEWFCHLCLKK 320 (528)
Q Consensus 271 d~C~VC~~~g-------~~~~LL~CD~C~r~yH~~Cl~Pp---L~~iP~g~W~C~~C~~~ 320 (528)
-+|..|-+.. -+++|+.|..|+|+=|.+|+.-- +-.+-...|.|..|..-
T Consensus 225 ~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~c 284 (336)
T KOG1244|consen 225 PYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYC 284 (336)
T ss_pred cccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeeccee
Confidence 4788887543 47799999999999999999531 12345568999999764
No 82
>smart00297 BROMO bromo domain.
Probab=28.07 E-value=8.2 Score=33.10 Aligned_cols=33 Identities=18% Similarity=0.206 Sum_probs=24.9
Q ss_pred ccccCCCccccCCCCCCCCCCCCCCCCCCccCCCC
Q 009705 367 SVRVGKGFQADIPDWLAPTNNDGYALGEPLELDTS 401 (528)
Q Consensus 367 cVR~G~~Fqa~VP~Wsg~~~~y~~~IgePMdLd~s 401 (528)
..+.+..|..+|.. ...++|+++|.+||+|.+-
T Consensus 21 ~~~~~~~F~~~~~~--~~~p~Y~~~i~~P~dl~~I 53 (107)
T smart00297 21 SHRLSWPFLKPVDR--KEAPDYYDIIKKPMDLSTI 53 (107)
T ss_pred hCccchhhccCCCh--hhccCHHHHhcCCCCHHHH
Confidence 44567788888765 2467899999999998754
No 83
>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=27.51 E-value=48 Score=25.12 Aligned_cols=31 Identities=23% Similarity=0.557 Sum_probs=23.7
Q ss_pred cccccccccc--cCCceEeccCCCCcccccccC
Q 009705 271 RSCKICGRSE--TALKLLLCDDCEEAFHVTCYT 301 (528)
Q Consensus 271 d~C~VC~~~g--~~~~LL~CD~C~r~yH~~Cl~ 301 (528)
.+|.+|+..- ....-+.|..|....|..|..
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 5788888753 455789999999999999984
No 84
>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=26.11 E-value=12 Score=33.55 Aligned_cols=28 Identities=11% Similarity=0.046 Sum_probs=19.6
Q ss_pred CccccCCCCCCCCCCCCCCCCCCccCCCCC
Q 009705 373 GFQADIPDWLAPTNNDGYALGEPLELDTSE 402 (528)
Q Consensus 373 ~Fqa~VP~Wsg~~~~y~~~IgePMdLd~se 402 (528)
.|...+.. ...++|+++|.+||+|++-+
T Consensus 28 ~F~~~p~~--~~~PdYy~iI~~Pmdl~tI~ 55 (113)
T cd05524 28 SFIRVPKR--RNEPEYYEVVSNPIDLLKIQ 55 (113)
T ss_pred HHhcCCCc--ccCCCHHHHhCCccCHHHHH
Confidence 45554332 35678999999999987653
No 85
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.40 E-value=34 Score=35.96 Aligned_cols=49 Identities=20% Similarity=0.440 Sum_probs=30.6
Q ss_pred ccccccccccccCCc-------eEeccCCCCcccccccCCC--cCCCCCCCccChhcccccc
Q 009705 270 SRSCKICGRSETALK-------LLLCDDCEEAFHVTCYTPR--IKIVPSDEWFCHLCLKKKH 322 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~-------LL~CD~C~r~yH~~Cl~Pp--L~~iP~g~W~C~~C~~~~~ 322 (528)
+..|+||++.-+.+. -+.==.|...||-+|..-- +.. .-.||.|..+-.
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGK----kqtCPYCKekVd 281 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGK----KQTCPYCKEKVD 281 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecC----CCCCchHHHHhh
Confidence 458999997642111 1122258899999998531 112 348999987643
No 86
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.80 E-value=38 Score=33.52 Aligned_cols=34 Identities=3% Similarity=0.097 Sum_probs=25.9
Q ss_pred CCcCCCcccccccCCcccccccccchhhhccCccc
Q 009705 211 GECSSSSAVMLETTGKDLSAKDLCISILRNEGMLE 245 (528)
Q Consensus 211 ~ECsss~I~~~e~~~ed~s~~D~C~sil~~~gl~~ 245 (528)
.+|..|+||+-.+.. ..-....|+|+||+.|+-.
