Query 030283
Match_columns 180
No_of_seqs 179 out of 1215
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 11:22:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030283hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00199 high mobility group p 99.9 7.3E-24 1.6E-28 153.1 10.7 85 40-124 8-93 (94)
2 cd01389 MATA_HMG-box MATA_HMG- 99.8 2.4E-20 5.2E-25 129.5 7.3 73 54-127 1-73 (77)
3 cd01388 SOX-TCF_HMG-box SOX-TC 99.8 9.2E-20 2E-24 125.2 7.4 71 54-125 1-71 (72)
4 PF00505 HMG_box: HMG (high mo 99.8 2.3E-19 5E-24 121.1 8.3 69 55-124 1-69 (69)
5 cd01390 HMGB-UBF_HMG-box HMGB- 99.8 8.7E-19 1.9E-23 117.2 8.4 65 55-120 1-65 (66)
6 smart00398 HMG high mobility g 99.8 1.2E-18 2.6E-23 117.2 8.7 70 54-124 1-70 (70)
7 COG5648 NHP6B Chromatin-associ 99.8 8.6E-19 1.9E-23 141.4 8.4 87 43-130 59-145 (211)
8 PF09011 HMG_box_2: HMG-box do 99.8 1.4E-18 3.1E-23 119.5 8.3 72 52-124 1-73 (73)
9 KOG0381 HMG box-containing pro 99.7 5.1E-17 1.1E-21 116.7 10.1 76 51-127 17-95 (96)
10 cd00084 HMG-box High Mobility 99.7 5.4E-17 1.2E-21 107.9 8.3 65 55-120 1-65 (66)
11 KOG0527 HMG-box transcription 99.7 6.9E-17 1.5E-21 139.7 6.2 87 47-134 55-141 (331)
12 KOG0526 Nucleosome-binding fac 99.6 9.1E-16 2E-20 137.6 6.5 77 44-125 525-601 (615)
13 KOG3248 Transcription factor T 99.3 2.4E-12 5.2E-17 110.4 5.6 75 53-128 190-264 (421)
14 KOG4715 SWI/SNF-related matrix 99.3 1.5E-11 3.2E-16 104.8 8.0 81 47-128 57-137 (410)
15 KOG0528 HMG-box transcription 99.1 3.3E-11 7.1E-16 107.5 2.5 81 46-127 317-397 (511)
16 KOG2746 HMG-box transcription 98.6 6.1E-08 1.3E-12 89.7 4.5 74 45-119 172-247 (683)
17 PF14887 HMG_box_5: HMG (high 98.2 1.3E-05 2.8E-10 55.6 7.6 75 54-130 3-77 (85)
18 PF04690 YABBY: YABBY protein; 96.8 0.0028 6.1E-08 50.4 5.5 48 50-98 117-164 (170)
19 COG5648 NHP6B Chromatin-associ 96.7 0.0013 2.7E-08 53.8 2.9 70 51-121 140-209 (211)
20 PF06382 DUF1074: Protein of u 96.3 0.011 2.3E-07 47.3 5.9 50 59-113 83-132 (183)
21 PF08073 CHDNT: CHDNT (NUC034) 95.4 0.015 3.3E-07 37.9 2.6 39 60-99 14-52 (55)
22 PF06244 DUF1014: Protein of u 94.5 0.053 1.1E-06 41.0 3.9 48 52-100 69-117 (122)
23 PF04769 MAT_Alpha1: Mating-ty 92.9 0.31 6.8E-06 39.8 6.0 56 49-111 38-93 (201)
24 KOG3223 Uncharacterized conser 92.6 0.099 2.1E-06 42.4 2.6 54 53-110 162-216 (221)
25 TIGR03481 HpnM hopanoid biosyn 86.6 1.5 3.1E-05 35.6 5.0 45 83-127 66-112 (198)
26 PRK15117 ABC transporter perip 82.6 3 6.6E-05 34.1 5.2 49 78-127 66-116 (211)
27 PF05494 Tol_Tol_Ttg2: Toluene 80.1 3.4 7.3E-05 32.2 4.5 47 78-125 36-84 (170)
28 COG2854 Ttg2D ABC-type transpo 58.1 16 0.00034 30.0 3.9 42 88-129 78-120 (202)
29 KOG0870 DNA polymerase epsilon 56.4 34 0.00074 27.2 5.4 63 57-127 41-105 (172)
30 PF12881 NUT_N: NUT protein N 52.4 35 0.00076 29.9 5.3 53 60-113 230-282 (328)
31 PF04147 Nop14: Nop14-like fam 47.4 17 0.00037 35.8 3.0 12 59-70 248-259 (840)
32 PF06524 NOA36: NOA36 protein; 46.4 22 0.00047 30.5 3.1 6 57-62 212-217 (314)
33 PF11304 DUF3106: Protein of u 44.8 65 0.0014 23.4 5.1 11 93-103 55-65 (107)
34 PF15243 ANAPC15: Anaphase-pro 36.7 59 0.0013 23.3 3.7 32 91-128 14-45 (92)
35 PF04147 Nop14: Nop14-like fam 36.6 27 0.00058 34.5 2.5 8 54-61 175-182 (840)
36 PF13875 DUF4202: Domain of un 35.9 35 0.00077 27.6 2.7 39 61-103 131-169 (185)
37 PF01352 KRAB: KRAB box; Inte 33.1 24 0.00052 21.3 1.0 28 83-110 3-31 (41)
38 COG4281 ACB Acyl-CoA-binding p 30.9 41 0.00089 23.5 2.0 61 54-116 16-85 (87)
39 PRK10363 cpxP periplasmic repr 30.8 1.3E+02 0.0028 23.9 5.1 40 85-125 112-151 (166)
40 PRK09706 transcriptional repre 29.9 1.1E+02 0.0023 22.7 4.4 43 85-127 87-129 (135)
41 PF00887 ACBP: Acyl CoA bindin 29.6 93 0.002 21.4 3.7 54 61-116 29-86 (87)
42 PRK12751 cpxP periplasmic stre 29.0 94 0.002 24.5 4.0 33 86-118 119-151 (162)
43 PF06945 DUF1289: Protein of u 28.5 64 0.0014 20.3 2.5 24 83-111 24-47 (51)
44 KOG2023 Nuclear transport rece 27.9 27 0.00058 33.9 0.9 6 56-61 169-174 (885)
45 PF05470 eIF-3c_N: Eukaryotic 27.3 1.7E+02 0.0038 27.8 6.1 47 83-129 82-137 (595)
46 PF04871 Uso1_p115_C: Uso1 / p 27.3 47 0.001 25.3 2.0 9 120-128 100-108 (136)
47 PRK12750 cpxP periplasmic repr 26.9 1.4E+02 0.003 23.6 4.7 34 87-120 127-160 (170)
48 PF15581 Imm35: Immunity prote 25.3 43 0.00093 23.9 1.3 20 83-102 32-51 (93)
49 PF06213 CobT: Cobalamin biosy 22.3 4.3E+02 0.0092 22.3 7.1 34 56-96 139-172 (282)
50 PF09164 VitD-bind_III: Vitami 21.4 2.7E+02 0.0059 18.8 4.6 33 60-93 9-41 (68)
No 1
>PTZ00199 high mobility group protein; Provisional
Probab=99.91 E-value=7.3e-24 Score=153.09 Aligned_cols=85 Identities=44% Similarity=0.694 Sum_probs=78.6
Q ss_pred cccccccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHH
Q 030283 40 RQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGK 118 (180)
Q Consensus 40 kk~kk~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~ 118 (180)
+.+++++++.+||++|+||+|||||||+++|..|..+||++. ++.+|+++||++|+.||+++|.+|+.+|..++.+|..
