Query psy10549
Match_columns 103
No_of_seqs 102 out of 514
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 21:16:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10549.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10549hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00888 Cullin: Cullin family 99.0 4.7E-10 1E-14 91.1 6.6 56 42-97 1-56 (588)
2 COG5647 Cullin, a subunit of E 98.7 5.5E-08 1.2E-12 82.5 8.4 74 22-97 6-98 (773)
3 KOG2166|consensus 98.7 5.2E-08 1.1E-12 83.1 6.7 68 33-100 12-83 (725)
4 KOG2284|consensus 97.9 3.1E-05 6.6E-10 63.6 5.6 64 35-98 8-75 (728)
5 KOG2166|consensus 90.8 0.18 3.8E-06 43.8 2.4 42 34-76 6-49 (725)
6 KOG2285|consensus 89.2 0.56 1.2E-05 39.5 4.0 62 34-95 9-73 (777)
7 PF10163 EnY2: Transcription f 87.7 4.2 9E-05 25.9 6.6 56 38-93 28-85 (86)
8 PF08328 ASL_C: Adenylosuccina 82.4 0.66 1.4E-05 31.7 1.0 45 19-66 32-76 (115)
9 PF08539 HbrB: HbrB-like; Int 78.5 7.3 0.00016 27.7 5.4 56 36-91 3-62 (158)
10 PF14164 YqzH: YqzH-like prote 76.0 8.7 0.00019 23.6 4.5 36 39-74 28-63 (64)
11 PF11020 DUF2610: Domain of un 74.2 13 0.00028 24.0 5.0 38 28-65 23-71 (82)
12 PTZ00015 histone H4; Provision 51.1 42 0.00091 22.3 4.4 43 58-100 29-71 (102)
13 smart00417 H4 Histone H4. 42.6 83 0.0018 19.7 4.6 43 58-100 12-54 (74)
14 PF03556 Cullin_binding: Culli 40.8 26 0.00057 23.5 2.3 34 43-76 2-36 (117)
15 KOG1086|consensus 40.1 79 0.0017 26.8 5.3 52 37-88 21-87 (594)
16 cd00076 H4 Histone H4, one of 39.6 73 0.0016 20.4 4.1 43 58-100 12-54 (85)
17 PF08066 PMC2NT: PMC2NT (NUC01 39.2 39 0.00085 21.4 2.8 23 34-56 59-81 (91)
18 PF13202 EF-hand_5: EF hand; P 38.6 34 0.00073 16.5 1.9 24 45-68 1-24 (25)
19 PF08511 COQ9: COQ9; InterPro 36.2 36 0.00078 21.5 2.2 21 35-55 54-74 (79)
20 PF03387 Herpes_UL46: Herpesvi 35.9 57 0.0012 27.1 3.9 35 21-55 147-181 (444)
21 PRK06922 hypothetical protein; 33.8 1.1E+02 0.0023 26.9 5.3 64 31-96 258-321 (677)
22 PLN00035 histone H4; Provision 33.0 1.1E+02 0.0024 20.4 4.2 41 60-100 30-70 (103)
23 PF12583 TPPII_N: Tripeptidyl 32.4 75 0.0016 22.4 3.5 47 37-96 67-113 (139)
24 PHA03195 tegument protein VP11 31.3 76 0.0017 27.8 4.0 35 21-55 154-188 (746)
25 PF00557 Peptidase_M24: Metall 29.9 1.9E+02 0.0042 20.0 5.8 42 34-75 100-141 (207)
26 PF10557 Cullin_Nedd8: Cullin 28.1 1.4E+02 0.003 17.7 5.6 35 43-78 7-41 (68)
27 cd01066 APP_MetAP A family inc 28.1 1.9E+02 0.0042 19.4 5.2 42 35-76 101-142 (207)
28 PF05066 HARE-HTH: HB1, ASXL, 26.3 87 0.0019 18.6 2.7 29 45-73 3-31 (72)
29 PF10808 DUF2542: Protein of u 25.6 1.1E+02 0.0023 19.6 3.0 33 37-69 19-64 (79)
30 PRK09646 RNA polymerase sigma 25.3 2.2E+02 0.0049 19.7 5.1 20 65-84 43-63 (194)
