Query psy14441
Match_columns 365
No_of_seqs 150 out of 214
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 19:57:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14441.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14441hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1142|consensus 100.0 7.3E-43 1.6E-47 328.6 12.1 111 254-364 148-258 (258)
2 PF03847 TFIID_20kDa: Transcri 100.0 2.6E-29 5.7E-34 195.9 6.6 68 262-329 1-68 (68)
3 COG5624 TAF61 Transcription in 99.9 4.6E-28 1E-32 240.6 -0.9 105 256-360 379-485 (505)
4 cd07981 TAF12 TATA Binding Pro 99.9 4.5E-24 9.7E-29 166.4 8.8 72 260-331 1-72 (72)
5 COG2036 HHT1 Histones H3 and H 98.1 7.7E-06 1.7E-10 68.0 5.9 70 256-326 15-84 (91)
6 PLN00035 histone H4; Provision 98.0 2.7E-05 5.8E-10 66.2 8.9 73 261-335 30-102 (103)
7 PTZ00015 histone H4; Provision 97.9 6.8E-05 1.5E-09 63.6 8.6 70 258-328 28-97 (102)
8 PF00125 Histone: Core histone 97.8 4.9E-05 1.1E-09 58.2 5.0 67 259-325 4-74 (75)
9 cd00076 H4 Histone H4, one of 97.7 0.00021 4.6E-09 58.7 8.4 73 260-334 13-85 (85)
10 smart00803 TAF TATA box bindin 97.6 0.00037 8.1E-09 54.3 7.9 64 260-324 2-65 (65)
11 PF00808 CBFD_NFYB_HMF: Histon 97.6 0.00024 5.3E-09 53.7 6.7 63 261-323 3-65 (65)
12 smart00428 H3 Histone H3. 97.5 0.00043 9.4E-09 59.0 7.3 68 256-323 25-98 (105)
13 cd07979 TAF9 TATA Binding Prot 97.3 0.0012 2.5E-08 56.6 8.1 66 265-331 6-71 (117)
14 smart00417 H4 Histone H4. 97.1 0.0017 3.6E-08 52.4 6.7 62 259-321 12-73 (74)
15 PLN00161 histone H3; Provision 97.0 0.0033 7.2E-08 56.0 7.7 76 256-332 51-131 (135)
16 PLN00121 histone H3; Provision 96.7 0.0045 9.8E-08 55.1 6.4 68 256-323 58-129 (136)
17 PLN00160 histone H3; Provision 96.6 0.0038 8.2E-08 52.8 4.9 68 256-323 17-89 (97)
18 PTZ00018 histone H3; Provision 96.5 0.0056 1.2E-07 54.5 6.1 68 256-323 58-129 (136)
19 PF02269 TFIID-18kDa: Transcri 96.5 0.0029 6.2E-08 52.2 4.0 61 266-326 7-67 (93)
20 PF02291 TFIID-31kDa: Transcri 96.3 0.014 3E-07 51.3 7.1 67 264-331 16-82 (129)
21 smart00576 BTP Bromodomain tra 96.1 0.044 9.5E-07 43.3 8.4 64 266-331 12-75 (77)
22 smart00427 H2B Histone H2B. 96.1 0.025 5.4E-07 47.4 7.3 59 266-324 7-65 (89)
23 cd08050 TAF6 TATA Binding Prot 95.4 0.091 2E-06 51.9 9.4 62 263-325 2-63 (343)
24 PTZ00463 histone H2B; Provisio 95.4 0.068 1.5E-06 46.9 7.4 65 266-334 34-98 (117)
25 PLN00158 histone H2B; Provisio 95.4 0.068 1.5E-06 46.8 7.4 59 266-324 33-91 (116)
26 PF02969 TAF: TATA box binding 94.6 0.19 4.2E-06 39.8 7.3 64 260-324 3-66 (66)
27 PF15630 CENP-S: Kinetochore c 94.6 0.11 2.3E-06 42.1 6.0 60 267-326 12-73 (76)
28 KOG3467|consensus 94.5 0.18 4E-06 42.9 7.4 78 257-336 26-103 (103)
29 KOG0869|consensus 94.4 0.15 3.2E-06 47.1 7.3 70 255-324 27-97 (168)
30 cd07978 TAF13 The TATA Binding 94.4 0.26 5.7E-06 41.0 8.0 61 264-325 6-66 (92)
31 KOG1744|consensus 93.8 0.19 4.1E-06 44.7 6.3 62 269-334 46-107 (127)
32 PF07524 Bromo_TP: Bromodomain 93.6 0.58 1.3E-05 36.6 8.2 63 266-329 8-73 (77)
33 cd08048 TAF11 TATA Binding Pro 92.7 0.82 1.8E-05 37.7 8.1 62 261-323 17-81 (85)
34 cd00074 H2A Histone 2A; H2A is 91.9 0.85 1.8E-05 39.6 7.6 73 253-325 13-85 (115)
35 PF09415 CENP-X: CENP-S associ 91.6 0.22 4.7E-06 39.9 3.5 59 264-322 3-64 (72)
36 KOG0871|consensus 90.5 1.5 3.3E-05 40.2 8.2 71 255-325 7-78 (156)
37 KOG3334|consensus 88.6 2.3 5E-05 38.9 7.8 67 266-333 19-85 (148)
38 KOG3423|consensus 87.1 5.1 0.00011 37.6 9.2 73 258-331 65-169 (176)
39 PF03540 TFIID_30kDa: Transcri 85.1 5.5 0.00012 30.5 7.1 50 260-310 2-51 (51)
40 KOG0870|consensus 83.3 5.6 0.00012 37.2 7.6 66 260-325 10-77 (172)
41 PF04719 TAFII28: hTAFII28-lik 83.3 5.4 0.00012 33.5 6.9 58 261-318 24-82 (90)
42 PF05236 TAF4: Transcription i 83.3 1.3 2.8E-05 42.1 3.7 59 256-314 39-100 (264)
43 cd08045 TAF4 TATA Binding Prot 83.1 3.1 6.7E-05 38.5 6.0 60 253-312 37-99 (212)
44 KOG1745|consensus 82.2 1.1 2.5E-05 40.3 2.7 68 256-323 59-130 (137)
45 PF05392 COX7B: Cytochrome C o 81.4 1.7 3.6E-05 36.2 3.2 31 161-191 39-69 (80)
46 COG5094 TAF9 Transcription ini 75.7 10 0.00022 34.4 6.6 66 266-332 20-88 (145)
47 COG5150 Class 2 transcription 74.1 15 0.00032 33.5 7.2 77 256-332 7-85 (148)
48 cd01403 Cyt_c_Oxidase_VIIb Cyt 70.0 0.87 1.9E-05 35.0 -1.2 31 161-191 11-41 (51)
49 KOG2549|consensus 69.7 30 0.00065 37.7 9.4 93 255-348 5-98 (576)
50 PF15511 CENP-T: Centromere ki 68.4 10 0.00022 38.9 5.6 61 258-318 349-414 (414)
51 KOG3901|consensus 66.9 13 0.00028 32.7 5.1 59 265-326 14-72 (109)
52 COG5248 TAF19 Transcription in 66.5 14 0.00031 32.8 5.4 48 277-326 26-73 (126)
53 KOG3489|consensus 64.6 27 0.00059 29.6 6.4 50 262-311 23-82 (86)
54 smart00350 MCM minichromosome 62.6 26 0.00056 36.5 7.3 66 259-324 416-502 (509)
55 PRK00411 cdc6 cell division co 62.6 27 0.00058 33.8 7.0 66 261-326 207-282 (394)
56 TIGR03015 pepcterm_ATPase puta 59.0 37 0.00081 30.8 6.9 67 259-325 190-265 (269)
57 TIGR02902 spore_lonB ATP-depen 50.5 47 0.001 34.9 6.9 64 261-324 263-330 (531)
58 COG5162 Transcription initiati 48.9 81 0.0017 30.0 7.4 47 264-310 73-137 (197)
59 PF08429 PLU-1: PLU-1-like pro 48.7 67 0.0015 31.0 7.2 119 197-334 30-154 (335)
60 KOG4782|consensus 48.5 14 0.0003 32.1 2.3 44 136-180 24-77 (108)
61 smart00414 H2A Histone 2A. 48.0 98 0.0021 26.6 7.3 69 257-325 6-74 (106)
62 TIGR02928 orc1/cdc6 family rep 45.8 85 0.0019 30.0 7.4 66 261-326 199-274 (365)
63 KOG3219|consensus 44.7 38 0.00082 32.4 4.7 65 258-323 110-175 (195)
64 PF05529 Bap31: B-cell recepto 42.1 14 0.0003 33.3 1.4 20 52-71 94-113 (192)
65 COG1224 TIP49 DNA helicase TIP 38.5 57 0.0012 34.5 5.2 63 262-324 362-430 (450)
66 PF15098 TMEM89: TMEM89 protei 37.9 22 0.00047 32.0 1.9 68 98-177 45-112 (134)
67 TIGR02639 ClpA ATP-dependent C 34.5 62 0.0013 35.3 5.0 77 262-338 346-441 (731)
68 COG5095 TAF6 Transcription ini 34.0 1.7E+02 0.0038 30.6 7.7 65 259-324 4-68 (450)
69 PTZ00017 histone H2A; Provisio 33.5 1.6E+02 0.0035 26.7 6.6 72 253-324 20-91 (134)
70 PF12767 SAGA-Tad1: Transcript 32.5 2.1E+02 0.0046 27.1 7.7 56 252-307 194-252 (252)
71 PF12911 OppC_N: N-terminal TM 32.0 59 0.0013 23.6 3.1 38 145-184 1-38 (56)
72 COG5208 HAP5 CCAAT-binding fac 31.0 76 0.0017 31.4 4.5 48 278-325 127-174 (286)
73 PRK14622 hypothetical protein; 30.4 41 0.00089 28.6 2.3 46 279-336 58-103 (103)
74 KOG4336|consensus 30.0 1.5E+02 0.0033 30.4 6.5 57 277-334 21-77 (323)
75 PF07942 N2227: N2227-like pro 29.1 18 0.00039 35.5 -0.0 89 121-209 122-229 (270)
76 KOG2680|consensus 29.1 98 0.0021 32.4 5.1 63 262-324 359-427 (454)
77 PF14846 DUF4485: Domain of un 28.5 33 0.0007 28.1 1.3 21 52-72 41-61 (85)
78 cd00922 Cyt_c_Oxidase_IV Cytoc 28.5 65 0.0014 28.6 3.3 46 105-152 28-77 (136)
79 PF05767 Pox_A14: Poxvirus vir 26.3 76 0.0016 27.3 3.2 34 157-196 8-41 (92)
80 PF11298 DUF3099: Protein of u 26.2 1.3E+02 0.0027 24.6 4.3 31 148-178 8-38 (73)
81 PRK13183 psbN photosystem II r 25.5 1.1E+02 0.0024 23.4 3.5 34 165-198 7-44 (46)
82 PF03908 Sec20: Sec20; InterP 25.3 1.2E+02 0.0025 24.7 4.0 27 153-179 62-88 (92)
83 PF09813 Coiled-coil_56: Coile 25.2 97 0.0021 27.0 3.6 21 155-175 45-65 (100)
84 KOG1748|consensus 25.1 84 0.0018 28.4 3.4 61 281-341 52-115 (131)
85 PTZ00171 acyl carrier protein; 25.1 28 0.00061 31.3 0.4 38 303-340 94-131 (148)
86 PF10183 ESSS: ESSS subunit of 25.0 1.7E+02 0.0036 24.8 5.0 10 138-147 42-51 (105)
87 TIGR03513 GldL_gliding gliding 24.2 4.1E+02 0.0089 25.6 8.0 28 263-294 88-115 (202)
88 PF09788 Tmemb_55A: Transmembr 23.5 53 0.0012 32.6 2.0 24 165-188 210-233 (256)
89 KOG3902|consensus 23.4 4.1E+02 0.009 27.5 8.2 58 265-324 29-88 (352)
90 PRK10692 hypothetical protein; 23.0 91 0.002 26.8 3.0 28 160-187 10-37 (92)
91 KOG1658|consensus 21.7 78 0.0017 29.6 2.6 69 262-331 61-130 (162)
92 PF10762 DUF2583: Protein of u 21.5 96 0.0021 26.5 2.9 32 160-193 10-41 (89)
93 PLN00154 histone H2A; Provisio 20.6 5E+02 0.011 23.7 7.4 71 254-324 32-103 (136)
No 1
>KOG1142|consensus
Probab=100.00 E-value=7.3e-43 Score=328.55 Aligned_cols=111 Identities=50% Similarity=0.855 Sum_probs=109.0
Q ss_pred CCCCCCCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCC
Q psy14441 254 STPNDQILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPG 333 (365)
Q Consensus 254 s~~~~~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPG 333 (365)
..+++++++|++|+|||++||+++.||+||||+|++||||||++|+++||+|||||||++||+|||+|||||+|||+|||
T Consensus 148 ~~~~~~il~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPg 227 (258)
T KOG1142|consen 148 EPGNNPILSKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPG 227 (258)
T ss_pred cCCCCccccccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCC
Confidence 35799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCcHHHHHHHHHHHHHhhc
Q psy14441 334 YGTDELKPYKRPMATEAHKQRLALIRKHLKK 364 (365)
Q Consensus 334 fgsDeirp~rK~~~teaHkqRMAlIrKtiKK 364 (365)
|++||+++++|+.|||+|+||||+|||++||
T Consensus 228 f~sd~~~~~~k~~pTe~hkqr~a~i~k~~~k 258 (258)
T KOG1142|consen 228 FSSDEKRSKKKALPTEEHKQRLALIRKQIKK 258 (258)
T ss_pred ccccccccccccCCcHHHHHHHHHHHHhhcC
Confidence 9999999999999999999999999999997
No 2
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=99.96 E-value=2.6e-29 Score=195.92 Aligned_cols=68 Identities=50% Similarity=0.837 Sum_probs=57.8
Q ss_pred ChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCc
Q psy14441 262 GKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNI 329 (365)
Q Consensus 262 ~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI 329 (365)
||++|+|||++|||+++||++|||+|+++|||||++|+++||+||||||+++||++||||||||+|||