T Consensus 8 ~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~ 87 (94)
T PTZ00199 8 VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEK 87 (94)
T ss_pred ccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence 444555667899999999999999999999999999999985 4889999999999999999999999999999999999
Q ss_pred HHHHHh
Q 030283 119 KMNAYN 124 (180)
Q Consensus 119 e~~~y~ 124 (180)
+|.+|.
T Consensus 88 e~~~Y~ 93 (94)
T PTZ00199 88 EKAEYA 93 (94)
T ss_pred HHHHHh
Confidence 999996
No 2
>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=99.82 E-value=2.4e-20 Score=129.55 Aligned_cols=73 Identities=30% Similarity=0.509 Sum_probs=70.2
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 030283 54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ 127 (180)
Q Consensus 54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~ 127 (180)
+|+||+|||||||+++|..|+.+||+++ +.+|+++||.+|+.|++++|.+|..+|..++.+|..+|+.|+...
T Consensus 1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~-~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p 73 (77)
T cd01389 1 KIPRPRNAFILYRQDKHAQLKTENPGLT-NNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTP 73 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccC
Confidence 5899999999999999999999999997 899999999999999999999999999999999999999998754
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=99.81 E-value=9.2e-20 Score=125.15 Aligned_cols=71 Identities=35% Similarity=0.522 Sum_probs=68.2
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283 54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK 125 (180)
Q Consensus 54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~ 125 (180)
+.|||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+++.|+.
T Consensus 1 ~iKrP~naf~~F~~~~r~~~~~~~p~~~-~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~y 71 (72)
T cd01388 1 HIKRPMNAFMLFSKRHRRKVLQEYPLKE-NRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYKW 71 (72)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence 4689999999999999999999999997 8999999999999999999999999999999999999999964
No 4
>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=99.80 E-value=2.3e-19 Score=121.11 Aligned_cols=69 Identities=43% Similarity=0.797 Sum_probs=65.6
Q ss_pred CCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283 55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN 124 (180)
Q Consensus 55 PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~ 124 (180)
|+||+|||+|||.+++..|+.+||+++ +.+|+++||++|+.|++++|.+|...|..++.+|..+|..|+
T Consensus 1 PkrP~~af~lf~~~~~~~~k~~~p~~~-~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~ 69 (69)
T PF00505_consen 1 PKRPPNAFMLFCKEKRAKLKEENPDLS-NKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK 69 (69)
T ss_dssp SSSS--HHHHHHHHHHHHHHHHSTTST-HHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCHHHHHHHHHHHHHHHHhcccc-cccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 899999999999999999999999998 899999999999999999999999999999999999999995
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=99.78 E-value=8.7e-19 Score=117.15 Aligned_cols=65 Identities=54% Similarity=0.836 Sum_probs=63.4
Q ss_pred CCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHH
Q 030283 55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM 120 (180)
Q Consensus 55 PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~ 120 (180)
|++|+|||+||++++|..++..||+++ +.+|++.||.+|+.||+++|.+|...|..++.+|..+|
T Consensus 1 Pkrp~saf~~f~~~~r~~~~~~~p~~~-~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~ 65 (66)
T cd01390 1 PKRPLSAYFLFSQEQRPKLKKENPDAS-VTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM 65 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999999997 89999999999999999999999999999999999887
No 6
>smart00398 HMG high mobility group.
Probab=99.78 E-value=1.2e-18 Score=117.20 Aligned_cols=70 Identities=47% Similarity=0.793 Sum_probs=67.8
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283 54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN 124 (180)
Q Consensus 54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~ 124 (180)
+|++|+|||+||++++|..+..+||+++ +.+|+++||.+|+.|++++|.+|..+|..++.+|..+|..|+
T Consensus 1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~-~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~ 70 (70)
T smart00398 1 KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70 (70)
T ss_pred CcCCCCcHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 5899999999999999999999999997 899999999999999999999999999999999999999984
No 7
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=99.77 E-value=8.6e-19 Score=141.41 Aligned_cols=87 Identities=43% Similarity=0.719 Sum_probs=81.9
Q ss_pred ccccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHH
Q 030283 43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNA 122 (180)
Q Consensus 43 kk~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~ 122 (180)
+..+++.++||.|+||+||||||+..+|..|...+|.++ |.+|+++||++|++|++++|++|...|..++.+|..++..
T Consensus 59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~-~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~ 137 (211)
T COG5648 59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEE 137 (211)
T ss_pred HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCC-hHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHh
Confidence 455677899999999999999999999999999999997 9999999999999999999999999999999999999999
Q ss_pred HhhhCCCC
Q 030283 123 YNKKQDGD 130 (180)
Q Consensus 123 y~~~~~~~ 130 (180)
|..++...