31 PRK11639 zinc uptake transcrip 25.1 1.8E+02 0.004 20.4 4.6 49 47-95 29-77 (169)
32 cd01092 APP-like Similar to Pr 25.1 2.4E+02 0.0051 19.5 5.4 41 34-74 101-141 (208)
33 PF05814 DUF843: Baculovirus p 24.9 74 0.0016 20.5 2.2 16 43-58 67-82 (83)
34 PF08542 Rep_fac_C: Replicatio 24.7 1.7E+02 0.0037 17.7 5.7 28 61-88 19-47 (89)
35 PF10929 DUF2811: Protein of u 24.6 55 0.0012 19.7 1.5 16 77-92 6-21 (57)
36 PRK12516 RNA polymerase sigma 24.1 2.6E+02 0.0055 19.5 5.4 14 81-94 65-78 (187)
37 PHA03193 tegument protein VP11 24.0 1.3E+02 0.0029 25.8 4.1 36 20-55 171-206 (594)
38 PF07034 ORC3_N: Origin recogn 23.8 1.3E+02 0.0028 23.4 3.9 37 36-73 33-69 (330)
39 PF07340 Herpes_IE1: Cytomegal 23.5 4.1E+02 0.009 21.8 6.7 38 36-73 118-155 (392)
40 KOG3533|consensus 22.5 4.4E+02 0.0096 26.1 7.3 80 14-95 505-602 (2706)
41 smart00803 TAF TATA box bindin 22.2 1.9E+02 0.0041 17.3 3.9 38 63-100 6-43 (65)
42 PF03613 EIID-AGA: PTS system 22.0 3.5E+02 0.0075 20.8 5.8 37 58-94 20-59 (264)
43 PF11123 DNA_Packaging_2: DNA 21.7 77 0.0017 20.3 1.8 19 76-94 28-46 (82)
44 PRK05572 sporulation sigma fac 21.6 3.3E+02 0.0072 19.9 8.6 25 31-55 12-40 (252)
45 cd03735 SOCS_SOCS1 SOCS (suppr 21.5 1.1E+02 0.0023 17.2 2.2 32 61-92 5-39 (43)
46 KOG3189|consensus 21.4 1.1E+02 0.0023 23.4 2.8 24 77-100 96-119 (252)
47 PRK05716 methionine aminopepti 21.2 3.2E+02 0.0069 19.7 5.4 41 35-75 117-157 (252)
48 COG2901 Fis Factor for inversi 21.1 2.6E+02 0.0056 18.5 4.6 58 10-85 8-66 (98)
49 PF10273 WGG: Pre-rRNA-process 21.0 98 0.0021 19.4 2.3 54 40-94 11-64 (82)
50 KOG0819|consensus 20.9 1.9E+02 0.004 23.2 4.2 27 61-87 233-262 (321)
51 PRK12537 RNA polymerase sigma 20.6 2.2E+02 0.0048 19.4 4.3 25 47-76 23-47 (182)
52 PRK15331 chaperone protein Sic 20.5 1.4E+02 0.0031 21.5 3.2 25 61-85 36-63 (165)
53 TIGR02396 diverge_rpsU rpsU-di 20.4 1E+02 0.0023 22.1 2.6 21 35-55 157-177 (184)
54 PF00036 EF-hand_1: EF hand; 20.4 1.3E+02 0.0027 15.0 2.2 27 45-71 2-28 (29)
55 PF07655 Secretin_N_2: Secreti 20.1 87 0.0019 20.1 1.9 15 40-54 70-84 (98)
No 1
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=99.03 E-value=4.7e-10 Score=91.12 Aligned_cols=56 Identities=41% Similarity=0.663 Sum_probs=52.8
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHhhhh
Q psy10549 42 WLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLETKV 97 (103)
Q Consensus 42 W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~~~~ 97 (103)
|+.|++||+.|+.+.....+||++|++||++|.+++|+.||+++++++.+|+..++
T Consensus 1 W~~l~~~i~~i~~~~~~~~~~~~lY~~vy~l~~~~~~~~LY~~l~~~i~~~~~~~~ 56 (588)
T PF00888_consen 1 WEILEEAIDQIFKKSISKLSYMELYTCVYNLCDNKYGEQLYDKLKEFISEYLKNII 56 (588)