T Consensus 1 ~K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~~ni 68 (68)
T PF03847_consen 1 SKRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERNWNI 68 (68)
T ss_dssp -HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHHS--
T ss_pred ChHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhhcCC
Confidence 69999999999999999999999999999999999999999999999999999999999999999997
No 3
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=99.93 E-value=4.6e-28 Score=240.59 Aligned_cols=105 Identities=32% Similarity=0.493 Sum_probs=101.8
Q ss_pred CCCCCCChhHHHHHHHhc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCCC
Q psy14441 256 PNDQILGKDKLDELMRQV-DSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPGY 334 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqI-Dp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPGf 334 (365)
...|+++|+||+||++.+ |..+++|+||||+||++||+||+.|+.|||+|||||+|+|||++|+|+||||+|||++|||
T Consensus 379 ~~~Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlErnwnIr~pGf 458 (505)
T COG5624 379 DLWRLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLERNWNIRCPGF 458 (505)
T ss_pred hhhhhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeeccccceecCcc
Confidence 458999999999999998 9999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCC-CCCCCCCcHHHHHHHHHHHH
Q psy14441 335 GTDELK-PYKRPMATEAHKQRLALIRK 360 (365)
Q Consensus 335 gsDeir-p~rK~~~teaHkqRMAlIrK 360 (365)
..|+|+ .|||+.||.++.|+...|+-
T Consensus 459 ~~d~I~~s~rk~~pt~~y~qk~~ai~t 485 (505)
T COG5624 459 VDDIIHMSYRKQKPTVEYCQKKLAIKT 485 (505)
T ss_pred hHHHHHHHHHhcCCChhHHHHHHhhhh
Confidence 999997 99999999999999999874
No 4
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=99.90 E-value=4.5e-24 Score=166.41 Aligned_cols=72 Identities=53% Similarity=0.867 Sum_probs=70.5
Q ss_pred CCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCccc
Q psy14441 260 ILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISI 331 (365)
Q Consensus 260 VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~I 331 (365)
+++|++|++|+++|||++++|++|+++|+++||+|+++|+++||++|||||++||+++||+|+|||+|||++
T Consensus 1 i~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~~~~~ 72 (72)
T cd07981 1 ILTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNWNISI 72 (72)
T ss_pred CCcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCC
Confidence 589999999999999999999999999999999999999999999999999999999999999999999975
No 5
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.07 E-value=7.7e-06 Score=68.04 Aligned_cols=70 Identities=19% Similarity=0.437 Sum_probs=65.8
Q ss_pred CCCCCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhc
Q psy14441 256 PNDQILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~ 326 (365)
.....|++..++.++++..+. .+..++.+.|.+.+++|+..+.+.|+.+|+|.|..||..+||++.+.+.
T Consensus 15 ~~~~~Lp~apv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~ 84 (91)
T COG2036 15 STDLLLPKAPVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRL 84 (91)
T ss_pred hhhhhcCchHHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHh
Confidence 467789999999999998777 9999999999999999999999999999999999999999999999764
No 6
>PLN00035 histone H4; Provisional
Probab=98.05 E-value=2.7e-05 Score=66.24 Aligned_cols=73 Identities=19% Similarity=0.410 Sum_probs=67.4
Q ss_pred CChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCCCC
Q psy14441 261 LGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPGYG 335 (365)
Q Consensus 261 L~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPGfg 335 (365)
||+..+..|++.- +-+.+..++.+.|.++.++|.++|+..|+.+|+|.+-.||+..||.+.|+|.+. .+=||+
T Consensus 30 ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~-~lyGf~ 102 (103)
T PLN00035 30 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR-TLYGFG 102 (103)
T ss_pred CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC-cCCCCC
Confidence 8899999999984 478999999999999999999999999999999999999999999999999988 666665
No 7
>PTZ00015 histone H4; Provisional
Probab=97.90 E-value=6.8e-05 Score=63.64 Aligned_cols=70 Identities=16% Similarity=0.329 Sum_probs=65.2
Q ss_pred CCCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccC
Q psy14441 258 DQILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWN 328 (365)
Q Consensus 258 ~~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wN 328 (365)
-+=|+|..+..|++. .+-..+.+|+.+.+-++.++|.++|+..|+.+|+|.+-.|++..||.+.|+|.+.
T Consensus 28 i~gI~k~~IrRLarr-~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~ 97 (102)
T PTZ00015 28 IRGITKGAIRRLARR-GGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred ccCCCHHHHHHHHHH-cCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 345899999999997 5668999999999999999999999999999999999999999999999999887
No 8
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=97.75 E-value=4.9e-05 Score=58.22 Aligned_cols=67 Identities=21% Similarity=0.413 Sum_probs=60.8
Q ss_pred CCCChhHHHHHHHhcCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh
Q psy14441 259 QILGKDKLDELMRQVDST----LQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK 325 (365)
Q Consensus 259 ~VL~KrkLqeLVrqIDp~----e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER 325 (365)
..+.|.-+..++++|..+ ..++.++-+.|..++|+|+.++++.|+.+|.|.|-.||..+||++.+..
T Consensus 4 ~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 4 RLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp HSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred cccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 456778888888888666 7999999999999999999999999999999999999999999998754
No 9
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=97.71 E-value=0.00021 Score=58.74 Aligned_cols=73 Identities=19% Similarity=0.416 Sum_probs=65.1
Q ss_pred CCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCCC
Q psy14441 260 ILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPGY 334 (365)
Q Consensus 260 VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPGf 334 (365)
-|||..+..|++. .+-..+..|+.+.+-++.++|.++|+..|+.+|+|.+-.||+..||.+.|+|.= ..+=||
T Consensus 13 gi~k~~I~RLarr-~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g-~~~ygf 85 (85)
T cd00076 13 GITKPAIRRLARR-GGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQG-RTLYGY 85 (85)
T ss_pred cCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCC-CCccCC
Confidence 3899999999998 457999999999999999999999999999999999999999999999998864 444343
No 10
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=97.59 E-value=0.00037 Score=54.27 Aligned_cols=64 Identities=19% Similarity=0.316 Sum_probs=59.2
Q ss_pred CCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 260 ILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 260 VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
++++..+..+.+.++-. .+.+|+.+.|.+.++.|+..|+..|+++++|=|-.||...||...|+
T Consensus 2 ~~p~~~i~ria~~~Gi~-ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGIG-NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 57889999999987554 89999999999999999999999999999999999999999998874
No 11
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=97.59 E-value=0.00024 Score=53.74 Aligned_cols=63 Identities=14% Similarity=0.349 Sum_probs=55.3
Q ss_pred CChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHh
Q psy14441 261 LGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVL 323 (365)
Q Consensus 261 L~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~L 323 (365)
|+..+++.+++.......+..|+.+++.+.++.||..++..|...|++.+..||..+||.-.|
T Consensus 3 lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 3 LPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp S-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 788999999999855578999999999999999999999999999999999999999997653
No 12
>smart00428 H3 Histone H3.
Probab=97.47 E-value=0.00043 Score=59.00 Aligned_cols=68 Identities=22% Similarity=0.386 Sum_probs=62.2
Q ss_pred CCCCCCChhHHHHHHHhcC----C--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHh
Q psy14441 256 PNDQILGKDKLDELMRQVD----S--TLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVL 323 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqID----p--~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~L 323 (365)
..+-+|+|.-.+.||++|. + +..+.+++.++|.+.+++|+-++.+.|-.+|+|.|--||.++|+++..
T Consensus 25 st~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ 98 (105)
T smart00428 25 STDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLAR 98 (105)
T ss_pred CcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHH
Confidence 4567889999999999984 2 458999999999999999999999999999999999999999999986
No 13
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=97.30 E-value=0.0012 Score=56.62 Aligned_cols=66 Identities=14% Similarity=0.367 Sum_probs=57.7
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCccc
Q psy14441 265 KLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISI 331 (365)
Q Consensus 265 kLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~I 331 (365)
-+..+++.. +-+..+++|...|+|++..++.+|+..|..+|+|-|.++|+..||++.++..-+..+
T Consensus 6 ~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f 71 (117)
T cd07979 6 VIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSF 71 (117)
T ss_pred HHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCC
Confidence 355566653 447899999999999999999999999999999999999999999999988877554
No 14
>smart00417 H4 Histone H4.