T Consensus 138 y~~k~~~~ 145 (211)
T COG5648 138 YNKKLPNK 145 (211)
T ss_pred hhcccCCC
Confidence 99988533
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=99.77 E-value=1.4e-18 Score=119.50 Aligned_cols=72 Identities=43% Similarity=0.785 Sum_probs=63.3
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHHh-CCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283 52 PNKPKRPPSAFFVFLEEFRKTFKKE-NPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN 124 (180)
Q Consensus 52 p~~PKrP~sAy~lF~~e~r~~ik~e-~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~ 124 (180)
|++||+|+|||+||+.+++..++.. ++.+. +.+|++.|+.+|+.||+++|.+|..+|..++.+|..+|..|+
T Consensus 1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~-~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~ 73 (73)
T PF09011_consen 1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQS-FREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN 73 (73)
T ss_dssp SSS--SSSSHHHHHHHHHHHHHHHHT-T-SS-HHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred CcCCCCCCCHHHHHHHHHHHHHHHhcccCCC-HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 7899999999999999999999988 66665 899999999999999999999999999999999999999995
No 9
>KOG0381 consensus HMG box-containing protein [General function prediction only]
Probab=99.72 E-value=5.1e-17 Score=116.70 Aligned_cols=76 Identities=49% Similarity=0.831 Sum_probs=72.2
Q ss_pred CC--CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHH-HHhhhC
Q 030283 51 DP--NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMN-AYNKKQ 127 (180)
Q Consensus 51 dp--~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~-~y~~~~ 127 (180)
+| +.|++|+|||++||.+.|..++.+||+++ +.+|+++||++|++|++++|.+|...|..++.+|..+|. .|+..+
T Consensus 17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~~-~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~~ 95 (96)
T KOG0381|consen 17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLS-VGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL 95 (96)
T ss_pred CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 56 59999999999999999999999999987 999999999999999999999999999999999999999 988754
No 10
>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=99.71 E-value=5.4e-17 Score=107.89 Aligned_cols=65 Identities=51% Similarity=0.807 Sum_probs=62.7
Q ss_pred CCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHH
Q 030283 55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM 120 (180)
Q Consensus 55 PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~ 120 (180)
|++|+|||+||++++|..++..||+++ +.+|++.||.+|+.|++++|.+|...|...+.+|...+
T Consensus 1 pkrp~~af~~f~~~~~~~~~~~~~~~~-~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~ 65 (66)
T cd00084 1 PKRPLSAYFLFSQEHRAEVKAENPGLS-VGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM 65 (66)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999999997 89999999999999999999999999999999999875
No 11
>KOG0527 consensus HMG-box transcription factor [Transcription]
Probab=99.67 E-value=6.9e-17 Score=139.68 Aligned_cols=87 Identities=30% Similarity=0.540 Sum_probs=79.1
Q ss_pred ccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283 47 KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK 126 (180)
Q Consensus 47 k~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~ 126 (180)
.......+.||||||||||++..|..|..+||.+. -.||++.||.+|+.|++++|.+|++.|++++..|.++++.|+.+
T Consensus 55 ~~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mH-NSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYR 133 (331)
T KOG0527|consen 55 KDKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMH-NSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYR 133 (331)
T ss_pred cCCCCccccCCCcchhhhhhHHHHHHHHHhCcchh-hHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcccc
Confidence 34566789999999999999999999999999997 58999999999999999999999999999999999999999998
Q ss_pred CCCCcccc
Q 030283 127 QDGDEASD 134 (180)
Q Consensus 127 ~~~~~~s~ 134 (180)
-.......
T Consensus 134 PRRKkk~~ 141 (331)
T KOG0527|consen 134 PRRKKKKR 141 (331)
T ss_pred cccccccc
Confidence 87554433
No 12
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=99.60 E-value=9.1e-16 Score=137.62 Aligned_cols=77 Identities=42% Similarity=0.722 Sum_probs=72.3
Q ss_pred cccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283 44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY 123 (180)
Q Consensus 44 k~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y 123 (180)
+..++.+|||+||||+||||||++..|..|+.. +++ +++|++.+|++|+.|+. |.+|...|+.++++|+.+|.+|
T Consensus 525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~-~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~y 599 (615)
T KOG0526|consen 525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GIS-VGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEY 599 (615)
T ss_pred cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--Cch-HHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhh
Confidence 445678999999999999999999999999987 887 99999999999999999 9999999999999999999999
Q ss_pred hh
Q 030283 124 NK 125 (180)
Q Consensus 124 ~~ 125 (180)
+.
T Consensus 600 k~ 601 (615)
T KOG0526|consen 600 KN 601 (615)
T ss_pred cC
Confidence 94
No 13
>KOG3248 consensus Transcription factor TCF-4 [Transcription]
Probab=99.31 E-value=2.4e-12 Score=110.41 Aligned_cols=75 Identities=21% Similarity=0.386 Sum_probs=68.8
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283 53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD 128 (180)
Q Consensus 53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~ 128 (180)
...|+|+||||||+++.|..|..++--.. -..|+++||++|..||.++..+|+++|.++++.|...+..|-++..
T Consensus 190 phiKKPLNAFmlyMKEmRa~vvaEctlKe-SAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdN 264 (421)
T KOG3248|consen 190 PHIKKPLNAFMLYMKEMRAKVVAECTLKE-SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDN 264 (421)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHhhhhh-HHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhh
Confidence 37899999999999999999999986443 5789999999999999999999999999999999999999988764
No 14
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]
Probab=99.26 E-value=1.5e-11 Score=104.84 Aligned_cols=81 Identities=27% Similarity=0.536 Sum_probs=76.2
Q ss_pred ccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283 47 KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK 126 (180)
Q Consensus 47 k~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~ 126 (180)
...+.|.+|-+|+-+||.|++..+.+|+..||.+. +++|.++||.+|..|++.+|..|...++..+..|.+.|.+|+..
T Consensus 57 t~pkpPkppekpl~pymrySrkvWd~VkA~nPe~k-LWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~s 135 (410)
T KOG4715|consen 57 TRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELK-LWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNS 135 (410)
T ss_pred cCCCCCCCCCcccchhhHHhhhhhhhhhccCcchH-HHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 44567888999999999999999999999999998 99999999999999999999999999999999999999999987
Q ss_pred CC
Q 030283 127 QD 128 (180)
Q Consensus 127 ~~ 128 (180)
..
T Consensus 136 p~ 137 (410)
T KOG4715|consen 136 PA 137 (410)
T ss_pred ch
Confidence 63
No 15
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription]
Probab=99.10 E-value=3.3e-11 Score=107.46 Aligned_cols=81 Identities=28% Similarity=0.475 Sum_probs=72.8
Q ss_pred cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283 46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK 125 (180)
Q Consensus 46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~ 125 (180)
+.....+++.||||||||+|.++.|..|...+|++.| ..|+++||.+|+.|+-.+|++|++.-..+-..|...++.|+.