T ss_dssp HHHHHHHHHHHHTT-GCCSHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHcCCCChhHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHH
Confidence 99999999999988889999999999999999999999999999999999998854
No 2
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.72 E-value=5.5e-08 Score=82.47 Aligned_cols=74 Identities=23% Similarity=0.313 Sum_probs=62.6
Q ss_pred CceeecCCCCCCChhHHHHHHHHHHHHHHHHHHhC---CCCCCHHHHHHHHHHhhccc----------------cHHHHH
Q psy10549 22 GHRTSRDHLMTMDEKYVQDIWLLLKNAIQEIQKKN---NSGLSFEELYRNAYTMVLHK----------------HGERLY 82 (103)
Q Consensus 22 ~kl~ik~~~~~~~~~~~e~~W~~L~~Ai~~I~~~~---~~~lsyeeLY~~VYnlC~~~----------------~g~~LY 82 (103)
.|+.+..+ ..+.++|+.+|+.++.||+.|+.+. ...++||++|+.+||+|++. .|+.||
T Consensus 6 ~ki~vp~~--~~~~~df~~~W~~i~~~I~~I~~~l~~~m~~l~~~evY~~IYn~c~n~tr~~~~~~~~~~~~~~~~s~li 83 (773)
T COG5647 6 IKIDVPRK--TLSEEDFESTWEFIERAIGQIFERLYDSMAILSLMEVYTKIYNYCTNKTRSLESDLRWKIDFIYLGSRLI 83 (773)
T ss_pred cccccCcc--CCchhhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhcccccchhcccchhHHHHHHHHHH
Confidence 45555442 5788999999999999999999653 46778999999999999887 789999
Q ss_pred HHHHHHHHHHHhhhh
Q psy10549 83 SGLKEVVTAHLETKV 97 (103)
Q Consensus 83 ~~lk~~i~~~l~~~~ 97 (103)
++|+.+.++++...-
T Consensus 84 ~~L~~~~k~~i~~~~ 98 (773)
T COG5647 84 QKLVDYAKNYIEEYN 98 (773)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999988765
No 3
>KOG2166|consensus
Probab=98.66 E-value=5.2e-08 Score=83.11 Aligned_cols=68 Identities=25% Similarity=0.330 Sum_probs=56.4
Q ss_pred CChhHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhccccH----HHHHHHHHHHHHHHHhhhhccC
Q psy10549 33 MDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHG----ERLYSGLKEVVTAHLETKVGVE 100 (103)
Q Consensus 33 ~~~~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~~~g----~~LY~~lk~~i~~~l~~~~~~~ 100 (103)
....+++++|..|..|++.+........+|+++|+++|++|++++| ++||+++++++.+|+.+.+.+.
T Consensus 12 ~~w~~~~~~~~~l~~~~~~~s~~~~~~~~~~~ly~t~~~~~~~k~~~~~~~~lY~~l~~~~~~yl~~~~~~~ 83 (725)
T KOG2166|consen 12 VGWSYIETGITKLKRIIEGLSEPAFEQYQFMYLYTTIYNMCLQKPPHDYSQQLYDKYREVIEEYLIQTVLPA 83 (725)
T ss_pred ccHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456777777777777775554445777899999999999999999 9999999999999999988765
No 4
>KOG2284|consensus
Probab=97.86 E-value=3.1e-05 Score=63.59 Aligned_cols=64 Identities=19% Similarity=0.433 Sum_probs=56.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHhhccc---cHHHHHHHHHHHHHHHHhhhhc
Q psy10549 35 EKYVQDIWLLLKNAIQEIQKKNN-SGLSFEELYRNAYTMVLHK---HGERLYSGLKEVVTAHLETKVG 98 (103)
Q Consensus 35 ~~~~e~~W~~L~~Ai~~I~~~~~-~~lsyeeLY~~VYnlC~~~---~g~~LY~~lk~~i~~~l~~~~~ 98 (103)
..+||++|..|...|..|.+-+. ....|-.-|..||++|..- .|+.||+.++.++++|+++.+.