Probab=97.12 E-value=0.0017 Score=52.43 Aligned_cols=62 Identities=23% Similarity=0.411 Sum_probs=57.7
Q ss_pred CCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHH
Q psy14441 259 QILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQF 321 (365)
Q Consensus 259 ~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql 321 (365)
+=|||..+..|++. .+-..+..++.+-+.++.++|.++|+..|+.+|+|.+-.|++..||.+
T Consensus 12 ~gI~k~~IrRLaRr-~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARR-GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 44899999999997 567899999999999999999999999999999999999999999975
No 15
>PLN00161 histone H3; Provisional
Probab=96.96 E-value=0.0033 Score=55.98 Aligned_cols=76 Identities=18% Similarity=0.264 Sum_probs=65.8
Q ss_pred CCCCCCChhHHHHHHHhcC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcc
Q psy14441 256 PNDQILGKDKLDELMRQVD-----STLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNIS 330 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqID-----p~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~ 330 (365)
..+-+|+|.-.+.||++|. ....+.+++.++|.+.+|.|+-+..+.+-..|-|.|--||..||++|.. |--|.+
T Consensus 51 st~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~-rirg~~ 129 (135)
T PLN00161 51 STELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR-RIRGPI 129 (135)
T ss_pred ccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH-Hhcccc
Confidence 5667889999999999993 2478899999999999999999999999999999999999999999986 443444
Q ss_pred cC
Q psy14441 331 IP 332 (365)
Q Consensus 331 IP 332 (365)
..
T Consensus 130 ~~ 131 (135)
T PLN00161 130 YG 131 (135)
T ss_pred cc
Confidence 33
No 16
>PLN00121 histone H3; Provisional
Probab=96.68 E-value=0.0045 Score=55.11 Aligned_cols=68 Identities=19% Similarity=0.324 Sum_probs=63.1
Q ss_pred CCCCCCChhHHHHHHHhcC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHh
Q psy14441 256 PNDQILGKDKLDELMRQVD----STLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVL 323 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqID----p~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~L 323 (365)
..+-+|+|.-.+.||++|. ++..+..++.++|.+.+|.|+-+..+.+-..|-|.|--||..||++|..
T Consensus 58 st~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 4677899999999999984 4579999999999999999999999999999999999999999999985
No 17
>PLN00160 histone H3; Provisional
Probab=96.56 E-value=0.0038 Score=52.81 Aligned_cols=68 Identities=18% Similarity=0.260 Sum_probs=61.8
Q ss_pred CCCCCCChhHHHHHHHhcCC-----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHh
Q psy14441 256 PNDQILGKDKLDELMRQVDS-----TLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVL 323 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqIDp-----~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~L 323 (365)
..+-+|+|.-.+.||++|.. ...+.+++-++|.+.|+.|+-+..+.+-..|-|.|--||..||+++..
T Consensus 17 st~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 17 STDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred chhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 34568899999999999943 368899999999999999999999999999999999999999999985
No 18
>PTZ00018 histone H3; Provisional
Probab=96.55 E-value=0.0056 Score=54.52 Aligned_cols=68 Identities=19% Similarity=0.324 Sum_probs=63.2
Q ss_pred CCCCCCChhHHHHHHHhcC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHh
Q psy14441 256 PNDQILGKDKLDELMRQVD----STLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVL 323 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqID----p~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~L 323 (365)
..+-+|+|.-.+.||++|. .+..+.+++.++|.+.||+|+-++.+.+-..|-|.|--||..||++|..
T Consensus 58 st~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 4577899999999999994 4679999999999999999999999999999999999999999999985
No 19
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.54 E-value=0.0029 Score=52.22 Aligned_cols=61 Identities=25% Similarity=0.437 Sum_probs=30.5
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhc
Q psy14441 266 LDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326 (365)
Q Consensus 266 LqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~ 326 (365)
|..|+--.+-.....+|..+++-++.-+||-+++..|+++|..||+.++.+.|+.|.|.++
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D 67 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKD 67 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcC
Confidence 4555555555667788999999999999999999999999999999999999999999864
No 20
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=96.30 E-value=0.014 Score=51.32 Aligned_cols=67 Identities=18% Similarity=0.367 Sum_probs=51.6
Q ss_pred hHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCccc
Q psy14441 264 DKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISI 331 (365)
Q Consensus 264 rkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~I 331 (365)
+-|..++++.+- ...+|.|...|+|+|=.|+.+|++.|-.+|.|.+..+++..||++.+.-..+..+
T Consensus 16 ~~i~~iL~~~Gv-~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f 82 (129)
T PF02291_consen 16 RVIHLILKSMGV-TEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSF 82 (129)
T ss_dssp HHHHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-----
T ss_pred HHHHHHHHHcCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhc
Confidence 457778887644 4579999999999999999999999999999999999999999999997766665
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=96.13 E-value=0.044 Score=43.30 Aligned_cols=64 Identities=16% Similarity=0.325 Sum_probs=53.6
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCccc
Q psy14441 266 LDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISI 331 (365)
Q Consensus 266 LqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~I 331 (365)
+-.+++. .+-+..++++-|.|.+++.+|+..+...+-+.|.|-|-.++.+.||.+.|++ .|+.+
T Consensus 12 Vaqil~~-~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~-~gi~~ 75 (77)
T smart00576 12 VAQILES-AGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN-LGISV 75 (77)
T ss_pred HHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH-hCccc
Confidence 3334443 3448999999999999999999999999999999988889999999999966 46654
No 22
>smart00427 H2B Histone H2B.
Probab=96.13 E-value=0.025 Score=47.38 Aligned_cols=59 Identities=22% Similarity=0.389 Sum_probs=55.1
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 266 LDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 266 LqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
+-..++||.|+..+...+..++--+++|..+.+...|++||+..+..||+.++||-..+
T Consensus 7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvr 65 (89)
T smart00427 7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVR 65 (89)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999997754
No 23
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=95.44 E-value=0.091 Score=51.89 Aligned_cols=62 Identities=15% Similarity=0.272 Sum_probs=54.5
Q ss_pred hhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh
Q psy14441 263 KDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK 325 (365)
Q Consensus 263 KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER 325 (365)
++.+.+..+++ +-+.+++|+.+.|.+-++.++..|+..|.++|+|-|..+|.+.||...|+.
T Consensus 2 ~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~ 63 (343)
T cd08050 2 QESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRL 63 (343)
T ss_pred hhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHH
Confidence 45566666665 346899999999999999999999999999999999999999999999965
No 24
>PTZ00463 histone H2B; Provisional
Probab=95.41 E-value=0.068 Score=46.90 Aligned_cols=65 Identities=20% Similarity=0.368 Sum_probs=59.3
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCCC
Q psy14441 266 LDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPGY 334 (365)
Q Consensus 266 LqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPGf 334 (365)
|-..++||-|...|...+..+|--+.+|..+.+.+.|++||+..+..||..+|||-..+ +-+||-
T Consensus 34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr----LlLpGE 98 (117)
T PTZ00463 34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR----LVLPGE 98 (117)
T ss_pred HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh----hcccHH
Confidence 78889999999999999999999999999999999999999999999999999998754 556653
No 25
>PLN00158 histone H2B; Provisional
Probab=95.39 E-value=0.068 Score=46.79 Aligned_cols=59 Identities=19% Similarity=0.353 Sum_probs=55.6
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 266 LDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 266 LqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
|-..++||.|...|...+..++--+.+|+.+.+...|++||+..+..||+.++||-..+
T Consensus 33 I~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvr 91 (116)
T PLN00158 33 IYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVR 91 (116)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 77889999999999999999999999999999999999999999999999999997654
No 26
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=94.60 E-value=0.19 Score=39.77 Aligned_cols=64 Identities=13% Similarity=0.313 Sum_probs=50.0
Q ss_pred CCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 260 ILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 260 VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
++++..++....+++- ..|++|+...|.+-++--|..|+..|.+.++|-+..+|...||...|+
T Consensus 3 ~~~~esvk~iAes~Gi-~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLGI-SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 5777888888877654 569999999999999999999999999999999999999999988764
No 27
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=94.60 E-value=0.11 Score=42.12 Aligned_cols=60 Identities=15% Similarity=0.397 Sum_probs=49.5
Q ss_pred HHHHHhc--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhc
Q psy14441 267 DELMRQV--DSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326 (365)
Q Consensus 267 qeLVrqI--Dp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~ 326 (365)
..++++. +.+..+.+++...|.|++=++++++...--..|||-|-+||...||.|...||
T Consensus 12 ~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn 73 (76)
T PF15630_consen 12 GKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRN 73 (76)
T ss_dssp HHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-
T ss_pred HHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcC
Confidence 3455555 45568999999999999999999999999999999999999999999998886
No 28
>KOG3467|consensus
Probab=94.51 E-value=0.18 Score=42.86 Aligned_cols=78 Identities=21% Similarity=0.376 Sum_probs=61.5
Q ss_pred CCCCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCCCCC
Q psy14441 257 NDQILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPGYGT 336 (365)
Q Consensus 257 ~~~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPGfgs 336 (365)
+-+=++|..|..|.+.-.- ..+..-.-|-.-..+.+|+++|+..||-.|-|-|-.|++..||...|+|+ |+.+=|||+
T Consensus 26 nIqgitKpaIRRlARr~GV-kRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~-G~~~~g~~~ 103 (103)
T KOG3467|consen 26 NIQGITKPAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ-GRTLYGFGG 103 (103)
T ss_pred hccccchHHHHHHHHhcCc-chhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHc-CceeeccCC
Confidence 3445778888888886433 34445555556788999999999999999999999999999999999986 666667663
No 29
>KOG0869|consensus
Probab=94.45 E-value=0.15 Score=47.06 Aligned_cols=70 Identities=16% Similarity=0.363 Sum_probs=64.3
Q ss_pred CCCCCCCChhHHHHHHHhc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 255 TPNDQILGKDKLDELMRQV-DSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 255 ~~~~~VL~KrkLqeLVrqI-Dp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
-+..|.|+=.++-.+++++ +++.+|.+|+.|.+.+.+-+||.=|+..|..-+-.-+-.||.-.||...+.
T Consensus 27 reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~ 97 (168)
T KOG0869|consen 27 REQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMS 97 (168)
T ss_pred chhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHH
Confidence 4678999999999999986 778999999999999999999999999999999999999999999987664
No 30
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=94.38 E-value=0.26 Score=40.96 Aligned_cols=61 Identities=21% Similarity=0.406 Sum_probs=50.1
Q ss_pred hHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh
Q psy14441 264 DKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK 325 (365)
Q Consensus 264 rkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER 325 (365)
..|+.|+--.+-...-.+|.-++|=++.-+||.+++..|++.|..|++. +.+.|+.|.+.+
T Consensus 6 ~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~~r~~k-~~~eD~~FliR~ 66 (92)
T cd07978 6 KEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGK-VKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC-CCHHHHHHHHhc
Confidence 3466777666656677888899999999999999999999999944444 699999999954
No 31
>KOG1744|consensus
Probab=93.75 E-value=0.19 Score=44.68 Aligned_cols=62 Identities=24% Similarity=0.447 Sum_probs=56.3
Q ss_pred HHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCCC
Q psy14441 269 LMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPGY 334 (365)
Q Consensus 269 LVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPGf 334 (365)
.+++|+|..-|..+...++--+.+|++++++..|-+||..+|-.|+..++||...+ +-+||-
T Consensus 46 vlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~r----LllPge 107 (127)
T KOG1744|consen 46 VLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVR----LLLPGE 107 (127)
T ss_pred hhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHH----HhCchH
Confidence 78999999999999999999999999999999999999999999999999998654 455653
No 32
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=93.59 E-value=0.58 Score=36.58 Aligned_cols=63 Identities=19% Similarity=0.321 Sum_probs=51.8
Q ss_pred HHHHHHhc---CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCc
Q psy14441 266 LDELMRQV---DSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNI 329 (365)
Q Consensus 266 LqeLVrqI---Dp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI 329 (365)
|+..|.+| .+=+...+.+-|.|.+++.+|+.++...+-+.|-|.+.....+.||...|+ +.|+
T Consensus 8 l~~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~-~~gi 73 (77)
T PF07524_consen 8 LRRSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALE-EMGI 73 (77)
T ss_pred HHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH-HhCC
Confidence 44444444 233788999999999999999999999999999999999899999999995 3444
No 33
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=92.67 E-value=0.82 Score=37.69 Aligned_cols=62 Identities=24% Similarity=0.400 Sum_probs=53.3
Q ss_pred CChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCC---CCCCchhhHHHh
Q psy14441 261 LGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGS---STLDPKDLQFVL 323 (365)
Q Consensus 261 L~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkS---dtLEvkDVql~L 323 (365)
++|+++..+++++.+ .++.++|..+|.-+|-.||-++++.|..+-..++. ..|..+.|.=.+
T Consensus 17 f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~ 81 (85)
T cd08048 17 FPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAY 81 (85)
T ss_pred ccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHH
Confidence 899999999999877 88999999999999999999999999999999887 455555554443
No 34
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=91.87 E-value=0.85 Score=39.58 Aligned_cols=73 Identities=8% Similarity=0.167 Sum_probs=65.7
Q ss_pred CCCCCCCCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh
Q psy14441 253 SSTPNDQILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK 325 (365)
Q Consensus 253 ~s~~~~~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER 325 (365)
.+...+=.++-.++..++++-...+.++.++-..|..+-|.+..+|++.|...||+-+..+|..+||++.+..