T Consensus 317 rg~~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHN-SnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrY 395 (511)
T KOG0528|consen 317 RGRASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRY 395 (511)
T ss_pred cCcCCCCccccCCcchhhcccchhhhhhhhcCccccc-cchhHHhcccccccccccccchHHHHHHHHHhhhccCccccc
Confidence 3445556788999999999999999999999999985 679999999999999999999999888888899999999998
Q ss_pred hC
Q 030283 126 KQ 127 (180)
Q Consensus 126 ~~ 127 (180)
+.
T Consensus 396 kP 397 (511)
T KOG0528|consen 396 KP 397 (511)
T ss_pred CC
Confidence 66
No 16
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription]
Probab=98.56 E-value=6.1e-08 Score=89.67 Aligned_cols=74 Identities=27% Similarity=0.468 Sum_probs=67.3
Q ss_pred ccccCCCCCCCCCCCChHHHHHHHHH--HHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHH
Q 030283 45 EKKAKKDPNKPKRPPSAFFVFLEEFR--KTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119 (180)
Q Consensus 45 ~kk~~kdp~~PKrP~sAy~lF~~e~r--~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e 119 (180)
+-..+.+..+.++|||||+||++.+| ..+.+.||+..| .-|++|||+.|-.|-+.+|..|.++|.+.+..|.++
T Consensus 172 rspnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DN-rtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka 247 (683)
T KOG2746|consen 172 RSPNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDN-RTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA 247 (683)
T ss_pred CCCCcCcchhhhhhhHHHHHHHhhcCCccchhccCccccc-hhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence 33456667788999999999999999 899999999985 779999999999999999999999999999999886
No 17
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=98.16 E-value=1.3e-05 Score=55.61 Aligned_cols=75 Identities=19% Similarity=0.268 Sum_probs=61.3
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCCCC
Q 030283 54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGD 130 (180)
Q Consensus 54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~~~ 130 (180)
.|..|.+|-.||.+..+..+...|+.-. ... -+.+...|++|+..+|-+|...|.++..+|+..|.+|+......
T Consensus 3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr-~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~~ 77 (85)
T PF14887_consen 3 LPETPKTAQEIWQQSVIGDYLAKFRNDR-KKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPADA 77 (85)
T ss_dssp -S----THHHHHHHHHHHHHHHHTTSTH-HHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCTT
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHhhHhH-HHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 5788999999999999999998998875 444 45889999999999999999999999999999999998876543
No 18
>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=96.80 E-value=0.0028 Score=50.43 Aligned_cols=48 Identities=33% Similarity=0.548 Sum_probs=41.7
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCC
Q 030283 50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98 (180)
Q Consensus 50 kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls 98 (180)
+.|.+-.|-+|||..|+++....|+..||+++ ..|+....+..|...+
T Consensus 117 kPPEKRqR~psaYn~f~k~ei~rik~~~p~is-hkeaFs~aAknW~h~p 164 (170)
T PF04690_consen 117 KPPEKRQRVPSAYNRFMKEEIQRIKAENPDIS-HKEAFSAAAKNWAHFP 164 (170)
T ss_pred CCccccCCCchhHHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHhhhhCc
Confidence 33444557789999999999999999999998 8999999999998765
No 19
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=96.71 E-value=0.0013 Score=53.82 Aligned_cols=70 Identities=21% Similarity=0.310 Sum_probs=61.8
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHH
Q 030283 51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMN 121 (180)
Q Consensus 51 dp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~ 121 (180)
-..+|..|.-+|+-|....|+.+...+|... ..+++++++..|.+|++.-|.+|.+.+.+.+..|...|+
T Consensus 140 ~k~~~~~~~~~~~e~~~~~r~~~~~~~~~~~-~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~ 209 (211)
T COG5648 140 KKLPNKAPIGPFIENEPKIRPKVEGPSPDKA-LVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP 209 (211)
T ss_pred cccCCCCCCchhhhccHHhccccCCCCcchh-hhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence 3456788888888888999999888888886 889999999999999999999999999999999987664
No 20
>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=96.33 E-value=0.011 Score=47.29 Aligned_cols=50 Identities=28% Similarity=0.496 Sum_probs=43.3
Q ss_pred CChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHH
Q 030283 59 PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLK 113 (180)
Q Consensus 59 ~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k 113 (180)
-+||+-|+.++|. .|.++. ..++....+..|..|++.+|..|..++....
T Consensus 83 nnaYLNFLReFRr----kh~~L~-p~dlI~~AAraW~rLSe~eK~rYrr~~~~~~ 132 (183)
T PF06382_consen 83 NNAYLNFLREFRR----KHCGLS-PQDLIQRAARAWCRLSEAEKNRYRRMAPSVR 132 (183)
T ss_pred chHHHHHHHHHHH----HccCCC-HHHHHHHHHHHHHhCCHHHHHHHHhhcchhh
Confidence 5799999999875 668897 8899999999999999999999998766443
No 21
>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=95.41 E-value=0.015 Score=37.91 Aligned_cols=39 Identities=21% Similarity=0.422 Sum_probs=34.9
Q ss_pred ChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCc
Q 030283 60 SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP 99 (180)
Q Consensus 60 sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~ 99 (180)
+.|-+|++-.|+.|...||++. +..|..+|+..|+..+.
T Consensus 14 t~yK~Fsq~vRP~l~~~NPk~~-~sKl~~l~~AKwrEF~~ 52 (55)
T PF08073_consen 14 TNYKAFSQHVRPLLAKANPKAP-MSKLMMLLQAKWREFQE 52 (55)
T ss_pred HHHHHHHHHHHHHHHHHCCCCc-HHHHHHHHHHHHHHHHh
Confidence 5688999999999999999997 89999999999987543
No 22
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=94.52 E-value=0.053 Score=41.00 Aligned_cols=48 Identities=23% Similarity=0.379 Sum_probs=41.5
Q ss_pred CCCCCCC-CChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCch
Q 030283 52 PNKPKRP-PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100 (180)
Q Consensus 52 p~~PKrP-~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~e 100 (180)
..+|-|. .-||.-|+....+.|+.+||++. ++++..+|-..|...|++
T Consensus 69 drHPErR~KAAy~afeE~~Lp~lK~E~PgLr-lsQ~kq~l~K~w~KSPeN 117 (122)
T PF06244_consen 69 DRHPERRMKAAYKAFEERRLPELKEENPGLR-LSQYKQMLWKEWQKSPEN 117 (122)
T ss_pred CCCcchhHHHHHHHHHHHHhHHHHhhCCCch-HHHHHHHHHHHHhcCCCC
Confidence 4456444 47899999999999999999998 999999999999988765
No 23
>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=92.93 E-value=0.31 Score=39.84 Aligned_cols=56 Identities=21% Similarity=0.357 Sum_probs=39.9
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHH
Q 030283 49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEK 111 (180)
Q Consensus 49 ~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~ 111 (180)
......++||+|+||+|+.=+- .-.|+.. ...++..|+..|..=+ -|..|.-+|..
