Query psy3267
Match_columns 105
No_of_seqs 112 out of 317
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 20:40:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3267.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3267hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5648 NHP6B Chromatin-associ 99.8 7.5E-19 1.6E-23 136.4 5.7 93 1-95 67-185 (211)
2 PTZ00199 high mobility group p 99.7 2.5E-18 5.4E-23 117.0 4.5 53 1-53 19-71 (94)
3 cd01388 SOX-TCF_HMG-box SOX-TC 99.5 2.9E-15 6.3E-20 96.3 3.1 66 5-82 2-69 (72)
4 cd01389 MATA_HMG-box MATA_HMG- 99.5 4.9E-15 1.1E-19 96.2 3.5 51 4-56 1-53 (77)
5 cd01390 HMGB-UBF_HMG-box HMGB- 99.5 1.1E-14 2.4E-19 90.1 4.1 47 5-53 1-47 (66)
6 smart00398 HMG high mobility g 99.5 7.3E-14 1.6E-18 86.4 4.2 48 4-53 1-48 (70)
7 KOG0526|consensus 99.4 6.4E-14 1.4E-18 120.9 4.3 52 1-56 532-583 (615)
8 PF09011 HMG_box_2: HMG-box do 99.4 8.4E-14 1.8E-18 89.7 3.7 52 2-55 1-55 (73)
9 cd00084 HMG-box High Mobility 99.4 2.7E-13 5.9E-18 83.0 4.0 47 5-53 1-47 (66)
10 PF00505 HMG_box: HMG (high mo 99.4 3.6E-13 7.9E-18 84.0 3.6 47 5-53 1-47 (69)
11 KOG0381|consensus 99.4 1E-12 2.2E-17 87.4 4.7 49 3-53 21-69 (96)
12 KOG0527|consensus 99.0 1.2E-10 2.6E-15 95.4 3.5 67 4-82 62-130 (331)
13 PTZ00199 high mobility group p 98.5 5.4E-08 1.2E-12 66.1 2.6 40 56-95 18-66 (94)
14 cd01389 MATA_HMG-box MATA_HMG- 98.2 9.5E-07 2.1E-11 57.1 2.5 37 59-95 4-43 (77)
15 cd01388 SOX-TCF_HMG-box SOX-TC 98.2 1.1E-06 2.3E-11 56.4 2.6 38 59-96 4-44 (72)
16 COG5648 NHP6B Chromatin-associ 98.1 2E-06 4.3E-11 67.3 3.2 42 56-97 66-114 (211)
17 cd01390 HMGB-UBF_HMG-box HMGB- 97.9 7E-06 1.5E-10 50.4 2.6 37 59-95 3-42 (66)
18 KOG0528|consensus 97.8 5.4E-06 1.2E-10 71.5 1.3 46 6-53 327-372 (511)
19 KOG4715|consensus 97.8 1.6E-05 3.5E-10 66.3 3.6 50 2-53 62-111 (410)
20 PF00505 HMG_box: HMG (high mo 97.8 1.8E-05 4E-10 49.0 2.6 37 59-95 3-42 (69)
21 cd00084 HMG-box High Mobility 97.6 4.1E-05 8.8E-10 46.4 2.6 38 60-97 4-44 (66)
22 smart00398 HMG high mobility g 97.6 5E-05 1.1E-09 46.5 2.4 36 60-95 5-43 (70)
23 KOG0381|consensus 97.5 8.4E-05 1.8E-09 49.1 2.7 36 62-97 28-66 (96)
24 KOG3248|consensus 97.1 0.00025 5.5E-09 59.7 2.3 72 6-89 193-266 (421)
25 PF08073 CHDNT: CHDNT (NUC034) 96.1 0.0055 1.2E-07 39.2 2.7 35 62-96 14-51 (55)
26 PF09011 HMG_box_2: HMG-box do 96.0 0.0053 1.1E-07 39.2 2.1 36 60-95 7-46 (73)
27 KOG2746|consensus 95.4 0.007 1.5E-07 54.2 1.3 48 6-55 183-234 (683)
28 KOG0526|consensus 95.3 0.017 3.6E-07 51.1 3.3 39 55-95 530-575 (615)
29 PF08073 CHDNT: CHDNT (NUC034) 95.1 0.048 1E-06 34.8 4.1 41 9-51 13-53 (55)
30 PF04690 YABBY: YABBY protein; 95.0 0.05 1.1E-06 41.5 4.9 43 4-48 121-163 (170)
31 KOG0527|consensus 93.3 0.047 1E-06 45.2 1.8 33 62-94 68-103 (331)
32 KOG2746|consensus 84.5 0.67 1.4E-05 42.0 2.2 32 62-93 187-223 (683)
33 PF14887 HMG_box_5: HMG (high 81.1 3 6.4E-05 28.8 3.8 45 5-52 4-48 (85)
34 PF04418 DUF543: Domain of unk 80.6 1.2 2.6E-05 29.7 1.8 18 84-101 14-31 (75)
35 PF06244 DUF1014: Protein of u 78.8 4.1 8.8E-05 29.6 4.2 43 5-49 73-115 (122)
36 KOG3497|consensus 73.9 1.3 2.8E-05 29.4 0.4 13 83-95 9-21 (69)
37 KOG4715|consensus 73.2 2.7 5.9E-05 35.7 2.3 33 62-94 70-105 (410)
38 PF06382 DUF1074: Protein of u 73.1 3.6 7.8E-05 32.0 2.8 40 10-55 84-125 (183)
39 PF06244 DUF1014: Protein of u 71.4 4.4 9.5E-05 29.4 2.7 33 62-94 78-110 (122)
40 PF12408 DUF3666: Ribose-5-pho 60.4 3.9 8.6E-05 25.4 0.6 26 71-96 7-32 (48)
41 PF14823 Sirohm_synth_C: Siroh 51.7 11 0.00023 24.7 1.6 35 70-105 13-48 (70)
42 KOG0528|consensus 41.6 11 0.00023 33.4 0.5 32 62-93 331-365 (511)
43 PF04769 MAT_Alpha1: Mating-ty 39.6 70 0.0015 24.8 4.7 60 3-68 42-115 (201)
44 KOG3248|consensus 37.1 21 0.00045 30.7 1.6 40 62-101 197-244 (421)
45 PF01194 RNA_pol_N: RNA polyme 34.6 16 0.00034 23.7 0.4 16 83-98 9-24 (60)
46 cd06257 DnaJ DnaJ domain or J- 32.6 98 0.0021 17.5 3.8 34 17-50 19-55 (55)
47 PF04690 YABBY: YABBY protein; 31.3 44 0.00094 25.6 2.4 28 59-86 124-151 (170)
48 PF00226 DnaJ: DnaJ domain; I 30.7 79 0.0017 18.7 3.1 37 16-52 18-58 (64)
49 PLN00032 DNA-directed RNA poly 27.4 29 0.00063 23.2 0.7 14 83-96 9-22 (71)
50 PLN02150 terpene synthase/cycl 26.0 55 0.0012 22.3 1.9 19 33-51 24-42 (96)
51 PF05047 L51_S25_CI-B8: Mitoch 24.8 61 0.0013 19.0 1.8 18 15-32 4-21 (52)
52 COG2879 Uncharacterized small 24.0 1.1E+02 0.0023 20.3 2.9 31 9-43 22-53 (65)
53 KOG3223|consensus 23.4 1.2E+02 0.0026 24.2 3.6 43 6-50 166-208 (221)
54 PF13875 DUF4202: Domain of un 23.1 78 0.0017 24.6 2.5 36 11-51 131-166 (185)
55 cd08317 Death_ank Death domain 22.8 58 0.0013 21.1 1.5 21 33-53 6-26 (84)
56 COG1644 RPB10 DNA-directed RNA 22.0 39 0.00085 22.2 0.5 13 83-95 9-21 (63)
57 KOG0371|consensus 21.9 45 0.00097 27.9 1.0 28 72-100 121-148 (319)
58 smart00271 DnaJ DnaJ molecular 21.8 1.7E+02 0.0038 16.8 4.2 35 17-51 20-58 (60)
59 KOG3223|consensus 21.3 1.1E+02 0.0024 24.4 3.0 33 62-94 170-202 (221)
60 PRK04016 DNA-directed RNA poly 20.0 44 0.00095 21.8 0.5 14 83-96 9-22 (62)
No 1
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=99.76 E-value=7.5e-19 Score=136.35 Aligned_cols=93 Identities=19% Similarity=0.168 Sum_probs=82.3
Q ss_pred CCCCCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCC--CCCC-----------------CC---
Q psy3267 1 MQNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVN--PFVG-----------------RK--- 58 (105)
Q Consensus 1 ~PnkPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~ee--ky~~-----------------e~--- 58 (105)
+||+||||+||||+|++.+|+++.+.||++ +|+|++|.+||+||.++++| +|.. .+
T Consensus 67 dpN~PKRp~sayf~y~~~~R~ei~~~~p~l--~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~ 144 (211)
T COG5648 67 DPNGPKRPLSAYFLYSAENRDEIRKENPKL--TFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPN 144 (211)
T ss_pred CCCCCCCchhHHHHHHHHHHHHHHHhCCCC--ChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCC
Confidence 699999999999999999999999999999 58999999999999999986 3441 12
Q ss_pred -CCchHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHHH
Q psy3267 59 -FAPVFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDEC 95 (105)
Q Consensus 59 -~APsa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~~ 95 (105)
+++..|.-+....|+.+.+.+|.. +.+++|++.|+|.