T Consensus 13 ~s~ragL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 13 RSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cccccCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 3445667899999999999755669999999999999999999999999999999999999999999999864
No 35
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=91.63 E-value=0.22 Score=39.93 Aligned_cols=59 Identities=22% Similarity=0.353 Sum_probs=46.4
Q ss_pred hHHHHHHHhc--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCC-CCchhhHHH
Q psy14441 264 DKLDELMRQV--DSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSST-LDPKDLQFV 322 (365)
Q Consensus 264 rkLqeLVrqI--Dp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdt-LEvkDVql~ 322 (365)
.-+..|++.- |.+.++.+|+-.++.++.|-||...+.+|...|+-.+++. ||+.|++=+
T Consensus 3 ~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki 64 (72)
T PF09415_consen 3 ELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKI 64 (72)
T ss_dssp HHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHH
T ss_pred HHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence 3445555531 6788999999999999999999999999999999999999 999998644
No 36
>KOG0871|consensus
Probab=90.52 E-value=1.5 Score=40.19 Aligned_cols=71 Identities=13% Similarity=0.311 Sum_probs=66.0
Q ss_pred CCCCCCCChhHHHHHHHhcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh
Q psy14441 255 TPNDQILGKDKLDELMRQVDS-TLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK 325 (365)
Q Consensus 255 ~~~~~VL~KrkLqeLVrqIDp-~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER 325 (365)
.+.+--|+|..++.+|+++=| +..+..|+.|++.+..=+||.-|.+.|-+.|-.+...|+...-|.=.||.
T Consensus 7 ~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~ 78 (156)
T KOG0871|consen 7 EDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALEN 78 (156)
T ss_pred ccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHH
Confidence 445667999999999999876 89999999999999999999999999999999999999999999999985
No 37
>KOG3334|consensus
Probab=88.59 E-value=2.3 Score=38.86 Aligned_cols=67 Identities=13% Similarity=0.281 Sum_probs=57.2
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCC
Q psy14441 266 LDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPG 333 (365)
Q Consensus 266 LqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPG 333 (365)
+..++++ -+=...||-|.-.|||+|=.++..|++.|--+|+|-+..++++.||++.++-.-+..+-|
T Consensus 19 i~~iL~s-~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~ 85 (148)
T KOG3334|consen 19 IASILKS-LGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTP 85 (148)
T ss_pred HHHHHHH-cCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCC
Confidence 4444544 344788999999999999999999999999999999999999999999998777777543
No 38
>KOG3423|consensus
Probab=87.07 E-value=5.1 Score=37.55 Aligned_cols=73 Identities=30% Similarity=0.373 Sum_probs=56.8
Q ss_pred CCCCChhHHHHHHHhcCCC------------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCC--------
Q psy14441 258 DQILGKDKLDELMRQVDST------------------LQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGS-------- 311 (365)
Q Consensus 258 ~~VL~KrkLqeLVrqIDp~------------------e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkS-------- 311 (365)
.....-.-|.||+.++|-- ..-|+-|..++.-.|-.||.+|+..|.+-+|-|..
T Consensus 65 ~~~~~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~ 144 (176)
T KOG3423|consen 65 NPTTKDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKK 144 (176)
T ss_pred CCCCcchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccc
Confidence 3344446688888887532 36688899999999999999999999999999984
Q ss_pred ------CCCCchhhHHHhhhccCccc
Q psy14441 312 ------STLDPKDLQFVLAKDWNISI 331 (365)
Q Consensus 312 ------dtLEvkDVql~LER~wNI~I 331 (365)
-||...|+.=.|+ +|||.|
T Consensus 145 ~~kdkK~tLtmeDL~~AL~-EyGinv 169 (176)
T KOG3423|consen 145 QAKDKKYTLTMEDLSPALA-EYGINV 169 (176)
T ss_pred cccccceeeeHHHHHHHHH-HhCccc
Confidence 2567777777774 677776
No 39
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=85.14 E-value=5.5 Score=30.53 Aligned_cols=50 Identities=22% Similarity=0.245 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhC
Q psy14441 260 ILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRG 310 (365)
Q Consensus 260 VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRk 310 (365)
+|+..-.+-.+++ .+-..-|+-+..++.=.|..||.+|+..|++.+|.|.
T Consensus 2 ~IPD~v~~~yL~~-~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r~ 51 (51)
T PF03540_consen 2 TIPDEVTDYYLER-SGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIRT 51 (51)
T ss_pred CCCHHHHHHHHHH-CCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3444444444444 4446689999999999999999999999999999883
No 40
>KOG0870|consensus
Probab=83.32 E-value=5.6 Score=37.17 Aligned_cols=66 Identities=20% Similarity=0.235 Sum_probs=60.7
Q ss_pred CCChhHHHHHHHhcCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh
Q psy14441 260 ILGKDKLDELMRQVDST--LQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK 325 (365)
Q Consensus 260 VL~KrkLqeLVrqIDp~--e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER 325 (365)
.|++.-+..||+++=|. ..+..|+-.++.+-|--||.-++..|-.+||--+-.|+.+.||.=.|+.
T Consensus 10 ~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~E 77 (172)
T KOG0870|consen 10 NLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDE 77 (172)
T ss_pred hccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHH
Confidence 57888899999998665 5899999999999999999999999999999999999999999988874
No 41
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=83.31 E-value=5.4 Score=33.47 Aligned_cols=58 Identities=26% Similarity=0.414 Sum_probs=43.6
Q ss_pred CChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCC-CCCchh
Q psy14441 261 LGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSS-TLDPKD 318 (365)
Q Consensus 261 L~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSd-tLEvkD 318 (365)
++|..+..|++++.++..+.+.|.-++.-+|--||-++++.|....+.++.. .|....
T Consensus 24 ~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~h 82 (90)
T PF04719_consen 24 FNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDH 82 (90)
T ss_dssp --HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHH
T ss_pred CCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHH
Confidence 7899999999999988999999999999999999999999999999977654 344433
No 42
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=83.29 E-value=1.3 Score=42.14 Aligned_cols=59 Identities=20% Similarity=0.403 Sum_probs=37.1
Q ss_pred CCCCCCChhHHHHHHHhcC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCC
Q psy14441 256 PNDQILGKDKLDELMRQVD---STLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTL 314 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqID---p~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtL 314 (365)
....+|...-|+..|++|. +...+++|+.++|.--+++++.++++.+..+|+||....-
T Consensus 39 ~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~ 100 (264)
T PF05236_consen 39 KEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSK 100 (264)
T ss_dssp -----S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------
T ss_pred ccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccC
Confidence 3456899999999999997 3457899999999999999999999999999999987643
No 43
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=83.10 E-value=3.1 Score=38.49 Aligned_cols=60 Identities=22% Similarity=0.381 Sum_probs=52.3
Q ss_pred CCCCCCCCCChhHHHHHHHhcCCCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCC
Q psy14441 253 SSTPNDQILGKDKLDELMRQVDSTL---QIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSS 312 (365)
Q Consensus 253 ~s~~~~~VL~KrkLqeLVrqIDp~e---~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSd 312 (365)
.+.....+|.+..|...+++|.... .+++|+.++|...+.+++-++++.+..+|+||...
T Consensus 37 ~~~~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~ 99 (212)
T cd08045 37 RSQKDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDS 99 (212)
T ss_pred cccchhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3456678999999999999985543 67999999999999999999999999999999665
No 44
>KOG1745|consensus
Probab=82.19 E-value=1.1 Score=40.30 Aligned_cols=68 Identities=21% Similarity=0.354 Sum_probs=60.1
Q ss_pred CCCCCCChhHHHHHHHhcC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHh
Q psy14441 256 PNDQILGKDKLDELMRQVD----STLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVL 323 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqID----p~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~L 323 (365)
..+-+|.|.-.+.||++|. ++..+-.++...|.+.++.|+-...+.+-..|-|=|--||..||+|+..
T Consensus 59 stdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlAr 130 (137)
T KOG1745|consen 59 STDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 130 (137)
T ss_pred hhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhh
Confidence 3455778888899999774 4578889999999999999999999999999999999999999999975
No 45
>PF05392 COX7B: Cytochrome C oxidase chain VIIB; InterPro: IPR008433 Cytochrome oxidase subunit VIIB is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. The X-ray structure of azide-bound fully oxidized cytochrome c oxidase from bovine heart at 2.9 A resolution has been determined [].; GO: 0004129 cytochrome-c oxidase activity, 0005746 mitochondrial respiratory chain; PDB: 3AG2_X 3ASO_K 3ABL_X 1V55_K 1OCR_K 2DYS_X 1OCO_X 2EIK_X 3AG1_K 2Y69_X ....
Probab=81.39 E-value=1.7 Score=36.18 Aligned_cols=31 Identities=29% Similarity=0.348 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHhhhcceeeecCCCC
Q psy14441 161 NIQLLVGTVSLAATIGYLAVSDVFIWNFFPP 191 (365)
Q Consensus 161 N~~Ll~Gi~~l~gTi~~~~~SGii~lN~~pP 191 (365)
|++|+.|.+|.+++.+|+.+.-=|.+|++|=
T Consensus 39 n~vL~~Ga~FC~~~W~y~~TQ~GIeWNlSPV 69 (80)
T PF05392_consen 39 NAVLASGATFCVAVWTYVATQIGIEWNLSPV 69 (80)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHSS------ST
T ss_pred ceeeecccchhhhhHhhhheecceeecCCcc
Confidence 8999999999999999999977777999985
No 46
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=75.71 E-value=10 Score=34.38 Aligned_cols=66 Identities=21% Similarity=0.312 Sum_probs=53.0
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCC---CCCCchhhHHHhhhccCcccC
Q psy14441 266 LDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGS---STLDPKDLQFVLAKDWNISIP 332 (365)
Q Consensus 266 LqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkS---dtLEvkDVql~LER~wNI~IP 332 (365)
|.=+++. -+-++-++.|-=-|+++|-.+-.+|++.|.-.|||-|+ .+|.++||.+.+.-.-|..+-
T Consensus 20 ihliL~S-lgi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~ 88 (145)
T COG5094 20 IHLILRS-LGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFV 88 (145)
T ss_pred HHHHHHh-cCchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcC
Confidence 3334443 33467788899999999999999999999999999854 367889999999888887763
No 47
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=74.09 E-value=15 Score=33.48 Aligned_cols=77 Identities=13% Similarity=0.267 Sum_probs=65.4
Q ss_pred CCCCCCChhHHHHHHHhc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh-ccCcccC
Q psy14441 256 PNDQILGKDKLDELMRQV-DSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK-DWNISIP 332 (365)
Q Consensus 256 ~~~~VL~KrkLqeLVrqI-Dp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER-~wNI~IP 332 (365)
+.+--|+|...|-+|..| +.+..+..|+.|++.+..=+||.-+.+.|-..|-.-...|+...-|-=.||. +|+-.||
T Consensus 7 dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 7 DDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred cccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 345568999999999998 5568999999999999999999999999999999999999999888777763 3444444
No 48
>cd01403 Cyt_c_Oxidase_VIIb Cytochrome C oxidase chain VIIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIb subunit is found only in eukaryotes and its specific function remains unclear. A rare polymorphism of the CcO VIIb gene may be associated with the high risk of nasopharyngeal carcinoma in a Cantonese family.