T Consensus 38 ~~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~-Qk~~S~~l~~lW~~dp--~k~~W~l~ak~ 93 (201)
T PF04769_consen 38 KRSPEKAKRPLNGFMAFRSYYS----PIFPPLP-QKELSGILTKLWEKDP--FKNKWSLMAKA 93 (201)
T ss_pred cccccccccchhHHHHHHHHHH----hhcCCcC-HHHHHHHHHHHHhCCc--cHhHHHHHhhh
Confidence 3345578999999999977665 3346665 6789999999998632 25556655543
No 24
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.56 E-value=0.099 Score=42.42 Aligned_cols=54 Identities=30% Similarity=0.463 Sum_probs=46.2
Q ss_pred CCC-CCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHH
Q 030283 53 NKP-KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAE 110 (180)
Q Consensus 53 ~~P-KrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~ 110 (180)
.+| +|=.-||.-|-....+.|+.+||++. +.++-.+|-.+|..-|+. ||.+++.
T Consensus 162 rHPEkRmrAA~~afEe~~LPrLK~e~P~lr-lsQ~Kqll~Kew~KsPDN---P~Nq~~~ 216 (221)
T KOG3223|consen 162 RHPEKRMRAAFKAFEEARLPRLKKENPGLR-LSQYKQLLKKEWQKSPDN---PFNQAAV 216 (221)
T ss_pred cChHHHHHHHHHHHHHhhchhhhhcCCCcc-HHHHHHHHHHHHhhCCCC---hhhHHhh
Confidence 566 45557899999999999999999998 899999999999999887 7777653
No 25
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.
Probab=86.63 E-value=1.5 Score=35.61 Aligned_cols=45 Identities=18% Similarity=0.511 Sum_probs=39.0
Q ss_pred HHHHHH-HHHhhhcCCCchhhhhHHHHHHH-HHHHHHHHHHHHhhhC
Q 030283 83 VSAVGK-AAGGKWKSMSPAEKAPYESKAEK-LKSEYGKKMNAYNKKQ 127 (180)
Q Consensus 83 ~~eisk-~l~e~Wk~Ls~eeK~~Y~~~A~~-~k~~y~~e~~~y~~~~ 127 (180)
|..|++ .||..|+.++++++..|...... ....|-..+..|....
T Consensus 66 f~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~~~ 112 (198)
T TIGR03481 66 LPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAGER 112 (198)
T ss_pred HHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCce
Confidence 667776 78999999999999999998888 7788999999997643
No 26
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=82.58 E-value=3 Score=34.06 Aligned_cols=49 Identities=29% Similarity=0.551 Sum_probs=40.2
Q ss_pred CCCccHHHHHH-HHHhhhcCCCchhhhhHHHHHHH-HHHHHHHHHHHHhhhC
Q 030283 78 PNVTAVSAVGK-AAGGKWKSMSPAEKAPYESKAEK-LKSEYGKKMNAYNKKQ 127 (180)
Q Consensus 78 P~~~~~~eisk-~l~e~Wk~Ls~eeK~~Y~~~A~~-~k~~y~~e~~~y~~~~ 127 (180)
|... |..|++ .||..|+.++++++..|...... +...|-..+..|....
T Consensus 66 p~~D-f~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~q~ 116 (211)
T PRK15117 66 PYVQ-VKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHGQT 116 (211)
T ss_pred ccCC-HHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCce
Confidence 4554 777776 68999999999999999987766 6678999999997653
No 27
>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []. Many proteins are involved in these processes. This family is a transporter which shows similarity to ABC transporters [].; PDB: 2QGU_A.
Probab=80.09 E-value=3.4 Score=32.17 Aligned_cols=47 Identities=21% Similarity=0.548 Sum_probs=35.5
Q ss_pred CCCccHHHHHH-HHHhhhcCCCchhhhhHHHHHHH-HHHHHHHHHHHHhh
Q 030283 78 PNVTAVSAVGK-AAGGKWKSMSPAEKAPYESKAEK-LKSEYGKKMNAYNK 125 (180)
Q Consensus 78 P~~~~~~eisk-~l~e~Wk~Ls~eeK~~Y~~~A~~-~k~~y~~e~~~y~~ 125 (180)
|.+. |..|++ .||..|+.|+++++..|...... ....|-..+..|..
T Consensus 36 ~~~D-~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~ 84 (170)
T PF05494_consen 36 PYFD-FERMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG 84 (170)
T ss_dssp GGB--HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred HhCC-HHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 4443 667766 58899999999999999987766 56778889998875
No 28
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=58.05 E-value=16 Score=29.98 Aligned_cols=42 Identities=19% Similarity=0.366 Sum_probs=36.0
Q ss_pred HHHHhhhcCCCchhhhhHHHHHHH-HHHHHHHHHHHHhhhCCC
Q 030283 88 KAAGGKWKSMSPAEKAPYESKAEK-LKSEYGKKMNAYNKKQDG 129 (180)
Q Consensus 88 k~l~e~Wk~Ls~eeK~~Y~~~A~~-~k~~y~~e~~~y~~~~~~ 129 (180)
..||.-|+.+++++++.|...... +...|-..+..|+.+...
T Consensus 78 ~vLGk~~k~aspeQ~~~F~~aF~~yl~q~Y~~aL~~Y~~q~~~ 120 (202)
T COG2854 78 LVLGKYYKTASPEQRQAFFKAFRTYLEQTYGQALLDYKGQTLK 120 (202)
T ss_pred HHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHccCCCce
Confidence 468999999999999999987766 667899999999987753
No 29
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=56.41 E-value=34 Score=27.22 Aligned_cols=63 Identities=16% Similarity=0.264 Sum_probs=37.0
Q ss_pred CCCChHHHHHHHHHHHHH--HhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 030283 57 RPPSAFFVFLEEFRKTFK--KENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ 127 (180)
Q Consensus 57 rP~sAy~lF~~e~r~~ik--~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~ 127 (180)
|..+-|++|...+-..|. +.|-.++ ..+|.+.|-++ +=..|..-.......|+.....-+...