T Consensus 145 ~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el 185 (211)
T COG5648 145 KAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSEL 185 (211)
T ss_pred CCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhh
Confidence 333888889999999999999987 8899999999984
No 2
>PTZ00199 high mobility group protein; Provisional
Probab=99.73 E-value=2.5e-18 Score=116.97 Aligned_cols=53 Identities=25% Similarity=0.236 Sum_probs=50.0
Q ss_pred CCCCCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC
Q psy3267 1 MQNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP 53 (105)
Q Consensus 1 ~PnkPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek 53 (105)
|||+||||+|||++|++++|.+++.+||+++.+|+||++.||++|+.|+++++
T Consensus 19 dp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK 71 (94)
T PTZ00199 19 DPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEK 71 (94)
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHH
Confidence 69999999999999999999999999999876689999999999999999873
No 3
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=99.55 E-value=2.9e-15 Score=96.34 Aligned_cols=66 Identities=15% Similarity=0.219 Sum_probs=55.4
Q ss_pred CCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC--CCCCCCCchHHHHhhhccchhhhhcCCcc
Q psy3267 5 LNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP--FVGRKFAPVFLTFLSRMKDSILFCVNPVL 82 (105)
Q Consensus 5 PKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek--y~~e~~APsa~~~f~~~~r~~l~~~nP~l 82 (105)
-|||+|||++|+++.|++++++||+++ ++||+|.||++|+.|+++++ |.. -+...+..-..+||+.
T Consensus 2 iKrP~naf~~F~~~~r~~~~~~~p~~~--~~eisk~l~~~Wk~ls~~eK~~y~~----------~a~~~k~~y~~~~p~y 69 (72)
T cd01388 2 IKRPMNAFMLFSKRHRRKVLQEYPLKE--NRAISKILGDRWKALSNEEKQPYYE----------EAKKLKELHMKLYPDY 69 (72)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCCCCC--HHHHHHHHHHHHHcCCHHHHHHHHH----------HHHHHHHHHHHHCcCC
Confidence 489999999999999999999999984 68999999999999999863 543 5666666666677764
No 4
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=99.54 E-value=4.9e-15 Score=96.20 Aligned_cols=51 Identities=18% Similarity=0.233 Sum_probs=46.5
Q ss_pred CCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC--CCC
Q psy3267 4 KLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP--FVG 56 (105)
Q Consensus 4 kPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek--y~~ 56 (105)
.||||++|||+|++++|.+++.+||+++ ++|||+.||++|+.|+++++ |..
T Consensus 1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~--~~eisk~~g~~Wk~ls~eeK~~y~~ 53 (77)
T cd01389 1 KIPRPRNAFILYRQDKHAQLKTENPGLT--NNEISRIIGRMWRSESPEVKAYYKE 53 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCC--HHHHHHHHHHHHhhCCHHHHHHHHH
Confidence 4899999999999999999999999984 78999999999999999873 553
No 5
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=99.52 E-value=1.1e-14 Score=90.06 Aligned_cols=47 Identities=28% Similarity=0.353 Sum_probs=44.4
Q ss_pred CCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC
Q psy3267 5 LNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP 53 (105)
Q Consensus 5 PKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek 53 (105)
||+|+|||++|+++.|..++.+||++ ++++|++.||++|+.|+++++
T Consensus 1 Pkrp~saf~~f~~~~r~~~~~~~p~~--~~~~i~~~~~~~W~~ls~~eK 47 (66)
T cd01390 1 PKRPLSAYFLFSQEQRPKLKKENPDA--SVTEVTKILGEKWKELSEEEK 47 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCC--CHHHHHHHHHHHHHhCCHHHH
Confidence 89999999999999999999999997 479999999999999999874
No 6
>smart00398 HMG high mobility group.
Probab=99.46 E-value=7.3e-14 Score=86.42 Aligned_cols=48 Identities=33% Similarity=0.377 Sum_probs=45.1
Q ss_pred CCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC
Q psy3267 4 KLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP 53 (105)
Q Consensus 4 kPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek 53 (105)
+||+|+|||++|++++|..++.+||+++ ++++++.||++|+.|+++++
T Consensus 1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~--~~~i~~~~~~~W~~l~~~ek 48 (70)
T smart00398 1 KPKRPMSAFMLFSQENRAKIKAENPDLS--NAEISKKLGERWKLLSEEEK 48 (70)
T ss_pred CcCCCCcHHHHHHHHHHHHHHHHCcCCC--HHHHHHHHHHHHHcCCHHHH
Confidence 5999999999999999999999999985 79999999999999999863
No 7
>KOG0526|consensus
Probab=99.44 E-value=6.4e-14 Score=120.90 Aligned_cols=52 Identities=21% Similarity=0.337 Sum_probs=48.6
Q ss_pred CCCCCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCCCCC
Q psy3267 1 MQNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNPFVG 56 (105)
Q Consensus 1 ~PnkPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eeky~~ 56 (105)
|||+|||+|||||+|+|..|+.+|++ ++ +++||+|++|++||+||++++|+.