Probab=69.99 E-value=0.87 Score=35.01 Aligned_cols=31 Identities=26% Similarity=0.403 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHHhhhcceeeecCCCC
Q psy14441 161 NIQLLVGTVSLAATIGYLAVSDVFIWNFFPP 191 (365)
Q Consensus 161 N~~Ll~Gi~~l~gTi~~~~~SGii~lN~~pP 191 (365)
|++|+.|.+|.++..+|+.+.-=|..|++|=
T Consensus 11 n~~l~~Ga~Fc~avw~~v~TQ~GIeWnlSPV 41 (51)
T cd01403 11 NAVLISGATFCTAVWTYVMTQTGIEWNLSPV 41 (51)
T ss_pred ceEEecccchhhhhhhheeeecceeeccccc
Confidence 8899999999999999999977778999985
No 49
>KOG2549|consensus
Probab=69.65 E-value=30 Score=37.67 Aligned_cols=93 Identities=15% Similarity=0.309 Sum_probs=71.8
Q ss_pred CCCCCCCC-hhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCC
Q psy14441 255 TPNDQILG-KDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPG 333 (365)
Q Consensus 255 ~~~~~VL~-KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPG 333 (365)
.....+.+ +..++.+.+++ +-+.|++|+..+|.+-.+.=|.+|+..|.+.-+|=|-.+|.+.||.-.|.-.-=-.+=|
T Consensus 5 ~~~~~v~s~~Es~k~vAEsl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg 83 (576)
T KOG2549|consen 5 KESPTVVSPKESVKVVAESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYG 83 (576)
T ss_pred cccccccCcHHHHHHHHHHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccC
Confidence 34556666 77777777775 34679999999999999999999999999999999999999999997775332222346
Q ss_pred CCCCCCCCCCCCCCc
Q psy14441 334 YGTDELKPYKRPMAT 348 (365)
Q Consensus 334 fgsDeirp~rK~~~t 348 (365)
|++-++-+.|+...+
T Consensus 84 ~~s~~~i~fr~a~~~ 98 (576)
T KOG2549|consen 84 FGAQEIIPFRKASGG 98 (576)
T ss_pred cccCceeeccccCCC
Confidence 666666666766554
No 50
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=68.41 E-value=10 Score=38.91 Aligned_cols=61 Identities=20% Similarity=0.339 Sum_probs=43.2
Q ss_pred CCCCChhHHHHHHHhcC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchh
Q psy14441 258 DQILGKDKLDELMRQVD-----STLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKD 318 (365)
Q Consensus 258 ~~VL~KrkLqeLVrqID-----p~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkD 318 (365)
+.-|+..-+..|+...- .+..|.+++-++|.+.-|.|-+.+...-...|||=|-+|||-.|
T Consensus 349 ~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 349 YPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ---S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 33344444455555442 46899999999999999999999999999999999999999877
No 51
>KOG3901|consensus
Probab=66.93 E-value=13 Score=32.65 Aligned_cols=59 Identities=20% Similarity=0.417 Sum_probs=43.3
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhc
Q psy14441 265 KLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326 (365)
Q Consensus 265 kLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~ 326 (365)
.|+-|+=-..-.-.-=++..++|=+|+=+||.++++.|...+ +-+.+.+.|+.|.|.|.
T Consensus 14 dl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRkD 72 (109)
T KOG3901|consen 14 DLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRKD 72 (109)
T ss_pred HHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHhC
Confidence 344444444333444567778999999999999988888888 33457899999999864
No 52
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=66.52 E-value=14 Score=32.80 Aligned_cols=48 Identities=19% Similarity=0.380 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhc
Q psy14441 277 LQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326 (365)
Q Consensus 277 e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~ 326 (365)
-.--+|..+.|-+++-|++..+++.|...|-.|+.- .+.|.+|.|.|.
T Consensus 26 v~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rnK~--k~eDfkfaLr~D 73 (126)
T COG5248 26 VAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKT--KTEDFKFALRRD 73 (126)
T ss_pred CCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcccc--hHHHHHHHHhhC
Confidence 344567888999999999999999999999988764 689999999864
No 53
>KOG3489|consensus
Probab=64.56 E-value=27 Score=29.56 Aligned_cols=50 Identities=22% Similarity=0.293 Sum_probs=43.0
Q ss_pred ChhHHHHHHHhc----------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCC
Q psy14441 262 GKDKLDELMRQV----------DSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGS 311 (365)
Q Consensus 262 ~KrkLqeLVrqI----------Dp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkS 311 (365)
.|.++++.|.+. +|+..||...|.-|...+|.|||.-.--.-++|+-+++
T Consensus 23 qk~k~~~~VHqft~~CWdKCi~~~~sklds~~e~ClsnCV~RfiDts~~I~~r~~~~~~~ 82 (86)
T KOG3489|consen 23 QKQKFQEQVHQFTEICWDKCIEKPGSKLDSSEETCLSNCVNRFIDTSLFIVKRLAQMNQG 82 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 377888888885 68899999999999999999999988777788877665
No 54
>smart00350 MCM minichromosome maintenance proteins.
Probab=62.64 E-value=26 Score=36.45 Aligned_cols=66 Identities=15% Similarity=0.203 Sum_probs=52.3
Q ss_pred CCCChhHHHHHHHhcCC--CCCCCHHHHHHHHHHHHHHH-------------------HHHHHHHHHHHhhhCCCCCCch
Q psy14441 259 QILGKDKLDELMRQVDS--TLQIDEEVYDTFSEIANDFV-------------------DNIVHRACQLAKHRGSSTLDPK 317 (365)
Q Consensus 259 ~VL~KrkLqeLVrqIDp--~e~LD~dVEElLLeLADDFV-------------------dsVvs~AC~LAKHRkSdtLEvk 317 (365)
.+++...|.+.+..+-. .-.+++++.+.|.+++.+-= +.++..|..+||-|.++.++..
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~ 495 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEA 495 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHH
Confidence 46787777777655432 23589999999998877643 6788899999999999999999
Q ss_pred hhHHHhh
Q psy14441 318 DLQFVLA 324 (365)
Q Consensus 318 DVql~LE 324 (365)
||+...+
T Consensus 496 Dv~~ai~ 502 (509)
T smart00350 496 DVEEAIR 502 (509)
T ss_pred HHHHHHH
Confidence 9987754
No 55
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=62.63 E-value=27 Score=33.85 Aligned_cols=66 Identities=18% Similarity=0.329 Sum_probs=50.0
Q ss_pred CChhHHHHHHHhcC----CCCCCCHHHHHHHHHHHHH------HHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhc
Q psy14441 261 LGKDKLDELMRQVD----STLQIDEEVYDTFSEIAND------FVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326 (365)
Q Consensus 261 L~KrkLqeLVrqID----p~e~LD~dVEElLLeLADD------FVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~ 326 (365)
.+...+.++++.-- ....+++++-+.+.+.+.. ..-+++..|+.+|..|++++|+.+||.-.+++.
T Consensus 207 y~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 207 YTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 34566666655421 1346899999999988854 345778899999999999999999999888765
No 56
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=59.03 E-value=37 Score=30.79 Aligned_cols=67 Identities=12% Similarity=0.219 Sum_probs=53.9
Q ss_pred CCCChhHHHHHHHhc------CCCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh
Q psy14441 259 QILGKDKLDELMRQV------DSTLQIDEEVYDTFSEIAND---FVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK 325 (365)
Q Consensus 259 ~VL~KrkLqeLVrqI------Dp~e~LD~dVEElLLeLADD---FVdsVvs~AC~LAKHRkSdtLEvkDVql~LER 325 (365)
.-++...+.+++... +....+++++.+.|.+.+.- .|+.++..+...|.-++++.++..||.-.+..
T Consensus 190 ~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~ 265 (269)
T TIGR03015 190 GPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAE 265 (269)
T ss_pred CCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 345666777766543 22346999999999999997 89999999999999999999999999887754
No 57
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=50.54 E-value=47 Score=34.94 Aligned_cols=64 Identities=17% Similarity=0.327 Sum_probs=50.2
Q ss_pred CChhHHHHHHHhcCC--CCCCCHHHHHHHHHHHHH--HHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 261 LGKDKLDELMRQVDS--TLQIDEEVYDTFSEIAND--FVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 261 L~KrkLqeLVrqIDp--~e~LD~dVEElLLeLADD--FVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
+++..+.++++..-. +..+++++-+.|.+.+.+ .+.+++..|+.+|..++..+++.+||.-+++
T Consensus 263 L~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~ 330 (531)
T TIGR02902 263 LLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE 330 (531)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence 456677777777532 357899999988777653 3557888999999999988999999999986
No 58
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=48.90 E-value=81 Score=29.98 Aligned_cols=47 Identities=32% Similarity=0.450 Sum_probs=40.2
Q ss_pred hHHHHHHHhcCCCC------------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhC
Q psy14441 264 DKLDELMRQVDSTL------------------QIDEEVYDTFSEIANDFVDNIVHRACQLAKHRG 310 (365)
Q Consensus 264 rkLqeLVrqIDp~e------------------~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRk 310 (365)
+.|.||++++|... +.|+-|..+|.-+|-.||.+|...|-+..|-|.
T Consensus 73 ktlee~l~~mDsy~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~ 137 (197)
T COG5162 73 KTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQ 137 (197)
T ss_pred HHHHHHHHhcccCCCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56899999988654 447778899999999999999999999888886
No 59
>PF08429 PLU-1: PLU-1-like protein; InterPro: IPR013637 This domain is found in the central region of lysine-specific demethylases, which are nuclear proteins that may have a role in DNA-binding and transcription, and are associated with malignant cancer phenotypes []. The domain is also found in various other Jumonji/ARID domain-containing proteins (see IPR013129 from INTERPRO, IPR001606 from INTERPRO). ; GO: 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process
Probab=48.68 E-value=67 Score=30.98 Aligned_cols=119 Identities=14% Similarity=0.287 Sum_probs=62.4
Q ss_pred hhhcCCccCc-hhhhhccchhhHHhhhccCcccccCCCccccCCCcccccccccCCCCCCCCCCCCChhHHHHHHHhcCC
Q psy14441 197 EVLSFPAKDL-SMLNSVDSDHSQVMNSFSNSMEVDQNSSQSSTQSPAAQVMQKTNMPSSTPNDQILGKDKLDELMRQVDS 275 (365)
Q Consensus 197 E~~~f~a~dl-~~L~~v~~~~~q~m~~~~~~~~i~q~~~~s~~p~P~~~~m~~~~~p~s~~~~~VL~KrkLqeLVrqIDp 275 (365)
|...||-+|+ ..|+..-.+|.+....-.. ++.++...+..+..+ .+.....-++=..|..|+++++.