T Consensus 129 ~~~~~CPiCl~~~se-k~~vsTkCGHvFC~~Cik~ 162 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSE-KVPVSTKCGHVFCSQCIKD 162 (187)
T ss_pred ccccCCCceecchhh-ccccccccchhHHHHHHHH
Confidence 469999999666554 4435679999999998765
No 87
>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=22.94 E-value=19 Score=24.05 Aligned_cols=28 Identities=25% Similarity=0.466 Sum_probs=16.6
Q ss_pred cccccccccCCceEeccCCCCcccccccCCC
Q 009705 273 CKICGRSETALKLLLCDDCEEAFHVTCYTPR 303 (528)
Q Consensus 273 C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~Pp 303 (528)
|.+|.... ....--.|...||..|+...
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 22333358888888887643
No 88
>PHA02929 N1R/p28-like protein; Provisional
Probab=21.90 E-value=37 Score=34.74 Aligned_cols=48 Identities=19% Similarity=0.439 Sum_probs=32.7
Q ss_pred ccccccccccccCCc-----eEeccCCCCcccccccCCCcCCCCCCCccChhccccc
Q 009705 270 SRSCKICGRSETALK-----LLLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLKKK 321 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~-----LL~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~~~ 321 (528)
+..|.+|...-.... +..=..|...||..|+...+...+ .||.|+...
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~----tCPlCR~~~ 226 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKN----TCPVCRTPF 226 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCC----CCCCCCCEe
Confidence 357999987532111 223347899999999987766433 699998754
No 89
>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=20.31 E-value=43 Score=30.03 Aligned_cols=50 Identities=22% Similarity=0.683 Sum_probs=29.3
Q ss_pred ccccccccccccCCceEec------cCC---CCcccccccCCCc-----CCCCCCCccChhcccc
Q 009705 270 SRSCKICGRSETALKLLLC------DDC---EEAFHVTCYTPRI-----KIVPSDEWFCHLCLKK 320 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~C------D~C---~r~yH~~Cl~PpL-----~~iP~g~W~C~~C~~~ 320 (528)
...|..|.+...... ..| ..| ...|=..||.-.- +.+..++|.||.|+..
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 456777776543223 345 555 6656555654322 2235678999999863
No 90
>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=20.31 E-value=68 Score=23.53 Aligned_cols=28 Identities=25% Similarity=0.616 Sum_probs=19.5
Q ss_pred EeccCCCCcccccccCCCcCCCCCCCccChhccc
Q 009705 286 LLCDDCEEAFHVTCYTPRIKIVPSDEWFCHLCLK 319 (528)
Q Consensus 286 L~CD~C~r~yH~~Cl~PpL~~iP~g~W~C~~C~~ 319 (528)
..|..|.+.||..=. .|..+..|..|-.
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 468999999995544 3555678888865
No 91
>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=20.29 E-value=64 Score=27.34 Aligned_cols=31 Identities=23% Similarity=0.615 Sum_probs=20.9
Q ss_pred ccccccccccccCCceEeccCCCCcccccccC
Q 009705 270 SRSCKICGRSETALKLLLCDDCEEAFHVTCYT 301 (528)
Q Consensus 270 ~d~C~VC~~~g~~~~LL~CD~C~r~yH~~Cl~ 301 (528)
+..|.+|++.-....+. ---|+..||..|..
T Consensus 78 ~~~C~vC~k~l~~~~f~-~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFV-VFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEE-EeCCCeEEeccccc
Confidence 45799999865443333 33455899999973
No 92
>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=20.26 E-value=72 Score=24.82 Aligned_cols=17 Identities=29% Similarity=0.917 Sum_probs=9.6
Q ss_pred cCCCCCCCccChhccccc
Q 009705 304 IKIVPSDEWFCHLCLKKK 321 (528)
Q Consensus 304 L~~iP~g~W~C~~C~~~~ 321 (528)
...+|+ +|.|+.|...+
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 345554 79999998754
Done!