T Consensus 532 dpnapkra~sa~m~w~~~~r~~ik~d--gi--~~~dv~kk~g~~wk~ms~k~~we~ 583 (615)
T KOG0526|consen 532 DPNAPKRATSAYMLWLNASRESIKED--GI--SVGDVAKKAGEKWKQMSAKEEWED 583 (615)
T ss_pred CCCCCccchhHHHHHHHhhhhhHhhc--Cc--hHHHHHHHHhHHHhhhcccchhhH
Confidence 79999999999999999999999998 76 579999999999999999988873
No 8
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=99.44 E-value=8.4e-14 Score=89.74 Aligned_cols=52 Identities=31% Similarity=0.484 Sum_probs=42.7
Q ss_pred CCCCCCCCchHHHhHHHHHHHHHHh-CCCCchhHHHHHHHHHHHhhhcccCC--CCC
Q psy3267 2 QNKLNMQGIAYAFFVQVCREEHKKK-HPEENVVFAEFSKKCAERWKSSRIVN--PFV 55 (105)
Q Consensus 2 PnkPKr~~SAY~fF~q~~Ree~Kkk-nPd~sv~faE~sKk~ge~WK~ms~ee--ky~ 55 (105)
||+|||++|||++|+++.|.+++.+ ++.. +++|+.+.||++|+.||++| +|+
T Consensus 1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~--~~~e~~k~~~~~Wk~Ls~~EK~~Y~ 55 (73)
T PF09011_consen 1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQ--SFREVMKEISERWKSLSEEEKEPYE 55 (73)
T ss_dssp SSS--SSSSHHHHHHHHHHHHHHHHT-T-S--SHHHHHHHHHHHHHHS-HHHHHHHH
T ss_pred CcCCCCCCCHHHHHHHHHHHHHHHhcccCC--CHHHHHHHHHHHHHhcCHHHHHHHH
Confidence 8999999999999999999999999 6644 57899999999999999986 355
No 9
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=99.40 E-value=2.7e-13 Score=82.98 Aligned_cols=47 Identities=32% Similarity=0.304 Sum_probs=44.1
Q ss_pred CCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC
Q psy3267 5 LNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP 53 (105)
Q Consensus 5 PKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek 53 (105)
||+|+|||++|+++.|..++.+||+. ++.+|++.||++|+.|+++++
T Consensus 1 pkrp~~af~~f~~~~~~~~~~~~~~~--~~~~i~~~~~~~W~~l~~~~k 47 (66)
T cd00084 1 PKRPLSAYFLFSQEHRAEVKAENPGL--SVGEISKILGEMWKSLSEEEK 47 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCC--CHHHHHHHHHHHHHhCCHHHH
Confidence 89999999999999999999999997 478999999999999999863
No 10
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=99.38 E-value=3.6e-13 Score=84.04 Aligned_cols=47 Identities=23% Similarity=0.292 Sum_probs=42.6
Q ss_pred CCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC
Q psy3267 5 LNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP 53 (105)
Q Consensus 5 PKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek 53 (105)
||||+|||++|+++.|..++.+||+++ .++|++.+|++|+.|+++++
T Consensus 1 PkrP~~af~lf~~~~~~~~k~~~p~~~--~~~i~~~~~~~W~~l~~~eK 47 (69)
T PF00505_consen 1 PKRPPNAFMLFCKEKRAKLKEENPDLS--NKEISKILAQMWKNLSEEEK 47 (69)
T ss_dssp SSSS--HHHHHHHHHHHHHHHHSTTST--HHHHHHHHHHHHHCSHHHHH
T ss_pred CcCCCCHHHHHHHHHHHHHHHHhcccc--cccchhhHHHHHhcCCHHHH
Confidence 899999999999999999999999996 68999999999999999863
No 11
>KOG0381|consensus
Probab=99.35 E-value=1e-12 Score=87.41 Aligned_cols=49 Identities=20% Similarity=0.234 Sum_probs=46.0
Q ss_pred CCCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC
Q psy3267 3 NKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP 53 (105)
Q Consensus 3 nkPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek 53 (105)
++||||+|||++|+++.|..++.+||+++ +.|++|.+|++|+.|+++++
T Consensus 21 ~~pkrp~sa~~~f~~~~~~~~k~~~p~~~--~~~v~k~~g~~W~~l~~~~k 69 (96)
T KOG0381|consen 21 QAPKRPLSAFFLFSSEQRSKIKAENPGLS--VGEVAKALGEMWKNLAEEEK 69 (96)
T ss_pred CCCCCCCcHHHHHHHHHHHHHHHhCCCCC--HHHHHHHHHHHHhcCCHHHH
Confidence 49999999999999999999999999975 68999999999999999875
No 12
>KOG0527|consensus
Probab=99.04 E-value=1.2e-10 Score=95.44 Aligned_cols=67 Identities=19% Similarity=0.225 Sum_probs=55.6
Q ss_pred CCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC--CCCCCCCchHHHHhhhccchhhhhcCCc
Q psy3267 4 KLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP--FVGRKFAPVFLTFLSRMKDSILFCVNPV 81 (105)
Q Consensus 4 kPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek--y~~e~~APsa~~~f~~~~r~~l~~~nP~ 81 (105)
.=||||-|||.|.|..|.++-++||++. | +||||.+|++||.|+++|| |+. .|.--|.+=..+||+
T Consensus 62 hIKRPMNAFMVWSq~~RRkma~qnP~mH-N-SEISK~LG~~WK~Lse~EKrPFi~----------EAeRLR~~HmkehPd 129 (331)
T KOG0527|consen 62 RIKRPMNAFMVWSQGQRRKLAKQNPKMH-N-SEISKRLGAEWKLLSEEEKRPFVD----------EAERLRAQHMKEYPD 129 (331)
T ss_pred ccCCCcchhhhhhHHHHHHHHHhCcchh-h-HHHHHHHHHHHhhcCHhhhccHHH----------HHHHHHHHHHHhCCC
Confidence 3599999999999999999999999996 4 9999999999999999885 664 455555555566665
Q ss_pred c
Q psy3267 82 L 82 (105)
Q Consensus 82 l 82 (105)
-
T Consensus 130 Y 130 (331)
T KOG0527|consen 130 Y 130 (331)
T ss_pred c
Confidence 4
No 13
>PTZ00199 high mobility group protein; Provisional
Probab=98.53 E-value=5.4e-08 Score=66.12 Aligned_cols=40 Identities=28% Similarity=0.395 Sum_probs=35.1
Q ss_pred CCCCCc----hHHHHhhhccchhhhhcCCcch-----hhhhhHhhHHHH
Q psy3267 56 GRKFAP----VFLTFLSRMKDSILFCVNPVLA-----VGSRILEKFDEC 95 (105)
Q Consensus 56 ~e~~AP----sa~~~f~~~~r~~l~~~nP~l~-----v~~v~~~~~~~~ 95 (105)
.|+|+| |||++|+++.|..|..+||++. |+.+||+.|..+
T Consensus 18 kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~l 66 (94)
T PTZ00199 18 KDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKL 66 (94)
T ss_pred CCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcC
Confidence 467777 9999999999999999999974 677899999865
No 14
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=98.21 E-value=9.5e-07 Score=57.13 Aligned_cols=37 Identities=16% Similarity=0.062 Sum_probs=32.8
Q ss_pred CCchHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHHH
Q psy3267 59 FAPVFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDEC 95 (105)
Q Consensus 59 ~APsa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~~ 95 (105)
-+|+||++|+++.|..|+.+||++ .|+.+||+.|...