T Consensus 30 e~~~~~~~~l~~~L~~~v~~a~~~~~~a~~-~l~~k~~~r~~~~~~-----------~~~~~~~~~~l~~l~~Ll~e~~~ 97 (335)
T PF08429_consen 30 EKIPFPLPELLENLRNFVKRAESWVEKAQQ-LLSRKQRTRRRNGKA-----------EDQKSRNKLTLEELEALLEEIES 97 (335)
T ss_pred HhCCCCCHHHHHHHHHHHHHHHHHHHHHHH-HhcccccccccCCcc-----------ccccccccCCHHHHHHHHHHHhc
Confidence 5566777787 7777776666554442111 111221111111111 12234556788899999999986
Q ss_pred CCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHh--hhccCcccCCC
Q psy14441 276 TLQIDEEVYDTFSEI---ANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVL--AKDWNISIPGY 334 (365)
Q Consensus 276 ~e~LD~dVEElLLeL---ADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~L--ER~wNI~IPGf 334 (365)
-..--|++ +.|.++ +++|...+-.. |.+ ....++.+++=-| ...+|+.+|..
T Consensus 98 L~~~~pEi-~~L~~l~~~ve~f~~~a~~~---L~~---~~~~~~~~le~Ll~~g~s~~v~lpel 154 (335)
T PF08429_consen 98 LPFDCPEI-DQLKELLEEVEEFQSRAQEA---LSD---PESPSLEELEELLEEGESFGVDLPEL 154 (335)
T ss_pred CCeeCchH-HHHHHHHHHHHHHHHHHHHH---Hhc---cccCCHHHHHHHHHhcccCceeChhH
Confidence 65555663 334444 44555443332 222 2233455665555 45667777754
No 60
>KOG4782|consensus
Probab=48.49 E-value=14 Score=32.09 Aligned_cols=44 Identities=30% Similarity=0.386 Sum_probs=32.9
Q ss_pred CCCcCCCCCCCCChHHHHHhhh--------hhh--HHHHHHHHHHHHHHHHHhhh
Q psy14441 136 PVTIDDLPVPQGSWKAHYDKQN--------TKY--NIQLLVGTVSLAATIGYLAV 180 (365)
Q Consensus 136 ~~TmnDLPvP~GdW~e~y~akq--------~kY--N~~Ll~Gi~~l~gTi~~~~~ 180 (365)
-+++.|||-|+--|++|..+-| ++. |.+-.+|++.++..| |+++
T Consensus 24 d~d~EdL~peQ~h~akQaE~an~ekV~~~~aknykN~is~a~i~alViaI-Y~YT 77 (108)
T KOG4782|consen 24 DIDIEDLPPEQKHFAKQAEKANQEKVKEIFAKNYKNHISFAGIGALVIAI-YGYT 77 (108)
T ss_pred CCchhhCChHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHh-hhhe
Confidence 5789999999999888876544 233 777788888888777 5443
No 61
>smart00414 H2A Histone 2A.
Probab=47.98 E-value=98 Score=26.63 Aligned_cols=69 Identities=10% Similarity=0.206 Sum_probs=60.8
Q ss_pred CCCCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh
Q psy14441 257 NDQILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK 325 (365)
Q Consensus 257 ~~~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER 325 (365)
.+=.++-.++..++++-.-...++..+--.|.-+-|-+..+|++.|...|+.-+...+..+++++.+..
T Consensus 6 agL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 6 AGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CCccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 344678889999999766678999999999999999999999999999999999999999999998843
No 62
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=45.81 E-value=85 Score=30.00 Aligned_cols=66 Identities=12% Similarity=0.191 Sum_probs=50.0
Q ss_pred CChhHHHHHHHhcC----CCCCCCHHHHHHHHHHHH------HHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhc
Q psy14441 261 LGKDKLDELMRQVD----STLQIDEEVYDTFSEIAN------DFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326 (365)
Q Consensus 261 L~KrkLqeLVrqID----p~e~LD~dVEElLLeLAD------DFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~ 326 (365)
.++..+.++++..- ....+|+++.+++.+++. ..+-+++..|..+|.-+++.+++..||.-.++..
T Consensus 199 ~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~ 274 (365)
T TIGR02928 199 YDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI 274 (365)
T ss_pred CCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 35667777776531 234689999999888875 2456688889999999999999999998776654
No 63
>KOG3219|consensus
Probab=44.66 E-value=38 Score=32.38 Aligned_cols=65 Identities=25% Similarity=0.400 Sum_probs=53.8
Q ss_pred CCCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCC-CCCchhhHHHh
Q psy14441 258 DQILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSS-TLDPKDLQFVL 323 (365)
Q Consensus 258 ~~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSd-tLEvkDVql~L 323 (365)
...++|..+..|+.+|.+.. +++-|.=++.-||.=||-.|++.|..+.--++.+ .|-.+.|.=.+
T Consensus 110 rs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~ 175 (195)
T KOG3219|consen 110 RSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAY 175 (195)
T ss_pred HhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHH
Confidence 45799999999999999888 9999999999999999999999999887776643 55555554333
No 64
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=42.14 E-value=14 Score=33.29 Aligned_cols=20 Identities=35% Similarity=0.576 Sum_probs=14.5
Q ss_pred cccchhccchhHHHHHHHHH
Q psy14441 52 HSFLFRKQRNVYLHCLLVML 71 (365)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~~~ 71 (365)
|.-+||.|||+|+.-....|
T Consensus 94 ~~~~fraQRN~YIsGf~LfL 113 (192)
T PF05529_consen 94 LAKKFRAQRNMYISGFALFL 113 (192)
T ss_pred HHHHHHHHHhHHHHHHHHHH
Confidence 36689999999996444433
No 65
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=38.48 E-value=57 Score=34.49 Aligned_cols=63 Identities=16% Similarity=0.460 Sum_probs=48.7
Q ss_pred ChhHHHHHHHhc--CCCCCCCHHHHHHHHHHHHH----HHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 262 GKDKLDELMRQV--DSTLQIDEEVYDTFSEIAND----FVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 262 ~KrkLqeLVrqI--Dp~e~LD~dVEElLLeLADD----FVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
+++.+.+.++-= .-+-.||+|+-|.|.++..+ +.-+.++-|..+||.||+.+++++||.-.-+
T Consensus 362 ~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~ 430 (450)
T COG1224 362 SREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE 430 (450)
T ss_pred CHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH
Confidence 456666666432 23458999999999998875 6777888888899999999999999976543
No 66
>PF15098 TMEM89: TMEM89 protein family
Probab=37.90 E-value=22 Score=31.98 Aligned_cols=68 Identities=25% Similarity=0.433 Sum_probs=49.2
Q ss_pred chhhHHHHHHHHHHHHhhhhhhhhHHhhhccCCCCCCCCCCcCCCCCCCCChHHHHHhhhhhhHHHHHHHHHHHHHHHHH
Q psy14441 98 MPVACHFVLSSLLKALLPVIGSQMVQQVRRSHAYSKKPPVTIDDLPVPQGSWKAHYDKQNTKYNIQLLVGTVSLAATIGY 177 (365)
Q Consensus 98 ~~~~~~~~~~~~~~~l~p~~~~~~~~q~r~~~~ps~~k~~TmnDLPvP~GdW~e~y~akq~kYN~~Ll~Gi~~l~gTi~~ 177 (365)
.|||.-.+-.. .+=.++|++++--|+-...+.++++|.+ |||+|+. +--.-...|+.|++-..-++..
T Consensus 45 YPVAGvtiTTT----Mml~~~r~~~~r~Rsq~tk~ehPqvtt~----p~g~wKr----r~piSDrtlll~VLHmLDalL~ 112 (134)
T PF15098_consen 45 YPVAGVTITTT----MMLMISRVMLQRWRSQATKGEHPQVTTS----PCGPWKR----RAPISDRTLLLGVLHMLDALLV 112 (134)
T ss_pred eeeccchHHHH----HHHHHHHHHHHHHHHhhcccCCCcccCC----CCCcccc----cCCcchhHHHHHHHHHHHHHHH
Confidence 58887555433 3346789999988988888888888875 9999974 3445567788898866655533
No 67
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=34.54 E-value=62 Score=35.26 Aligned_cols=77 Identities=14% Similarity=0.321 Sum_probs=56.2
Q ss_pred ChhHHHHHHHhcCC------CCCCCHHHHHHHHHHHHHHHHH---------HHHHHHHHHhhhC----CCCCCchhhHHH
Q psy14441 262 GKDKLDELMRQVDS------TLQIDEEVYDTFSEIANDFVDN---------IVHRACQLAKHRG----SSTLDPKDLQFV 322 (365)
Q Consensus 262 ~KrkLqeLVrqIDp------~e~LD~dVEElLLeLADDFVds---------Vvs~AC~LAKHRk----SdtLEvkDVql~ 322 (365)
+.....++++.+-. +..+++++.+.+.++++.|+.+ ++..||..++-+. ...++..||.-+
T Consensus 346 ~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~~~~~~~~~~v~~~~i~~~ 425 (731)
T TIGR02639 346 SIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPKAKKKANVSVKDIENV 425 (731)
T ss_pred CHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhcCcccccccccCHHHHHHH
Confidence 55555666664322 2479999999999999999844 5778887666543 345899999999
Q ss_pred hhhccCcccCCCCCCC
Q psy14441 323 LAKDWNISIPGYGTDE 338 (365)
Q Consensus 323 LER~wNI~IPGfgsDe 338 (365)
+++--||++...+.+|
T Consensus 426 i~~~tgiP~~~~~~~~ 441 (731)
T TIGR02639 426 VAKMAHIPVKTVSVDD 441 (731)
T ss_pred HHHHhCCChhhhhhHH
Confidence 9998888776655544
No 68
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=33.99 E-value=1.7e+02 Score=30.58 Aligned_cols=65 Identities=14% Similarity=0.310 Sum_probs=54.4
Q ss_pred CCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 259 QILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 259 ~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
-+.++..+.+..+.. +-+.||+|+-.+|..=.+==|..|++.|.+.-.|-|-++|.+-||...|.
T Consensus 4 t~ws~et~KdvAesl-Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr 68 (450)
T COG5095 4 TLWSKETLKDVAESL-GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALR 68 (450)
T ss_pred eeecHHHHHHHHHHc-CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHH
Confidence 356677788777654 34678999888887777778999999999999999999999999999884
No 69
>PTZ00017 histone H2A; Provisional
Probab=33.51 E-value=1.6e+02 Score=26.68 Aligned_cols=72 Identities=8% Similarity=0.167 Sum_probs=63.6
Q ss_pred CCCCCCCCCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 253 SSTPNDQILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 253 ~s~~~~~VL~KrkLqeLVrqIDp~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
.+.-.+=.++-.++..++++-.-...+...+--.|.-+-|-+..+|++.|...|+.-+...|..++|++.+.