T Consensus 41 raAtVFv~~Lts~s~e~A~~q~rKt~s-adDVl~aL~Ei-------efs~f~~plk~~Le~yk~~~k~Kk~~~ 105 (172)
T KOG0870|consen 41 RAATVFVIFLTSVSNEIAKDQKRKTIS-ADDVLKALDEI-------EFSSFVNPLKSALEAYKKAVKQKKLAK 105 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccCccc-HHHHHHHHHHh-------chHHHhhHHHHHHHHHHHHHHHHHHhc
Confidence 445669999887777663 3345554 77777766654 223444445555566666555544433
No 30
>PF12881 NUT_N: NUT protein N terminus; InterPro: IPR024309 This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins. It is also found in FAM22, which are a family of uncharacterised mammalian proteins.
Probab=52.45 E-value=35 Score=29.87 Aligned_cols=53 Identities=21% Similarity=0.270 Sum_probs=36.7
Q ss_pred ChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHH
Q 030283 60 SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLK 113 (180)
Q Consensus 60 sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k 113 (180)
.||-.|.--..-.|....|.++ +.|-....-+.|...|--+|..|+++|++-+
T Consensus 230 EAlSCFLIpvLrsLar~kPtMt-lEeGl~ra~qEW~~~SnfdRmifyemaekFm 282 (328)
T PF12881_consen 230 EALSCFLIPVLRSLARLKPTMT-LEEGLWRAVQEWQHTSNFDRMIFYEMAEKFM 282 (328)
T ss_pred hhhhhhHHHHHHHHHhcCCCcc-HHHHHHHHHHHhhccccccHHHHHHHHHHHc
Confidence 3444444444444444556665 6666666778899999999999999999854
No 31
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=47.42 E-value=17 Score=35.79 Aligned_cols=12 Identities=8% Similarity=0.213 Sum_probs=6.1
Q ss_pred CChHHHHHHHHH
Q 030283 59 PSAFFVFLEEFR 70 (180)
Q Consensus 59 ~sAy~lF~~e~r 70 (180)
...|-+++.+..
T Consensus 248 ~ddYD~~vrel~ 259 (840)
T PF04147_consen 248 DDDYDKLVRELA 259 (840)
T ss_pred ccHHHHHHHHhc
Confidence 445555555443
No 32
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=46.35 E-value=22 Score=30.51 Aligned_cols=6 Identities=17% Similarity=0.584 Sum_probs=2.2
Q ss_pred CCCChH
Q 030283 57 RPPSAF 62 (180)
Q Consensus 57 rP~sAy 62 (180)
=|.-.|
T Consensus 212 CPKCg~ 217 (314)
T PF06524_consen 212 CPKCGY 217 (314)
T ss_pred CCCCCC
Confidence 333333
No 33
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=44.79 E-value=65 Score=23.44 Aligned_cols=11 Identities=27% Similarity=1.041 Sum_probs=4.5
Q ss_pred hhcCCCchhhh
Q 030283 93 KWKSMSPAEKA 103 (180)
Q Consensus 93 ~Wk~Ls~eeK~ 103 (180)
.|..|+++++.
T Consensus 55 ~W~~LspeqR~ 65 (107)
T PF11304_consen 55 RWAALSPEQRQ 65 (107)
T ss_pred HHHhCCHHHHH
Confidence 34444444443
No 34
>PF15243 ANAPC15: Anaphase-promoting complex subunit 15
Probab=36.73 E-value=59 Score=23.33 Aligned_cols=32 Identities=13% Similarity=0.258 Sum_probs=18.6
Q ss_pred HhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283 91 GGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD 128 (180)
Q Consensus 91 ~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~ 128 (180)
...|=+|. .+..+.+. ..+++.++.+|.....
T Consensus 14 ~~lwf~~d----~pc~dE~E--L~~~Eq~~q~Wl~sI~ 45 (92)
T PF15243_consen 14 DPLWFNLD----RPCVDETE--LQQQEQQHQAWLQSIA 45 (92)
T ss_pred CcccccCC----CccchHHH--HHHHHHHHHHHHHHHH
Confidence 34587775 34444333 3366677778876654
No 35
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=36.56 E-value=27 Score=34.47 Aligned_cols=8 Identities=38% Similarity=0.638 Sum_probs=3.5
Q ss_pred CCCCCCCh
Q 030283 54 KPKRPPSA 61 (180)
Q Consensus 54 ~PKrP~sA 61 (180)
.|-|+.|-
T Consensus 175 ~~~r~ksk 182 (840)
T PF04147_consen 175 EPERKKSK 182 (840)
T ss_pred cCccccCH
Confidence 34444443
No 36
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=35.93 E-value=35 Score=27.58 Aligned_cols=39 Identities=23% Similarity=0.397 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhh
Q 030283 61 AFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKA 103 (180)
Q Consensus 61 Ay~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~ 103 (180)
+-++|...+...+...|. -.-|..+|...|+.||+.-+.
T Consensus 131 acLVFL~~~f~~F~~~~d----eeK~v~Il~KTw~KMS~~g~~ 169 (185)
T PF13875_consen 131 ACLVFLEYYFEDFAAKHD----EEKIVDILRKTWRKMSERGHE 169 (185)
T ss_pred HHHHhHHHHHHHHHhcCC----HHHHHHHHHHHHHHCCHHHHH
Confidence 567899999999988872 345888999999999987664
No 37
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=33.13 E-value=24 Score=21.31 Aligned_cols=28 Identities=21% Similarity=0.369 Sum_probs=15.7
Q ss_pred HHHHHHHHH-hhhcCCCchhhhhHHHHHH
Q 030283 83 VSAVGKAAG-GKWKSMSPAEKAPYESKAE 110 (180)
Q Consensus 83 ~~eisk~l~-e~Wk~Ls~eeK~~Y~~~A~ 110 (180)
|.+|+.-++ +.|..|.+.+|..|.+.-.