T Consensus 4 RP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~l 43 (77)
T cd01389 4 RPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSE 43 (77)
T ss_pred CCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhC
Confidence 466999999999999999999999 5777899999754
No 15
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=98.19 E-value=1.1e-06 Score=56.36 Aligned_cols=38 Identities=5% Similarity=0.023 Sum_probs=32.3
Q ss_pred CCchHHHHhhhccchhhhhcCCcchh---hhhhHhhHHHHh
Q psy3267 59 FAPVFLTFLSRMKDSILFCVNPVLAV---GSRILEKFDECL 96 (105)
Q Consensus 59 ~APsa~~~f~~~~r~~l~~~nP~l~v---~~v~~~~~~~~~ 96 (105)
-+|+||++|+++.|++++.+||++++ +.+||++|...-
T Consensus 4 rP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls 44 (72)
T cd01388 4 RPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALS 44 (72)
T ss_pred CCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence 46799999999999999999999855 555899998653
No 16
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=98.12 E-value=2e-06 Score=67.33 Aligned_cols=42 Identities=26% Similarity=0.248 Sum_probs=37.5
Q ss_pred CCCCCc----hHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHHHhh
Q psy3267 56 GRKFAP----VFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDECLD 97 (105)
Q Consensus 56 ~e~~AP----sa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~~~~ 97 (105)
.+||+| ||||+||.+.|.+|+.+||.+ .||.+|+|+|.+.-|
T Consensus 66 ~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd 114 (211)
T COG5648 66 KDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTD 114 (211)
T ss_pred cCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccH
Confidence 578999 999999999999999999988 677789999987644
No 17
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=97.94 E-value=7e-06 Score=50.36 Aligned_cols=37 Identities=22% Similarity=0.085 Sum_probs=32.1
Q ss_pred CCchHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHHH
Q psy3267 59 FAPVFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDEC 95 (105)
Q Consensus 59 ~APsa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~~ 95 (105)
.++++|++|+.+.|..++.+||++ .|+.++|+.|..+
T Consensus 3 rp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~l 42 (66)
T cd01390 3 RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKEL 42 (66)
T ss_pred CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhC
Confidence 355999999999999999999986 5777889999864
No 18
>KOG0528|consensus
Probab=97.85 E-value=5.4e-06 Score=71.48 Aligned_cols=46 Identities=17% Similarity=0.246 Sum_probs=43.2
Q ss_pred CCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC
Q psy3267 6 NMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP 53 (105)
Q Consensus 6 Kr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek 53 (105)
||||.|||.|..+.|.++-+..||.. + ..|||.+|.|||.||-.||
T Consensus 327 KRPMNAFMVWAkDERRKILqA~PDMH-N-SnISKILGSRWKaMSN~eK 372 (511)
T KOG0528|consen 327 KRPMNAFMVWAKDERRKILQAFPDMH-N-SNISKILGSRWKAMSNTEK 372 (511)
T ss_pred cCCcchhhcccchhhhhhhhcCcccc-c-cchhHHhcccccccccccc
Confidence 99999999999999999999999986 3 6899999999999999875
No 19
>KOG4715|consensus
Probab=97.82 E-value=1.6e-05 Score=66.32 Aligned_cols=50 Identities=14% Similarity=0.155 Sum_probs=46.7
Q ss_pred CCCCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC
Q psy3267 2 QNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP 53 (105)
Q Consensus 2 PnkPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek 53 (105)
|..|-+|+-+||-|+...+.++|.+||++. +=||+|++|.+|+.|.++||
T Consensus 62 Pkppekpl~pymrySrkvWd~VkA~nPe~k--LWeiGK~Ig~mW~dLpd~EK 111 (410)
T KOG4715|consen 62 PKPPEKPLMPYMRYSRKVWDQVKASNPELK--LWEIGKIIGGMWLDLPDEEK 111 (410)
T ss_pred CCCCCcccchhhHHhhhhhhhhhccCcchH--HHHHHHHHHHHHhhCcchHH
Confidence 567889999999999999999999999996 68999999999999999986
No 20
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=97.79 E-value=1.8e-05 Score=48.99 Aligned_cols=37 Identities=16% Similarity=0.211 Sum_probs=30.5
Q ss_pred CCchHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHHH
Q psy3267 59 FAPVFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDEC 95 (105)
Q Consensus 59 ~APsa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~~ 95 (105)
.|++||++|+.+.|..|..+||++ .|+.+|++.|...
T Consensus 3 rP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l 42 (69)
T PF00505_consen 3 RPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNL 42 (69)
T ss_dssp SS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCS
T ss_pred CCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcC
Confidence 355999999999999999999998 6677789999763
No 21
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=97.65 E-value=4.1e-05 Score=46.41 Aligned_cols=38 Identities=13% Similarity=0.101 Sum_probs=33.1
Q ss_pred CchHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHHHhh
Q psy3267 60 APVFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDECLD 97 (105)
Q Consensus 60 APsa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~~~~ 97 (105)
++++|++|+.+.|..+..+||++ .|+.++++.|..+-+
T Consensus 4 p~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~ 44 (66)
T cd00084 4 PLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSE 44 (66)
T ss_pred CCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCH
Confidence 44999999999999999999985 678889999987644
No 22
>smart00398 HMG high mobility group.
Probab=97.58 E-value=5e-05 Score=46.49 Aligned_cols=36 Identities=14% Similarity=0.221 Sum_probs=31.2
Q ss_pred CchHHHHhhhccchhhhhcCCcch---hhhhhHhhHHHH
Q psy3267 60 APVFLTFLSRMKDSILFCVNPVLA---VGSRILEKFDEC 95 (105)
Q Consensus 60 APsa~~~f~~~~r~~l~~~nP~l~---v~~v~~~~~~~~ 95 (105)
++++|++|+++.|+.+..+||+++ |+.++++.|..+
T Consensus 5 p~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l 43 (70)
T smart00398 5 PMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLL 43 (70)
T ss_pred CCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcC
Confidence 449999999999999999999985 667789999764
No 23
>KOG0381|consensus
Probab=97.49 E-value=8.4e-05 Score=49.15 Aligned_cols=36 Identities=19% Similarity=0.206 Sum_probs=30.9
Q ss_pred hHHHHhhhccchhhhhcCCcchh---hhhhHhhHHHHhh
Q psy3267 62 VFLTFLSRMKDSILFCVNPVLAV---GSRILEKFDECLD 97 (105)
Q Consensus 62 sa~~~f~~~~r~~l~~~nP~l~v---~~v~~~~~~~~~~ 97 (105)
||||+|+.+.|..+..+||+++| +..||+.|...-+
T Consensus 28 sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~ 66 (96)
T KOG0381|consen 28 SAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAE 66 (96)
T ss_pred cHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCH
Confidence 99999999999999999999865 4568899976544
No 24
>KOG3248|consensus
Probab=97.14 E-value=0.00025 Score=59.66 Aligned_cols=72 Identities=11% Similarity=0.147 Sum_probs=56.2
Q ss_pred CCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCC--CCCCCCCCchHHHHhhhccchhhhhcCCcch
Q psy3267 6 NMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVN--PFVGRKFAPVFLTFLSRMKDSILFCVNPVLA 83 (105)
Q Consensus 6 Kr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~ee--ky~~e~~APsa~~~f~~~~r~~l~~~nP~l~ 83 (105)
|.++-|||+|+.++|..+-.+.- ++ .-++|-+.+|.||-.||-|| ||-+ .+...|+.-.+-+|+|+
T Consensus 193 KKPLNAFmlyMKEmRa~vvaEct-lK-eSAaiNqiLGrRWH~LSrEEQAKYyE----------lArKerqlH~qlYP~WS 260 (421)
T KOG3248|consen 193 KKPLNAFMLYMKEMRAKVVAECT-LK-ESAAINQILGRRWHALSREEQAKYYE----------LARKERQLHMQLYPGWS 260 (421)
T ss_pred cccHHHHHHHHHHHHHHHHHHhh-hh-hHHHHHHHHhHHHhhhhHHHHHHHHH----------HHHHHHHHHHHhcCCcc
Confidence 78999999999999999999875 33 23899999999999999987 5544 66666666667777775
Q ss_pred hhhhhH
Q psy3267 84 VGSRIL 89 (105)
Q Consensus 84 v~~v~~ 89 (105)
.-+--|
T Consensus 261 ARdNYg 266 (421)
T KOG3248|consen 261 ARDNYG 266 (421)
T ss_pred hhhhhh
Confidence 554443
No 25
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=96.12 E-value=0.0055 Score=39.16 Aligned_cols=35 Identities=17% Similarity=0.107 Sum_probs=31.1
Q ss_pred hHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHHHh
Q psy3267 62 VFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDECL 96 (105)
Q Consensus 62 sa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~~~ 96 (105)
+.|-.|++-+||.|...||.. ++.-+++.||.|--
T Consensus 14 t~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~ 51 (55)
T PF08073_consen 14 TNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQ 51 (55)
T ss_pred HHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHH
Confidence 678899999999999999999 66678999999854
No 26
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=95.97 E-value=0.0053 Score=39.19 Aligned_cols=36 Identities=11% Similarity=0.052 Sum_probs=28.6
Q ss_pred CchHHHHhhhccchhhhhc-CCc---chhhhhhHhhHHHH
Q psy3267 60 APVFLTFLSRMKDSILFCV-NPV---LAVGSRILEKFDEC 95 (105)
Q Consensus 60 APsa~~~f~~~~r~~l~~~-nP~---l~v~~v~~~~~~~~ 95 (105)
+||||+||+.+.+..++.+ ++. ..+...|++.|-.+
T Consensus 7 ~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~L 46 (73)
T PF09011_consen 7 PPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSL 46 (73)
T ss_dssp SSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS
T ss_pred CCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhc
Confidence 4499999999999999988 444 36778899999754
No 27
>KOG2746|consensus
Probab=95.37 E-value=0.007 Score=54.23 Aligned_cols=48 Identities=19% Similarity=0.280 Sum_probs=43.3
Q ss_pred CCCCchHHHhHHHHH--HHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC--CC
Q psy3267 6 NMQGIAYAFFVQVCR--EEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP--FV 55 (105)
Q Consensus 6 Kr~~SAY~fF~q~~R--ee~KkknPd~sv~faE~sKk~ge~WK~ms~eek--y~ 55 (105)
+|||++|++|.+-.| +.+...||+-. -..|+|.+||+|-++-..|+ |.