T Consensus 20 rS~ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 20 RSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred ccccCCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 345566788999999999986667899999888999999999999999999999999999999999999984
No 70
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=32.49 E-value=2.1e+02 Score=27.15 Aligned_cols=56 Identities=11% Similarity=0.221 Sum_probs=44.2
Q ss_pred CCCCCCCCCCChhHHHHHHHhcCC--C-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy14441 252 PSSTPNDQILGKDKLDELMRQVDS--T-LQIDEEVYDTFSEIANDFVDNIVHRACQLAK 307 (365)
Q Consensus 252 p~s~~~~~VL~KrkLqeLVrqIDp--~-e~LD~dVEElLLeLADDFVdsVvs~AC~LAK 307 (365)
+...+...+-+-..|.+=+..|.- + ..+++|+-++|.--.|.|+.++++..+.++|
T Consensus 194 ~lc~es~~LPD~~~L~~Rm~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~r 252 (252)
T PF12767_consen 194 PLCSESGELPDTQSLRKRMEQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLDLVR 252 (252)
T ss_pred ccHHHhCcCCCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 344456777777777777766632 2 5889999999999999999999999998875
No 71
>PF12911 OppC_N: N-terminal TM domain of oligopeptide transport permease C
Probab=31.99 E-value=59 Score=23.57 Aligned_cols=38 Identities=13% Similarity=0.286 Sum_probs=26.3
Q ss_pred CCCChHHHHHhhhhhhHHHHHHHHHHHHHHHHHhhhccee
Q psy14441 145 PQGSWKAHYDKQNTKYNIQLLVGTVSLAATIGYLAVSDVF 184 (365)
Q Consensus 145 P~GdW~e~y~akq~kYN~~Ll~Gi~~l~gTi~~~~~SGii 184 (365)
|.+.|++.|++=.+ |..-++|+++++.-+..+.....+
T Consensus 1 ~~s~~~~~~~~f~~--nk~a~~gl~il~~~vl~ai~~p~~ 38 (56)
T PF12911_consen 1 SRSPWKDAWRRFRR--NKLAVIGLIILLILVLLAIFAPFI 38 (56)
T ss_pred CCCHHHHHHHHHHh--CchHHHHHHHHHHHHHHHHHHHHc
Confidence 57889998876543 667777777776666666655555
No 72
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=30.96 E-value=76 Score=31.39 Aligned_cols=48 Identities=25% Similarity=0.326 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhh
Q psy14441 278 QIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAK 325 (365)
Q Consensus 278 ~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER 325 (365)
-+..||--+...+.+.||+.++.+|--.|+..+-.||--.||.-.+++
T Consensus 127 MisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~k 174 (286)
T COG5208 127 MISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKK 174 (286)
T ss_pred heecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHH
Confidence 345555667889999999999999999999999999999999877753
No 73
>PRK14622 hypothetical protein; Provisional
Probab=30.40 E-value=41 Score=28.63 Aligned_cols=46 Identities=22% Similarity=0.276 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCCCCC
Q psy14441 279 IDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPGYGT 336 (365)
Q Consensus 279 LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPGfgs 336 (365)
+||+=.|.|-++.=.=+++.+..+.++++.+=+.. .=|+.+|||++
T Consensus 58 l~~ed~e~LeDLI~aA~N~A~~k~~~~~~~~m~~~------------tgg~~lPG~~~ 103 (103)
T PRK14622 58 VDPNDKAMLEDLVTAAVNAAVEKARTAADESMSKA------------TGGIKIPGIAG 103 (103)
T ss_pred cCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------hCCCCCCCCCC
Confidence 34333445555555556666666666655544331 12677899874
No 74
>KOG4336|consensus
Probab=29.98 E-value=1.5e+02 Score=30.41 Aligned_cols=57 Identities=16% Similarity=0.308 Sum_probs=46.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCCC
Q psy14441 277 LQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPGY 334 (365)
Q Consensus 277 e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPGf 334 (365)
+.+++.+.|-|+++.+..++.+-..+--.+-|-|-......||.|.| +++||.++..
T Consensus 21 d~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~L-i~mnI~v~sL 77 (323)
T KOG4336|consen 21 DSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTL-IEMNIKVSSL 77 (323)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHH-HHhCCChhhh
Confidence 56899999999999999999998777666666666777899999998 4577777643
No 75
>PF07942 N2227: N2227-like protein; InterPro: IPR012901 This family features sequences that are similar to a region of hypothetical yeast gene product N2227 (P53934 from SWISSPROT). This is thought to be expressed during meiosis and may be involved in the defence response to stressful conditions [].
Probab=29.14 E-value=18 Score=35.50 Aligned_cols=89 Identities=15% Similarity=0.209 Sum_probs=68.1
Q ss_pred hHHhhhccCCCCCCC---CCCcCCCCCCCCChHHHHHhh--hhhhHHHH-------HHHHHHHHHHHHHhhhcceeeecC
Q psy14441 121 MVQQVRRSHAYSKKP---PVTIDDLPVPQGSWKAHYDKQ--NTKYNIQL-------LVGTVSLAATIGYLAVSDVFIWNF 188 (365)
Q Consensus 121 ~~~q~r~~~~ps~~k---~~TmnDLPvP~GdW~e~y~ak--q~kYN~~L-------l~Gi~~l~gTi~~~~~SGii~lN~ 188 (365)
..+|.|+...|+-.+ ..--++|-.=.|||.+-|... +.+|+.+. +--++-.+-||.-++.-|=++.|+
T Consensus 122 ~~dqlr~v~iPDv~p~~~~~~~~~~sm~aGDF~e~y~~~~~~~~~d~VvT~FFIDTA~Ni~~Yi~tI~~lLkpgG~WIN~ 201 (270)
T PF07942_consen 122 REDQLRPVRIPDVDPSSELPSPSNLSMCAGDFLEVYGPDENKGSFDVVVTCFFIDTAENIIEYIETIEHLLKPGGYWINF 201 (270)
T ss_pred HHHhCCceEeCCcCcccccCCCCceeEecCccEEecCCcccCCcccEEEEEEEeechHHHHHHHHHHHHHhccCCEEEec
Confidence 467899999996533 223567777899999999887 78888654 335667788888888888899999
Q ss_pred CCCCCChhhh-------hcCCccCchhh
Q psy14441 189 FPPTLPKNEV-------LSFPAKDLSML 209 (365)
Q Consensus 189 ~pP~~P~~E~-------~~f~a~dl~~L 209 (365)
+|-.|-++++ +.+...|+..|
T Consensus 202 GPLlyh~~~~~~~~~~sveLs~eEi~~l 229 (270)
T PF07942_consen 202 GPLLYHFEPMSIPNEMSVELSLEEIKEL 229 (270)
T ss_pred CCccccCCCCCCCCCcccCCCHHHHHHH
Confidence 9999999987 66666665544
No 76
>KOG2680|consensus
Probab=29.10 E-value=98 Score=32.43 Aligned_cols=63 Identities=11% Similarity=0.352 Sum_probs=48.7
Q ss_pred ChhHHHHHHHhc--CCCCCCCHHHHHHHHHHHHH----HHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 262 GKDKLDELMRQV--DSTLQIDEEVYDTFSEIAND----FVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 262 ~KrkLqeLVrqI--Dp~e~LD~dVEElLLeLADD----FVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
+++.+.++++-= .-.-.|++|+-++|..+..+ +--..++.|...|..||..++++.||+-.++
T Consensus 359 ~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 359 TEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred cHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 445555555422 23357899999999999875 6778889999999999999999999976554
No 77
>PF14846 DUF4485: Domain of unknown function (DUF4485)
Probab=28.53 E-value=33 Score=28.08 Aligned_cols=21 Identities=38% Similarity=0.448 Sum_probs=19.3
Q ss_pred cccchhccchhHHHHHHHHHh
Q psy14441 52 HSFLFRKQRNVYLHCLLVMLN 72 (365)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~~~~ 72 (365)
++...++.||.|+.+|+++++
T Consensus 41 ~~~~~~~~RN~Y~~~Ll~~l~ 61 (85)
T PF14846_consen 41 HNVEEKKNRNEYASLLLHCLQ 61 (85)
T ss_pred CCHHHHHHHHHHHHHHHHHHh
Confidence 778889999999999999986
No 78
>cd00922 Cyt_c_Oxidase_IV Cytochrome c oxidase subunit IV. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit IV is the largest of the nuclear-encoded subunits. It binds ATP at the matrix side, leading to an allosteric inhibition of enzyme activity at high intramitochondrial ATP/ADP ratios. In mammals, subunit IV has a lung-specific isoform and a ubiquitously expressed isoform.
Probab=28.49 E-value=65 Score=28.63 Aligned_cols=46 Identities=24% Similarity=0.242 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhhh----hhhhHHhhhccCCCCCCCCCCcCCCCCCCCChHHH
Q psy14441 105 VLSSLLKALLPVI----GSQMVQQVRRSHAYSKKPPVTIDDLPVPQGSWKAH 152 (365)
Q Consensus 105 ~~~~~~~~l~p~~----~~~~~~q~r~~~~ps~~k~~TmnDLPvP~GdW~e~ 152 (365)
....+...|.-+- +.+..+=.+.-|--+-+ .|.-+++.|.|+|+..
T Consensus 28 e~~~~~~~Lrekek~dW~~LT~~EKkAlY~isfg--~~~~e~~~~~~ewk~v 77 (136)
T cd00922 28 ELSAEIKALREKEKGDWKQLTLEEKKALYRISFG--ETGPEMNAPTGEWKTV 77 (136)
T ss_pred cchHHHHHHHHHhhCCHhhCCHHHHhhHhhhhhc--cccccccCCCccHHHH
Confidence 5566666666554 55666655555544432 5778899999999864
No 79
>PF05767 Pox_A14: Poxvirus virion envelope protein A14; InterPro: IPR008785 This family consists of several Poxvirus virion envelope protein A14-like sequences. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate in vivo and in vitro. A14 is hyperphosphorylated on serine residues in the absence of H1 expression [].; GO: 0019031 viral envelope
Probab=26.29 E-value=76 Score=27.28 Aligned_cols=34 Identities=21% Similarity=0.251 Sum_probs=27.9
Q ss_pred hhhhHHHHHHHHHHHHHHHHHhhhcceeeecCCCCCCChh
Q psy14441 157 NTKYNIQLLVGTVSLAATIGYLAVSDVFIWNFFPPTLPKN 196 (365)
Q Consensus 157 q~kYN~~Ll~Gi~~l~gTi~~~~~SGii~lN~~pP~~P~~ 196 (365)
...|+-+|+.|++.++.+..+++ +.++-+++|.+
T Consensus 8 ~n~~S~vli~GiiLL~~aCIfAf------idfsK~~~~~~ 41 (92)
T PF05767_consen 8 SNYFSGVLIGGIILLIAACIFAF------IDFSKNTKPTD 41 (92)
T ss_pred HhccchHHHHHHHHHHHHHHHHh------hhhccCCCCch
Confidence 45688999999999999998876 57777777765
No 80
>PF11298 DUF3099: Protein of unknown function (DUF3099); InterPro: IPR021449 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Probab=26.23 E-value=1.3e+02 Score=24.60 Aligned_cols=31 Identities=10% Similarity=0.100 Sum_probs=23.5
Q ss_pred ChHHHHHhhhhhhHHHHHHHHHHHHHHHHHh
Q psy14441 148 SWKAHYDKQNTKYNIQLLVGTVSLAATIGYL 178 (365)
Q Consensus 148 dW~e~y~akq~kYN~~Ll~Gi~~l~gTi~~~ 178 (365)
+-.+++++|+++|.....+-++.|+++..+.