T Consensus 3 f~Dvav~fs~eEW~~L~~~Qk~ly~dvm~ 31 (41)
T PF01352_consen 3 FEDVAVYFSQEEWELLDPAQKNLYRDVML 31 (41)
T ss_dssp ----TT---HHHHHTS-HHHHHHHHHHHH
T ss_pred EEEEEEEcChhhcccccceecccchhHHH
Confidence 445554444 5699999999999887543
No 38
>COG4281 ACB Acyl-CoA-binding protein [Lipid metabolism]
Probab=30.86 E-value=41 Score=23.52 Aligned_cols=61 Identities=20% Similarity=0.390 Sum_probs=38.1
Q ss_pred CCCCCCCh-----HHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCC----chhhhhHHHHHHHHHHHH
Q 030283 54 KPKRPPSA-----FFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS----PAEKAPYESKAEKLKSEY 116 (180)
Q Consensus 54 ~PKrP~sA-----y~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls----~eeK~~Y~~~A~~~k~~y 116 (180)
-+.+|.|- |.||-+......-.+.|++- .-+.+.--+.|..|- +.-++.|..+..+++..|
T Consensus 16 L~~kP~~d~LLkLYAL~KQ~s~GD~~~ekPG~~--d~~gr~K~eAW~~LKGksqedA~qeYialVeeLkak~ 85 (87)
T COG4281 16 LSEKPSNDELLKLYALFKQGSVGDNDGEKPGFF--DIVGRYKYEAWAGLKGKSQEDARQEYIALVEELKAKY 85 (87)
T ss_pred hccCCCcHHHHHHHHHHHhccccccCCCCCCcc--ccccchhHHHHhhccCccHHHHHHHHHHHHHHHHhhc
Confidence 45677665 77776666555555567774 334444557787765 334567777777777655
No 39
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=30.78 E-value=1.3e+02 Score=23.94 Aligned_cols=40 Identities=13% Similarity=0.315 Sum_probs=31.3
Q ss_pred HHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283 85 AVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK 125 (180)
Q Consensus 85 eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~ 125 (180)
++.++-.+++.-|+|++|..|+....+-...+.. +..+..
T Consensus 112 em~k~~nqmy~lLTPEQKaq~~~~~~~rm~~~~~-~~~~q~ 151 (166)
T PRK10363 112 EMAKVRNQMYRLLTPEQQAVLNEKHQQRMEQLRD-VTQWQK 151 (166)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH-HHhcCc
Confidence 4667778999999999999999888888777754 554433
No 40
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=29.90 E-value=1.1e+02 Score=22.69 Aligned_cols=43 Identities=12% Similarity=0.085 Sum_probs=37.6
Q ss_pred HHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 030283 85 AVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ 127 (180)
Q Consensus 85 eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~ 127 (180)
.-...|-..|+.|+++++.............|...+.+|-...
T Consensus 87 ~~~~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~ 129 (135)
T PRK09706 87 EDQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLKAR 129 (135)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456788899999999999999999999999999999997754
No 41
>PF00887 ACBP: Acyl CoA binding protein; InterPro: IPR000582 Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters []. ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor []. ACBP is a highly conserved protein of about 90 residues that is found in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and in some eubacterial species []. Although ACBP occurs as a completely independent protein, intact ACB domains have been identified in a number of large, multifunctional proteins in a variety of eukaryotic species. These include large membrane-associated proteins with N-terminal ACB domains, multifunctional enzymes with both ACB and peroxisomal enoyl-CoA Delta(3), Delta(2)-enoyl-CoA isomerase domains, and proteins with both an ACB domain and ankyrin repeats (IPR002110 from INTERPRO) []. The ACB domain consists of four alpha-helices arranged in a bowl shape with a highly exposed acyl-CoA-binding site. The ligand is bound through specific interactions with residues on the protein, most notably several conserved positive charges that interact with the phosphate group on the adenosine-3'phosphate moiety, and the acyl chain is sandwiched between the hydrophobic surfaces of CoA and the protein []. Other proteins containing an ACB domain include: Endozepine-like peptide (ELP) (gene DBIL5) from mouse []. ELP is a testis-specific ACBP homologue that may be involved in the energy metabolism of the mature sperm. MA-DBI, a transmembrane protein of unknown function which has been found in mammals. MA-DBI contains a N-terminal ACB domain. DRS-1 [], a human protein of unknown function that contains a N-terminal ACB domain and a C-terminal enoyl-CoA isomerase/hydratase domain. ; GO: 0000062 fatty-acyl-CoA binding; PDB: 2CB8_A 2FJ9_A 2LBB_A 1ST7_A 3EPY_B 2FDQ_C 1NTI_A 1HB8_A 1ACA_A 1NVL_A ....
Probab=29.58 E-value=93 Score=21.36 Aligned_cols=54 Identities=17% Similarity=0.327 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCC----chhhhhHHHHHHHHHHHH
Q 030283 61 AFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS----PAEKAPYESKAEKLKSEY 116 (180)
Q Consensus 61 Ay~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls----~eeK~~Y~~~A~~~k~~y 116 (180)
-|-||.+.....+....|+.-+ -+.+.--..|+.|. .+-+..|..+.......|
T Consensus 29 LYalyKQAt~Gd~~~~~P~~~d--~~~~~K~~AW~~l~gms~~eA~~~Yi~~v~~~~~~~ 86 (87)
T PF00887_consen 29 LYALYKQATHGDCDTPRPGFFD--IEGRAKWDAWKALKGMSKEEAMREYIELVEELIPKY 86 (87)
T ss_dssp HHHHHHHHHTSS--S-CTTTTC--HHHHHHHHHHHTTTTTHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCcCCCCcchh--HHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHhc
Confidence 3777777776666555676543 34444456797776 334566776666665555
No 42
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=28.98 E-value=94 Score=24.49 Aligned_cols=33 Identities=12% Similarity=0.270 Sum_probs=25.8
Q ss_pred HHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHH
Q 030283 86 VGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGK 118 (180)
Q Consensus 86 isk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~ 118 (180)
+.+...+++..|++++|..|.+..++-..+...
T Consensus 119 ~~~~~~qmy~lLTPEQra~l~~~~e~r~~~~~~ 151 (162)
T PRK12751 119 MAKVRNQMYNLLTPEQKEALNKKHQERIEKLQQ 151 (162)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence 445667888999999999999888777665543
No 43
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=28.52 E-value=64 Score=20.27 Aligned_cols=24 Identities=25% Similarity=0.488 Sum_probs=16.9
Q ss_pred HHHHHHHHHhhhcCCCchhhhhHHHHHHH
Q 030283 83 VSAVGKAAGGKWKSMSPAEKAPYESKAEK 111 (180)
Q Consensus 83 ~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~ 111 (180)
..||.. |..|++.+|.........