T Consensus 183 rrPMnaf~ifskrhr~~g~vhq~~pn~D--NrtIskiLgewWytL~~~Ekq~yh 234 (683)
T KOG2746|consen 183 RRPMNAFHIFSKRHRGEGRVHQRHPNQD--NRTISKILGEWWYTLGPNEKQKYH 234 (683)
T ss_pred hhhhHHHHHHHhhcCCccchhccCcccc--chhHHHHHhhhHhhhCchhhhhHH
Confidence 789999999999999 89999999974 47899999999999999884 66
No 28
>KOG0526|consensus
Probab=95.28 E-value=0.017 Score=51.15 Aligned_cols=39 Identities=15% Similarity=0.049 Sum_probs=33.1
Q ss_pred CCCCCCc----hHHHHhhhccchhhhhcCCcchhhhh---hHhhHHHH
Q psy3267 55 VGRKFAP----VFLTFLSRMKDSILFCVNPVLAVGSR---ILEKFDEC 95 (105)
Q Consensus 55 ~~e~~AP----sa~~~f~~~~r~~l~~~nP~l~v~~v---~~~~~~~~ 95 (105)
..||||| ||||++.+.-|..|+.+ +.+|++| +||||.+.
T Consensus 530 ~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~~dv~kk~g~~wk~m 575 (615)
T KOG0526|consen 530 KKDPNAPKRATSAYMLWLNASRESIKED--GISVGDVAKKAGEKWKQM 575 (615)
T ss_pred CCCCCCCccchhHHHHHHHhhhhhHhhc--CchHHHHHHHHhHHHhhh
Confidence 3578999 99999999999999999 7766665 69999764
No 29
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=95.07 E-value=0.048 Score=34.84 Aligned_cols=41 Identities=17% Similarity=0.250 Sum_probs=36.2
Q ss_pred CchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccC
Q psy3267 9 GIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIV 51 (105)
Q Consensus 9 ~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~e 51 (105)
.|.|=.|.|..|..+.++||++. .+.+-..++++||.-++.
T Consensus 13 lt~yK~Fsq~vRP~l~~~NPk~~--~sKl~~l~~AKwrEF~~~ 53 (55)
T PF08073_consen 13 LTNYKAFSQHVRPLLAKANPKAP--MSKLMMLLQAKWREFQEH 53 (55)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCc--HHHHHHHHHHHHHHHHhc
Confidence 56788999999999999999996 579999999999987654
No 30
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=95.05 E-value=0.05 Score=41.49 Aligned_cols=43 Identities=21% Similarity=0.228 Sum_probs=37.7
Q ss_pred CCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhc
Q psy3267 4 KLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSS 48 (105)
Q Consensus 4 kPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~m 48 (105)
|-.|..|||--|+.+.=.++|..||+++- .|.=+.+...|+..
T Consensus 121 KRqR~psaYn~f~k~ei~rik~~~p~ish--keaFs~aAknW~h~ 163 (170)
T PF04690_consen 121 KRQRVPSAYNRFMKEEIQRIKAENPDISH--KEAFSAAAKNWAHF 163 (170)
T ss_pred ccCCCchhHHHHHHHHHHHHHhcCCCCCH--HHHHHHHHHhhhhC
Confidence 34688999999999999999999999974 78888899999864
No 31
>KOG0527|consensus
Probab=93.31 E-value=0.047 Score=45.23 Aligned_cols=33 Identities=15% Similarity=0.148 Sum_probs=31.6
Q ss_pred hHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHH
Q psy3267 62 VFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDE 94 (105)
Q Consensus 62 sa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~ 94 (105)
=|||++|+..|.+|.++||.+ +|+..+|..|..
T Consensus 68 NAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~ 103 (331)
T KOG0527|consen 68 NAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKL 103 (331)
T ss_pred chhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhh
Confidence 899999999999999999998 999999999974
No 32
>KOG2746|consensus
Probab=84.52 E-value=0.67 Score=41.98 Aligned_cols=32 Identities=9% Similarity=0.055 Sum_probs=30.7
Q ss_pred hHHHHhhhccc--hhhhhcCCcc---hhhhhhHhhHH
Q psy3267 62 VFLTFLSRMKD--SILFCVNPVL---AVGSRILEKFD 93 (105)
Q Consensus 62 sa~~~f~~~~r--~~l~~~nP~l---~v~~v~~~~~~ 93 (105)
+||.+||...| ..+...|||+ +|++|.||+|-
T Consensus 187 naf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWy 223 (683)
T KOG2746|consen 187 NAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWY 223 (683)
T ss_pred HHHHHHHhhcCCccchhccCccccchhHHHHHhhhHh
Confidence 99999999999 9999999998 99999999995
No 33
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=81.14 E-value=3 Score=28.79 Aligned_cols=45 Identities=11% Similarity=0.093 Sum_probs=34.7
Q ss_pred CCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCC
Q psy3267 5 LNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVN 52 (105)
Q Consensus 5 PKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~ee 52 (105)
|..|.++=-+|-|..+..+-+.+++... .+ -+.+...|++|++++
T Consensus 4 PE~PKt~qe~Wqq~vi~dYla~~~~dr~--K~-~kam~~~W~~me~Ke 48 (85)
T PF14887_consen 4 PETPKTAQEIWQQSVIGDYLAKFRNDRK--KA-LKAMEAQWSQMEKKE 48 (85)
T ss_dssp S----THHHHHHHHHHHHHHHHTTSTHH--HH-HHHHHHHHHTTGGGH
T ss_pred CCCCCCHHHHHHHHHHHHHHHHhhHhHH--HH-HHHHHHHHHHhhhhh
Confidence 5666788889999999999999999863 33 568888999999986
No 34
>PF04418 DUF543: Domain of unknown function (DUF543); InterPro: IPR007512 This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long. However the Arabidopsis homologue is over 300 residues long. These proteins contain a conserved N-terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important.