T Consensus 8 s~~~d~~~R~r~Y~i~M~~Ri~~fvlA~~~~ 38 (73)
T PF11298_consen 8 SLSQDQRRRRRRYLIMMGIRIPCFVLAAVVY 38 (73)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4467888999999999888877666655443
No 81
>PRK13183 psbN photosystem II reaction center protein N; Provisional
Probab=25.48 E-value=1.1e+02 Score=23.39 Aligned_cols=34 Identities=15% Similarity=0.035 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHhhhcceeeecCCCCC----CChhhh
Q psy14441 165 LVGTVSLAATIGYLAVSDVFIWNFFPPT----LPKNEV 198 (365)
Q Consensus 165 l~Gi~~l~gTi~~~~~SGii~lN~~pP~----~P~~E~ 198 (365)
+..++++++.+.++.+---+|--|+||. -|+||=
T Consensus 7 A~~~~i~i~~lL~~~TgyaiYtaFGppSk~LrDPFeeH 44 (46)
T PRK13183 7 ALSLAITILAILLALTGFGIYTAFGPPSKELDDPFDDH 44 (46)
T ss_pred hHHHHHHHHHHHHHHhhheeeeccCCcccccCCchhhc
Confidence 3455667777777777778899999994 355553
No 82
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=25.30 E-value=1.2e+02 Score=24.67 Aligned_cols=27 Identities=7% Similarity=0.237 Sum_probs=18.8
Q ss_pred HHhhhhhhHHHHHHHHHHHHHHHHHhh
Q psy14441 153 YDKQNTKYNIQLLVGTVSLAATIGYLA 179 (365)
Q Consensus 153 y~akq~kYN~~Ll~Gi~~l~gTi~~~~ 179 (365)
+.++...==..+.+|+++|+++++|++
T Consensus 62 l~r~~~~D~~li~~~~~~f~~~v~yI~ 88 (92)
T PF03908_consen 62 LERRDKTDRILIFFAFLFFLLVVLYIL 88 (92)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHh
Confidence 334444444566789999999999875
No 83
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=25.16 E-value=97 Score=26.99 Aligned_cols=21 Identities=10% Similarity=0.116 Sum_probs=14.7
Q ss_pred hhhhhhHHHHHHHHHHHHHHH
Q psy14441 155 KQNTKYNIQLLVGTVSLAATI 175 (365)
Q Consensus 155 akq~kYN~~Ll~Gi~~l~gTi 175 (365)
++.|+=|....+|+++++.+|
T Consensus 45 ~~~R~rN~~Tgl~L~~~v~gI 65 (100)
T PF09813_consen 45 QRRRRRNLLTGLALGAFVVGI 65 (100)
T ss_pred HHHhhhhHHHHHHHHHHHHHH
Confidence 345667888777877777766
No 84
>KOG1748|consensus
Probab=25.14 E-value=84 Score=28.42 Aligned_cols=61 Identities=23% Similarity=0.434 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCcccCCCCCCCCCC
Q psy14441 281 EEVYDTFSEIANDFV---DNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISIPGYGTDELKP 341 (365)
Q Consensus 281 ~dVEElLLeLADDFV---dsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~IPGfgsDeirp 341 (365)
++++|-++++.-.|- .+.++-.....|-=|.|.||.=.|-..||.+||+.||---+|+|++
T Consensus 52 ~~v~~RVl~VVk~~dki~~~k~~~~s~f~~DLGlDSLD~VEiVMAlEEEFgiEIpd~dAdki~t 115 (131)
T KOG1748|consen 52 KEVVDRVLDVVKKFDKIDPSKLTTDSDFFKDLGLDSLDTVEIVMALEEEFGIEIPDEDADKIKT 115 (131)
T ss_pred HHHHHHHHHHHHHhhcCCccccchhhHHHHhcCCcccccchhhhhhHHHhCCccCcchhhhhCC
Confidence 346666666655443 3445566677788899999999999999999999999888887764
No 85
>PTZ00171 acyl carrier protein; Provisional
Probab=25.09 E-value=28 Score=31.32 Aligned_cols=38 Identities=24% Similarity=0.564 Sum_probs=29.1
Q ss_pred HHHHhhhCCCCCCchhhHHHhhhccCcccCCCCCCCCC
Q psy14441 303 CQLAKHRGSSTLDPKDLQFVLAKDWNISIPGYGTDELK 340 (365)
Q Consensus 303 C~LAKHRkSdtLEvkDVql~LER~wNI~IPGfgsDeir 340 (365)
+.+..--+-|.|+.=++-..||++||+.||---.++++
T Consensus 94 s~~~~dLg~DSLd~veLv~~LEdeFgI~Ipded~~~i~ 131 (148)
T PTZ00171 94 SNFVKDLGADSLDVVELLIAIEQEFNLTIPDHDAEKIK 131 (148)
T ss_pred cchhhhcCCCHHHHHHHHHHHHHHHCCccCHHHHHHCC
Confidence 34555678899999999999999999999953333344
No 86
>PF10183 ESSS: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) ; InterPro: IPR019329 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry represents the ESSS subunit from mitochondrial NADH:ubiquinone oxidoreductase (complex I). It carries mitochondrial import sequences [].
Probab=25.03 E-value=1.7e+02 Score=24.82 Aligned_cols=10 Identities=20% Similarity=0.332 Sum_probs=8.7
Q ss_pred CcCCCCCCCC
Q psy14441 138 TIDDLPVPQG 147 (365)
Q Consensus 138 TmnDLPvP~G 147 (365)
-|+.=|.+.|
T Consensus 42 l~~~~p~~~G 51 (105)
T PF10183_consen 42 LFGKNPPSPG 51 (105)
T ss_pred ccCCCCCcCC
Confidence 4888999999
No 87
>TIGR03513 GldL_gliding gliding motility-associated protein GldL. This protein family, GldL, is named for the member from Flavobacterium johnsoniae, which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes. However, members are found also in several members of the Bacteriodetes that appear not to be motile
Probab=24.23 E-value=4.1e+02 Score=25.63 Aligned_cols=28 Identities=21% Similarity=0.485 Sum_probs=19.4
Q ss_pred hhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHH
Q psy14441 263 KDKLDELMRQVDSTLQIDEEVYDTFSEIANDF 294 (365)
Q Consensus 263 KrkLqeLVrqIDp~e~LD~dVEElLLeLADDF 294 (365)
-.+|+.++++ ..+|++..|.|..-.+.|
T Consensus 88 s~kld~~l~e----akid~~l~esl~~~i~~~ 115 (202)
T TIGR03513 88 SQKLDAMLKE----AKKDATLMQSLGNGINNF 115 (202)
T ss_pred hHhHHHHHHH----cccCHHHHHHHHHHHHHH
Confidence 4678888874 668888777766655554
No 88
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=23.54 E-value=53 Score=32.58 Aligned_cols=24 Identities=8% Similarity=0.039 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHhhhcceeeecC
Q psy14441 165 LVGTVSLAATIGYLAVSDVFIWNF 188 (365)
Q Consensus 165 l~Gi~~l~gTi~~~~~SGii~lN~ 188 (365)
++|++..+||+.+++..|-+|+-|
T Consensus 210 iiaigltvGT~~~A~~~~giY~~w 233 (256)
T PF09788_consen 210 IIAIGLTVGTWTYAKTYGGIYVSW 233 (256)
T ss_pred HHHHHHhhhhHHHHhhcCcEeHHH
Confidence 345555667777777777676544
No 89
>KOG3902|consensus
Probab=23.43 E-value=4.1e+02 Score=27.53 Aligned_cols=58 Identities=22% Similarity=0.289 Sum_probs=38.0
Q ss_pred HHHHHHHhcCCCCCCCHHHH--HHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 265 KLDELMRQVDSTLQIDEEVY--DTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 265 kLqeLVrqIDp~e~LD~dVE--ElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
.+|.++=+. ++.-||-+| .++-+++--=|-...-.|..+|-.||+..|...|+-|-..
T Consensus 29 eiQqmmf~s--Gei~~P~pett~Lved~V~gqvie~l~qa~eia~lrgsr~Itpedliflir 88 (352)
T KOG3902|consen 29 EIQQMMFQS--GEIPDPLPETTNLVEDNVRGQVIESLVQANEIADLRGSRSITPEDLIFLIR 88 (352)
T ss_pred HHHHHHHHh--CCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccccChHHHHHHhh
Confidence 455555443 333444444 3444444444556677889999999999999999987653
No 90
>PRK10692 hypothetical protein; Provisional
Probab=23.03 E-value=91 Score=26.80 Aligned_cols=28 Identities=21% Similarity=0.341 Sum_probs=23.8
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcceeeec
Q psy14441 160 YNIQLLVGTVSLAATIGYLAVSDVFIWN 187 (365)
Q Consensus 160 YN~~Ll~Gi~~l~gTi~~~~~SGii~lN 187 (365)
=|.....|.+..+++|+|...+-+.-||
T Consensus 10 GN~lMglGmv~Mv~gigysi~~~i~~L~ 37 (92)
T PRK10692 10 GNVLMGLGLVVMVVGVGYSILNQLPQLN 37 (92)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhcccCC
Confidence 4888889999999999999988887444
No 91
>KOG1658|consensus
Probab=21.73 E-value=78 Score=29.59 Aligned_cols=69 Identities=14% Similarity=0.233 Sum_probs=56.4
Q ss_pred ChhHHHHHHHhcCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhhhccCccc
Q psy14441 262 GKDKLDELMRQVDSTL-QIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKDWNISI 331 (365)
Q Consensus 262 ~KrkLqeLVrqIDp~e-~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LER~wNI~I 331 (365)
+=.+++++++. ||.. -+.+++.-++..-|+.||..+...+-.-|-.|+-.++..+|+--..+..|-..+
T Consensus 61 pL~rik~vvkl-~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~f 130 (162)
T KOG1658|consen 61 PLARIKQVVKL-DPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAF 130 (162)
T ss_pred cHHHHHhhccC-CcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHH
Confidence 33455666653 6664 456778999999999999999999999999999999999999988888877653
No 92
>PF10762 DUF2583: Protein of unknown function (DUF2583) ; InterPro: IPR019698 Some members in this entry are annotated as YchH however currently no function is known.
Probab=21.49 E-value=96 Score=26.52 Aligned_cols=32 Identities=25% Similarity=0.383 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcceeeecCCCCCC
Q psy14441 160 YNIQLLVGTVSLAATIGYLAVSDVFIWNFFPPTL 193 (365)
Q Consensus 160 YN~~Ll~Gi~~l~gTi~~~~~SGii~lN~~pP~~ 193 (365)
=|.....|.+..+++|+|...+-+. .++.|++
T Consensus 10 GN~lMglGmv~Mv~gigysi~~~~~--~L~Lp~~ 41 (89)
T PF10762_consen 10 GNVLMGLGMVVMVGGIGYSILSQIP--QLGLPQF 41 (89)
T ss_pred hhHHHHHhHHHHHHhHHHHHHHhcc--cCCCcHH
Confidence 3888889999999999999998887 4445544
No 93
>PLN00154 histone H2A; Provisional
Probab=20.62 E-value=5e+02 Score=23.71 Aligned_cols=71 Identities=11% Similarity=0.144 Sum_probs=61.8
Q ss_pred CCCCCCCCChhHHHHHHHhcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCchhhHHHhh
Q psy14441 254 STPNDQILGKDKLDELMRQVD-STLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLA 324 (365)
Q Consensus 254 s~~~~~VL~KrkLqeLVrqID-p~e~LD~dVEElLLeLADDFVdsVvs~AC~LAKHRkSdtLEvkDVql~LE 324 (365)
+....=.++=.+++.++++-. -...+...+--.|..+-|=..-+|++-|...|+.-+...|..++|++.+.
T Consensus 32 S~rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 32 SSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred ccccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 444556788899999999865 35799999988999999999999999999999999999999999999884
Done!