T Consensus 24 ~dEI~~-----W~~~s~~er~~i~~~l~~ 47 (51)
T PF06945_consen 24 LDEIRD-----WKSMSDDERRAILARLRA 47 (51)
T ss_pred HHHHHH-----HhhCCHHHHHHHHHHHHH
Confidence 456654 999999998776654443
No 44
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.87 E-value=27 Score=33.91 Aligned_cols=6 Identities=33% Similarity=0.567 Sum_probs=2.9
Q ss_pred CCCCCh
Q 030283 56 KRPPSA 61 (180)
Q Consensus 56 KrP~sA 61 (180)
.||+++
T Consensus 169 ~rpl~~ 174 (885)
T KOG2023|consen 169 TRPLNI 174 (885)
T ss_pred cCchHH
Confidence 455444
No 45
>PF05470 eIF-3c_N: Eukaryotic translation initiation factor 3 subunit 8 N-terminus; InterPro: IPR008905 The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA [].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation, 0005852 eukaryotic translation initiation factor 3 complex
Probab=27.35 E-value=1.7e+02 Score=27.81 Aligned_cols=47 Identities=17% Similarity=0.386 Sum_probs=27.8
Q ss_pred HHHHHHHHHhhh------cCCCchhhhhHHHH---HHHHHHHHHHHHHHHhhhCCC
Q 030283 83 VSAVGKAAGGKW------KSMSPAEKAPYESK---AEKLKSEYGKKMNAYNKKQDG 129 (180)
Q Consensus 83 ~~eisk~l~e~W------k~Ls~eeK~~Y~~~---A~~~k~~y~~e~~~y~~~~~~ 129 (180)
+.+|-..|.+.| +.|+...=.-|..+ -.+....|+..+..|+.....
T Consensus 82 l~~Led~v~e~~~~ke~~Kkms~~nakaln~lkQklkK~~k~~e~~i~~yrenPe~ 137 (595)
T PF05470_consen 82 LVELEDFVNETWADKEAKKKMSKNNAKALNTLKQKLKKYNKEYEAQIAKYRENPEA 137 (595)
T ss_pred HHHHHHHHHHHHhhhHhhhhcCHHhHHHHHHHHHHHHhhhhhHHHHHHHHHhCCcc
Confidence 334455566666 44554444555543 334455788899999887753
No 46
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=27.28 E-value=47 Score=25.30 Aligned_cols=9 Identities=11% Similarity=0.375 Sum_probs=4.0
Q ss_pred HHHHhhhCC
Q 030283 120 MNAYNKKQD 128 (180)
Q Consensus 120 ~~~y~~~~~ 128 (180)
+..|+.++.
T Consensus 100 ~~kyk~rLk 108 (136)
T PF04871_consen 100 RKKYKERLK 108 (136)
T ss_pred HHHHHHHHH
Confidence 344444443
No 47
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=26.89 E-value=1.4e+02 Score=23.62 Aligned_cols=34 Identities=18% Similarity=0.222 Sum_probs=28.0
Q ss_pred HHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHH
Q 030283 87 GKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM 120 (180)
Q Consensus 87 sk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~ 120 (180)
.+...+.+..|++++|..|.++...-...|...+
T Consensus 127 ~~~~~~~~~vLTpEQRak~~e~~~~r~~~~~~~~ 160 (170)
T PRK12750 127 LEKRHQMLSILTPEQKAKFQELQQERMQECQDKM 160 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445568999999999999999888888877766
No 48
>PF15581 Imm35: Immunity protein 35
Probab=25.32 E-value=43 Score=23.93 Aligned_cols=20 Identities=5% Similarity=0.346 Sum_probs=16.0
Q ss_pred HHHHHHHHHhhhcCCCchhh
Q 030283 83 VSAVGKAAGGKWKSMSPAEK 102 (180)
Q Consensus 83 ~~eisk~l~e~Wk~Ls~eeK 102 (180)
+.-+...|...|+.|+.++=
T Consensus 32 i~~l~~lIe~eWRGl~~~qV 51 (93)
T PF15581_consen 32 IRNLESLIEHEWRGLPEEQV 51 (93)
T ss_pred HHHHHHHHHHHHcCCCHHHH
Confidence 44577889999999998754
No 49
>PF06213 CobT: Cobalamin biosynthesis protein CobT; InterPro: IPR006538 These proteins are CobT subunits of the aerobic cobalt chelatase (aerobic cobalamin biosynthesis pathway). Pseudomonas denitrificans CobT has been experimentally characterised [, ]. Aerobic cobalt chelatase consists of three subunits, CobT, CobN (IPR003672 from INTERPRO) and CobS (IPR006537 from INTERPRO). Cobalamin (vitamin B12) can be complexed with metal via the ATP-dependent reactions (aerobic pathway) (e.g., in P. denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium) [, ]. The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively []. CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus) []. Nomenclature note: CobT of the aerobic pathway P. denitrificans is not a homologue of CobT of the anaerobic pathway (Salmonella typhimurium, Escherichia coli). Therefore, annotation of any members of this family as nicotinate-mononucleotide--5,6-dimethylbenzimidazole phosphoribosyltransferases is erroneous.
Probab=22.34 E-value=4.3e+02 Score=22.29 Aligned_cols=34 Identities=18% Similarity=0.402 Sum_probs=16.1
Q ss_pred CCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcC
Q 030283 56 KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKS 96 (180)
Q Consensus 56 KrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~ 96 (180)
-.|+..++.|+ .|..|....+. .....+-..|+.
T Consensus 139 ~~~l~~al~l~--lr~rl~g~~~p-----~~~~~~~~~~R~ 172 (282)
T PF06213_consen 139 DAPLSEALALL--LRERLTGQPPP-----ESAEKVVELWRP 172 (282)
T ss_pred cccHHHHHHHH--HHHHHhCCCCc-----HHHHHHHHHHHH
Confidence 34555444444 45556554332 234444445654
No 50
>PF09164 VitD-bind_III: Vitamin D binding protein, domain III; InterPro: IPR015247 This domain is predominantly found in Vitamin D binding proteins, and adopts a multihelical structure. It is required for formation of an actin 'clamp', allowing the protein to bind to actin []. ; PDB: 1MA9_A 1KW2_A 1KXP_D 1J7E_A 1J78_A 1LOT_A.
Probab=21.37 E-value=2.7e+02 Score=18.82 Aligned_cols=33 Identities=9% Similarity=0.280 Sum_probs=24.0
Q ss_pred ChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhh
Q 030283 60 SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGK 93 (180)
Q Consensus 60 sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~ 93 (180)
+.|.=|-+..+..++...|+++ ..+|..++.++
T Consensus 9 ~tFtEyKKrL~e~l~~k~P~at-~~~l~~lve~R 41 (68)
T PF09164_consen 9 NTFTEYKKRLAERLRAKLPDAT-PTELKELVEKR 41 (68)
T ss_dssp S-HHHHHHHHHHHHHHH-TTS--HHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHH
Confidence 5678888888999999999997 67777766554
Done!