Probab=80.59 E-value=1.2 Score=29.74 Aligned_cols=18 Identities=28% Similarity=0.397 Sum_probs=14.3
Q ss_pred hhhhhHhhHHHHhhhhhc
Q psy3267 84 VGSRILEKFDECLDYFGL 101 (105)
Q Consensus 84 v~~v~~~~~~~~~~~~~~ 101 (105)
-.+.+.+|||.||+-+-+
T Consensus 14 se~~~~~kwD~cl~~~l~ 31 (75)
T PF04418_consen 14 SEDELGEKWDRCLSDTLV 31 (75)
T ss_pred cHHHHHHHHHHHHHHHHH
Confidence 346899999999987644
No 35
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=78.78 E-value=4.1 Score=29.57 Aligned_cols=43 Identities=19% Similarity=0.287 Sum_probs=36.4
Q ss_pred CCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcc
Q psy3267 5 LNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSR 49 (105)
Q Consensus 5 PKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms 49 (105)
-||-.-||.-|....-.++|++||++. .+.+-..+-..|+.-.
T Consensus 73 ErR~KAAy~afeE~~Lp~lK~E~PgLr--lsQ~kq~l~K~w~KSP 115 (122)
T PF06244_consen 73 ERRMKAAYKAFEERRLPELKEENPGLR--LSQYKQMLWKEWQKSP 115 (122)
T ss_pred chhHHHHHHHHHHHHhHHHHhhCCCch--HHHHHHHHHHHHhcCC
Confidence 345557899999999999999999996 5789999999998744
No 36
>KOG3497|consensus
Probab=73.85 E-value=1.3 Score=29.37 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=10.4
Q ss_pred hhhhhhHhhHHHH
Q psy3267 83 AVGSRILEKFDEC 95 (105)
Q Consensus 83 ~v~~v~~~~~~~~ 95 (105)
+-|.|||+||+.-
T Consensus 9 tCGKvig~KWe~Y 21 (69)
T KOG3497|consen 9 TCGKVIGDKWETY 21 (69)
T ss_pred eccccccccHHHH
Confidence 4588999999853
No 37
>KOG4715|consensus
Probab=73.18 E-value=2.7 Score=35.70 Aligned_cols=33 Identities=21% Similarity=0.101 Sum_probs=30.7
Q ss_pred hHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHH
Q psy3267 62 VFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDE 94 (105)
Q Consensus 62 sa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~ 94 (105)
-.|+-||..+=+.|++.||++ .||.|||--|-.
T Consensus 70 ~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~d 105 (410)
T KOG4715|consen 70 MPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLD 105 (410)
T ss_pred chhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhh
Confidence 889999999999999999998 899999999964
No 38
>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta. The function of this family is unknown.
Probab=73.10 E-value=3.6 Score=31.95 Aligned_cols=40 Identities=20% Similarity=0.291 Sum_probs=32.1
Q ss_pred chHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC--CC
Q psy3267 10 IAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP--FV 55 (105)
Q Consensus 10 SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek--y~ 55 (105)
.+|+=|+.+.|. +|.+++ ..|+....+..|..|++.++ |.
T Consensus 84 naYLNFLReFRr----kh~~L~--p~dlI~~AAraW~rLSe~eK~rYr 125 (183)
T PF06382_consen 84 NAYLNFLREFRR----KHCGLS--PQDLIQRAARAWCRLSEAEKNRYR 125 (183)
T ss_pred hHHHHHHHHHHH----HccCCC--HHHHHHHHHHHHHhCCHHHHHHHH
Confidence 468889988766 467875 47999999999999999864 55
No 39
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=71.36 E-value=4.4 Score=29.40 Aligned_cols=33 Identities=15% Similarity=0.010 Sum_probs=28.8
Q ss_pred hHHHHhhhccchhhhhcCCcchhhhhhHhhHHH
Q psy3267 62 VFLTFLSRMKDSILFCVNPVLAVGSRILEKFDE 94 (105)
Q Consensus 62 sa~~~f~~~~r~~l~~~nP~l~v~~v~~~~~~~ 94 (105)
-||.-|....=|.|+.+||+|..+++.+==|.+
T Consensus 78 AAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~ 110 (122)
T PF06244_consen 78 AAYKAFEERRLPELKEENPGLRLSQYKQMLWKE 110 (122)
T ss_pred HHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHH
Confidence 899999999999999999999998877655544
No 40
>PF12408 DUF3666: Ribose-5-phosphate isomerase ; InterPro: IPR022133 This domain family is found in bacteria, and is approximately 50 amino acids in length. The family is found in association with PF02502 from PFAM. There are two completely conserved residues (D and F) that may be functionally important. ; PDB: 3ONO_A 3C5Y_N 2PPW_A.
Probab=60.38 E-value=3.9 Score=25.42 Aligned_cols=26 Identities=27% Similarity=0.346 Sum_probs=20.8
Q ss_pred cchhhhhcCCcchhhhhhHhhHHHHh
Q psy3267 71 KDSILFCVNPVLAVGSRILEKFDECL 96 (105)
Q Consensus 71 ~r~~l~~~nP~l~v~~v~~~~~~~~~ 96 (105)
.=..|++-+|+|.-+-|.||+|.||+
T Consensus 7 ll~iLk~iDqdLvK~AisGe~Fqe~F 32 (48)
T PF12408_consen 7 LLDILKAIDQDLVKTAISGERFQECF 32 (48)
T ss_dssp HHHHHHHS-HHHHHHHT-SHHHHHHH
T ss_pred HHHHHHHhCHHHHHHHhccHHHHHHH
Confidence 34568889999999999999999997
No 41
>PF14823 Sirohm_synth_C: Sirohaem biosynthesis protein C-terminal; PDB: 1KYQ_B.
Probab=51.69 E-value=11 Score=24.67 Aligned_cols=35 Identities=31% Similarity=0.357 Sum_probs=23.1
Q ss_pred ccchhhhhcCCcchhhhhhHhhH-HHHhhhhhccccC
Q psy3267 70 MKDSILFCVNPVLAVGSRILEKF-DECLDYFGLRALA 105 (105)
Q Consensus 70 ~~r~~l~~~nP~l~v~~v~~~~~-~~~~~~~~~~~~~ 105 (105)
..|.+||...|+.+.+.- -=+| -.|-|||||+-|+
T Consensus 13 ~LR~~LR~~ap~~~~~~~-RM~Wm~~vcd~w~l~~l~ 48 (70)
T PF14823_consen 13 ELRSRLREVAPDPEDGKR-RMRWMSQVCDYWSLEELA 48 (70)
T ss_dssp HHHHHHHHHS-SCCCHHH-HHHHHHHHHHHHHHHHGG
T ss_pred HHHHHHHhcCCCchhHHH-HHHHHHHHhcccCHHHHH
Confidence 458889999998855543 3345 4577888887653
No 42
>KOG0528|consensus
Probab=41.59 E-value=11 Score=33.45 Aligned_cols=32 Identities=3% Similarity=0.095 Sum_probs=30.4
Q ss_pred hHHHHhhhccchhhhhcCCcc---hhhhhhHhhHH
Q psy3267 62 VFLTFLSRMKDSILFCVNPVL---AVGSRILEKFD 93 (105)
Q Consensus 62 sa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~ 93 (105)
-|||..+++.|.+|....|+- -|++|.|-.|.
T Consensus 331 NAFMVWAkDERRKILqA~PDMHNSnISKILGSRWK 365 (511)
T KOG0528|consen 331 NAFMVWAKDERRKILQAFPDMHNSNISKILGSRWK 365 (511)
T ss_pred chhhcccchhhhhhhhcCccccccchhHHhccccc
Confidence 899999999999999999988 89999999995
No 43
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT). MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus
Probab=39.62 E-value=70 Score=24.81 Aligned_cols=60 Identities=17% Similarity=0.153 Sum_probs=42.6
Q ss_pred CCCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC-------------CCCCCCCc-hHHHHhh
Q psy3267 3 NKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP-------------FVGRKFAP-VFLTFLS 68 (105)
Q Consensus 3 nkPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek-------------y~~e~~AP-sa~~~f~ 68 (105)
.++||+.-+||.|. .-+..-.|+.. -.++|..++..|+.=.-+.+ ..+..++| ..|+-|+
T Consensus 42 ~~~kr~lN~Fm~FR----syy~~~~~~~~--Qk~~S~~l~~lW~~dp~k~~W~l~ak~ys~iRd~~gk~~~~L~~Fl~~~ 115 (201)
T PF04769_consen 42 EKAKRPLNGFMAFR----SYYSPIFPPLP--QKELSGILTKLWEKDPFKNKWSLMAKAYSFIRDQLGKDKAPLDQFLAFA 115 (201)
T ss_pred cccccchhHHHHHH----HHHHhhcCCcC--HHHHHHHHHHHHhCCccHhHHHHHhhhhhhhccccccccCCHHHHHHHh
Confidence 45788999999884 44556677764 58999999999987333331 22456888 7777776
No 44
>KOG3248|consensus
Probab=37.07 E-value=21 Score=30.70 Aligned_cols=40 Identities=10% Similarity=0.167 Sum_probs=33.3
Q ss_pred hHHHHhhhccchhhhhcCCcc---hhhhhhHhhHH-----HHhhhhhc
Q psy3267 62 VFLTFLSRMKDSILFCVNPVL---AVGSRILEKFD-----ECLDYFGL 101 (105)
Q Consensus 62 sa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~-----~~~~~~~~ 101 (105)
-||++|-.+.|.+|.+|-... .|.+|+|.+|- |-..||-|
T Consensus 197 NAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyEl 244 (421)
T KOG3248|consen 197 NAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYEL 244 (421)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHH
Confidence 999999999999999998854 78899999996 34456654
No 45
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=34.58 E-value=16 Score=23.68 Aligned_cols=16 Identities=31% Similarity=0.486 Sum_probs=12.3
Q ss_pred hhhhhhHhhHHHHhhh
Q psy3267 83 AVGSRILEKFDECLDY 98 (105)
Q Consensus 83 ~v~~v~~~~~~~~~~~ 98 (105)
+=|.||+.||++.+..
T Consensus 9 TCGkvi~~~~e~y~~~ 24 (60)
T PF01194_consen 9 TCGKVIGNKWEEYLER 24 (60)
T ss_dssp TTTSBTCGHHHHHHHH
T ss_pred CCCCChhHhHHHHHHH
Confidence 4578999999987643
No 46
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=32.63 E-value=98 Score=17.48 Aligned_cols=34 Identities=24% Similarity=0.182 Sum_probs=22.7
Q ss_pred HHHHHHHHHhCCCCchh---HHHHHHHHHHHhhhccc
Q psy3267 17 QVCREEHKKKHPEENVV---FAEFSKKCAERWKSSRI 50 (105)
Q Consensus 17 q~~Ree~KkknPd~sv~---faE~sKk~ge~WK~ms~ 50 (105)
...|.-.++-|||...+ -.+....+.+.|..+++
T Consensus 19 ~~y~~l~~~~HPD~~~~~~~~~~~~~~l~~Ay~~L~d 55 (55)
T cd06257 19 KAYRKLALKYHPDKNPDDPEAEEKFKEINEAYEVLSD 55 (55)
T ss_pred HHHHHHHHHHCcCCCCCcHHHHHHHHHHHHHHHHhcC
Confidence 45677778889997542 34556677777777653
No 47
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=31.26 E-value=44 Score=25.55 Aligned_cols=28 Identities=11% Similarity=0.033 Sum_probs=24.6
Q ss_pred CCchHHHHhhhccchhhhhcCCcchhhh
Q psy3267 59 FAPVFLTFLSRMKDSILFCVNPVLAVGS 86 (105)
Q Consensus 59 ~APsa~~~f~~~~r~~l~~~nP~l~v~~ 86 (105)
-+||||=.|-.+.=+.|+++||+++=-|
T Consensus 124 R~psaYn~f~k~ei~rik~~~p~ishke 151 (170)
T PF04690_consen 124 RVPSAYNRFMKEEIQRIKAENPDISHKE 151 (170)
T ss_pred CCchhHHHHHHHHHHHHHhcCCCCCHHH
Confidence 6779999999999999999999995443
No 48
>PF00226 DnaJ: DnaJ domain; InterPro: IPR001623 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Such a structure is shown in the following schematic representation: +------------+-+-------+-----+-----------+--------------------------------+ | N-terminal | | Gly-R | | CXXCXGXG | C-terminal | +------------+-+-------+-----+-----------+--------------------------------+ It is thought that the 'J' domain of DnaJ mediates the interaction with the dnaK protein and consists of four helices, the second of which has a charged surface that includes at least one pair of basic residues that are essential for interaction with the ATPase domain of Hsp70. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins [], either together or separately. In yeast, J-domains have been classified into 3 groups; the class III proteins are functionally distinct and do not appear to act as molecular chaperones []. ; GO: 0031072 heat shock protein binding; PDB: 2GUZ_C 2L6L_A 1HDJ_A 2EJ7_A 1FPO_C 2CUG_A 2QSA_A 2OCH_A 3BVO_B 3APQ_A ....
Probab=30.71 E-value=79 Score=18.72 Aligned_cols=37 Identities=19% Similarity=0.133 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhCCCCchhHH----HHHHHHHHHhhhcccCC
Q psy3267 16 VQVCREEHKKKHPEENVVFA----EFSKKCAERWKSSRIVN 52 (105)
Q Consensus 16 ~q~~Ree~KkknPd~sv~fa----E~sKk~ge~WK~ms~ee 52 (105)
-+..|.-.+.-|||....-+ +....+.+.|+.|++.+
T Consensus 18 k~~y~~l~~~~HPD~~~~~~~~~~~~~~~i~~Ay~~L~~~~ 58 (64)
T PF00226_consen 18 KKAYRRLSKQYHPDKNSGDEAEAEEKFARINEAYEILSDPE 58 (64)
T ss_dssp HHHHHHHHHHTSTTTGTSTHHHHHHHHHHHHHHHHHHHSHH
T ss_pred HHHHHhhhhccccccchhhhhhhhHHHHHHHHHHHHhCCHH
Confidence 45567777888999743334 77888899999988753
No 49
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=27.41 E-value=29 Score=23.20 Aligned_cols=14 Identities=36% Similarity=0.494 Sum_probs=10.9
Q ss_pred hhhhhhHhhHHHHh
Q psy3267 83 AVGSRILEKFDECL 96 (105)
Q Consensus 83 ~v~~v~~~~~~~~~ 96 (105)
+=|.|||+||++-+
T Consensus 9 TCGkvig~~we~y~ 22 (71)
T PLN00032 9 TCGKVIGNKWDTYL 22 (71)
T ss_pred CCCCCcHHHHHHHH
Confidence 45789999998654
No 50
>PLN02150 terpene synthase/cyclase family protein
Probab=25.98 E-value=55 Score=22.25 Aligned_cols=19 Identities=16% Similarity=0.148 Sum_probs=16.8
Q ss_pred hHHHHHHHHHHHhhhcccC
Q psy3267 33 VFAEFSKKCAERWKSSRIV 51 (105)
Q Consensus 33 ~faE~sKk~ge~WK~ms~e 51 (105)
...+|.+.+.+.||.|+.+
T Consensus 24 A~~~i~~li~~~WK~iN~e 42 (96)
T PLN02150 24 AVSELKKMIRDNYKIVMEE 42 (96)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5778999999999999985
No 51
>PF05047 L51_S25_CI-B8: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain ; InterPro: IPR007741 Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) 1.6.5.3 from EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.; PDB: 1S3A_A.
Probab=24.83 E-value=61 Score=18.99 Aligned_cols=18 Identities=17% Similarity=0.237 Sum_probs=14.2
Q ss_pred hHHHHHHHHHHhCCCCch
Q psy3267 15 FVQVCREEHKKKHPEENV 32 (105)
Q Consensus 15 F~q~~Ree~KkknPd~sv 32 (105)
|+..+-..++..||++.+
T Consensus 4 F~~~~lp~l~~~NP~v~~ 21 (52)
T PF05047_consen 4 FLKNNLPTLKYHNPQVQF 21 (52)
T ss_dssp HHHHTHHHHHHHSTT--E
T ss_pred HHHHhHHHHHHHCCCcEE
Confidence 778888999999999876
No 52
>COG2879 Uncharacterized small protein [Function unknown]
Probab=24.03 E-value=1.1e+02 Score=20.25 Aligned_cols=31 Identities=29% Similarity=0.643 Sum_probs=20.3
Q ss_pred CchHHHhHHHHHHHHHHhCCCCch-hHHHHHHHHHH
Q psy3267 9 GIAYAFFVQVCREEHKKKHPEENV-VFAEFSKKCAE 43 (105)
Q Consensus 9 ~SAY~fF~q~~Ree~KkknPd~sv-~faE~sKk~ge 43 (105)
++.|=-|+.. ++++|||..+ +-.||=+.|.+
T Consensus 22 vpdYdnYVeh----mr~~hPd~p~mT~~EFfrec~d 53 (65)
T COG2879 22 VPDYDNYVEH----MRKKHPDKPPMTYEEFFRECQD 53 (65)
T ss_pred CCcHHHHHHH----HHHhCcCCCcccHHHHHHHHHH
Confidence 3445555544 4667898764 67788888765
No 53
>KOG3223|consensus
Probab=23.40 E-value=1.2e+02 Score=24.21 Aligned_cols=43 Identities=16% Similarity=0.289 Sum_probs=34.2
Q ss_pred CCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhccc
Q psy3267 6 NMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRI 50 (105)
Q Consensus 6 Kr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~ 50 (105)
||=.-||--|-+..-.++|.+||++. +++.-..+-..|+.-.|
T Consensus 166 kRmrAA~~afEe~~LPrLK~e~P~lr--lsQ~Kqll~Kew~KsPD 208 (221)
T KOG3223|consen 166 KRMRAAFKAFEEARLPRLKKENPGLR--LSQYKQLLKKEWQKSPD 208 (221)
T ss_pred HHHHHHHHHHHHhhchhhhhcCCCcc--HHHHHHHHHHHHhhCCC
Confidence 33445699999999999999999996 56887888888987443
No 54
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=23.08 E-value=78 Score=24.57 Aligned_cols=36 Identities=22% Similarity=0.342 Sum_probs=27.4
Q ss_pred hHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccC
Q psy3267 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIV 51 (105)
Q Consensus 11 AY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~e 51 (105)
+.+.|++..=+.+-.+|.+. .+-..+...|+.||++
T Consensus 131 acLVFL~~~f~~F~~~~dee-----K~v~Il~KTw~KMS~~ 166 (185)
T PF13875_consen 131 ACLVFLEYYFEDFAAKHDEE-----KIVDILRKTWRKMSER 166 (185)
T ss_pred HHHHhHHHHHHHHHhcCCHH-----HHHHHHHHHHHHCCHH
Confidence 46778888889999998443 3555667799999985
No 55
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=22.83 E-value=58 Score=21.09 Aligned_cols=21 Identities=14% Similarity=0.131 Sum_probs=18.0
Q ss_pred hHHHHHHHHHHHhhhcccCCC
Q psy3267 33 VFAEFSKKCAERWKSSRIVNP 53 (105)
Q Consensus 33 ~faE~sKk~ge~WK~ms~eek 53 (105)
.|..|++.+|..|+.+-.+-.
T Consensus 6 ~l~~ia~~lG~dW~~LAr~Lg 26 (84)
T cd08317 6 RLADISNLLGSDWPQLARELG 26 (84)
T ss_pred hHHHHHHHHhhHHHHHHHHcC
Confidence 588999999999999877654
No 56
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=21.99 E-value=39 Score=22.18 Aligned_cols=13 Identities=31% Similarity=0.473 Sum_probs=10.4
Q ss_pred hhhhhhHhhHHHH
Q psy3267 83 AVGSRILEKFDEC 95 (105)
Q Consensus 83 ~v~~v~~~~~~~~ 95 (105)
+-|.+|+++|++-
T Consensus 9 sCGkvi~~~w~~y 21 (63)
T COG1644 9 SCGKVIGHKWEEY 21 (63)
T ss_pred cCCCCHHHHHHHH
Confidence 4578999999864
No 57
>KOG0371|consensus
Probab=21.95 E-value=45 Score=27.89 Aligned_cols=28 Identities=25% Similarity=0.317 Sum_probs=24.6
Q ss_pred chhhhhcCCcchhhhhhHhhHHHHhhhhh
Q psy3267 72 DSILFCVNPVLAVGSRILEKFDECLDYFG 100 (105)
Q Consensus 72 r~~l~~~nP~l~v~~v~~~~~~~~~~~~~ 100 (105)
=..|+++|-...|++|.| -+||||.-.|
T Consensus 121 vtilrGNHEsrqitqvyg-fydeclRkyg 148 (319)
T KOG0371|consen 121 VTILRGNHESRQITQVYG-FYDECLRKYG 148 (319)
T ss_pred eEEecCchHHHHHHHHHh-hHHHHHhhcc
Confidence 356899999999999999 8999998776
No 58
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=21.84 E-value=1.7e+02 Score=16.76 Aligned_cols=35 Identities=23% Similarity=0.170 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCCCch----hHHHHHHHHHHHhhhcccC
Q psy3267 17 QVCREEHKKKHPEENV----VFAEFSKKCAERWKSSRIV 51 (105)
Q Consensus 17 q~~Ree~KkknPd~sv----~faE~sKk~ge~WK~ms~e 51 (105)
+..|...+.-|||... .-.+..+.+.+.|..+++.
T Consensus 20 ~ay~~l~~~~HPD~~~~~~~~~~~~~~~l~~Ay~~L~~~ 58 (60)
T smart00271 20 KAYRKLALKYHPDKNPGDKEEAEEKFKEINEAYEVLSDP 58 (60)
T ss_pred HHHHHHHHHHCcCCCCCchHHHHHHHHHHHHHHHHHcCC
Confidence 4456666777999753 2456778888888888775
No 59
>KOG3223|consensus
Probab=21.30 E-value=1.1e+02 Score=24.39 Aligned_cols=33 Identities=15% Similarity=-0.033 Sum_probs=27.6
Q ss_pred hHHHHhhhccchhhhhcCCcchhhhhhHhhHHH
Q psy3267 62 VFLTFLSRMKDSILFCVNPVLAVGSRILEKFDE 94 (105)
Q Consensus 62 sa~~~f~~~~r~~l~~~nP~l~v~~v~~~~~~~ 94 (105)
-||.-|-...=|.|+.+||++.+++.-+=-|.|
T Consensus 170 AA~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Ke 202 (221)
T KOG3223|consen 170 AAFKAFEEARLPRLKKENPGLRLSQYKQLLKKE 202 (221)
T ss_pred HHHHHHHHhhchhhhhcCCCccHHHHHHHHHHH
Confidence 899999999999999999999988755444443
No 60
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=20.01 E-value=44 Score=21.76 Aligned_cols=14 Identities=36% Similarity=0.522 Sum_probs=10.5
Q ss_pred hhhhhhHhhHHHHh
Q psy3267 83 AVGSRILEKFDECL 96 (105)
Q Consensus 83 ~v~~v~~~~~~~~~ 96 (105)
+=|.||+++|++-+
T Consensus 9 TCGkvi~~~we~y~ 22 (62)
T PRK04016 9 TCGKVIAEKWEEFK 22 (62)
T ss_pred CCCCChHHHHHHHH
Confidence 44789999998743
Done!