T Consensus 8 vv~fd~~w~~l~~si~~ii~l~~i~~~~w~~~fsdvy~icvs~p~pl~erly~e~k~~i~~hvrq~~~ 75 (728)
T KOG2284|consen 8 VVEFDKVWVQLRPSIIDIINLRPITNVQWHHKFSDVYDICVSIPTPLSERLYNEVKACIQEHVRQKRQ 75 (728)
T ss_pred eeeHHHHHHHHHHHHHHHHhccchhccccccchhhHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHhh
Confidence 47899999999999999988775 5678999999999999664 8999999999999999986544
No 5
>KOG2166|consensus
Probab=90.77 E-value=0.18 Score=43.79 Aligned_cols=42 Identities=21% Similarity=0.283 Sum_probs=37.1
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHhhccc
Q psy10549 34 DEKYVQDIWLLLKNAIQEIQKKNNSGLS--FEELYRNAYTMVLHK 76 (103)
Q Consensus 34 ~~~~~e~~W~~L~~Ai~~I~~~~~~~ls--yeeLY~~VYnlC~~~ 76 (103)
.+++++..|..++.+++.++.... ..+ +|++|+.+|.+|+.-
T Consensus 6 ~~~~~~~~w~~~~~~~~~l~~~~~-~~s~~~~~~~~~~~ly~t~~ 49 (725)
T KOG2166|consen 6 KEIDLEVGWSYIETGITKLKRIIE-GLSEPAFEQYQFMYLYTTIY 49 (725)
T ss_pred cccchhccHHHHHHHHHHHHHHHH-hhccccccHHHHHHHHHHHH
Confidence 468999999999999999999875 555 999999999999873
No 6
>KOG2285|consensus
Probab=89.23 E-value=0.56 Score=39.51 Aligned_cols=62 Identities=8% Similarity=0.270 Sum_probs=51.3
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHhhccc--cHHHHHHHHHHHHHHHHhh
Q psy10549 34 DEKYVQDIWLLLKNAIQEIQKKNN-SGLSFEELYRNAYTMVLHK--HGERLYSGLKEVVTAHLET 95 (103)
Q Consensus 34 ~~~~~e~~W~~L~~Ai~~I~~~~~-~~lsyeeLY~~VYnlC~~~--~g~~LY~~lk~~i~~~l~~ 95 (103)
+..-||+.|.+-+.-+-++....+ .+-.|++||-+||..|.-. -..++|+.|+..|-+++.+
T Consensus 9 ~r~qFee~W~~~rpIVlkLLrQ~sVt~~~WqDLF~~Vh~vclWddkGpaKI~d~L~~dI~efi~q 73 (777)
T KOG2285|consen 9 DRDQFEEEWSKARPIVLKLLRQKSVTPAAWQDLFYHVHKVCLWDDKGPAKIRDILTRDINEFIHQ 73 (777)
T ss_pred chhhhhhhccccchHHHHHHhhccCCHHHHHHHHhhheeeeeecCCCcHHHHHHHHHHHHHHHHH
Confidence 456899999999999998888764 4556999999999999654 5578999999988888764
No 7
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=87.73 E-value=4.2 Score=25.88 Aligned_cols=56 Identities=18% Similarity=0.252 Sum_probs=40.8
Q ss_pred HHHHH-HHHHHHHHHHHHh-CCCCCCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHH
Q psy10549 38 VQDIW-LLLKNAIQEIQKK-NNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHL 93 (103)
Q Consensus 38 ~e~~W-~~L~~Ai~~I~~~-~~~~lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l 93 (103)
.+.+| +.++..+..+.+. ....++|++|+..|--.+.....+.+...+...|..+|
T Consensus 28 ~e~GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~Ir~~L 85 (86)
T PF10163_consen 28 IECGWRDEVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQRIRAFL 85 (86)
T ss_dssp HHTTHHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHH
T ss_pred HHCChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHh
Confidence 46678 5666666666666 45789999999999999888877777766666666655
No 8
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=82.43 E-value=0.66 Score=31.69 Aligned_cols=45 Identities=18% Similarity=0.299 Sum_probs=31.6
Q ss_pred CCCCceeecCCCCCCChhHHHHHHHHHHHHHHHHHHhCCCCCCHHHHH
Q psy10549 19 KSNGHRTSRDHLMTMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELY 66 (103)
Q Consensus 19 ~~~~kl~ik~~~~~~~~~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY 66 (103)
+|-+||.++.- .-..++++.|+.|.++|+.|+++....-.||.|=
T Consensus 32 kGl~Kl~vn~~---~l~~dL~~nWeVlaEpIQTvmRr~g~~~pYE~LK 76 (115)
T PF08328_consen 32 KGLGKLEVNEE---RLAEDLDENWEVLAEPIQTVMRRYGIPNPYEKLK 76 (115)
T ss_dssp HHHHTEEE-HH---HHHHHHCT-GGGGHHHHHHHHHHTT-SSHHHHHH
T ss_pred HHHhcccCCHH---HHHHHHHHCHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 45667777751 2257899999999999999999876666666653
No 9
>PF08539 HbrB: HbrB-like; InterPro: IPR013745 HbrB is involved in hyphal growth and polarity [].
Probab=78.55 E-value=7.3 Score=27.73 Aligned_cols=56 Identities=16% Similarity=0.234 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHH---hhccccH-HHHHHHHHHHHHH
Q psy10549 36 KYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYT---MVLHKHG-ERLYSGLKEVVTA 91 (103)
Q Consensus 36 ~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYn---lC~~~~g-~~LY~~lk~~i~~ 91 (103)
...++.|..+..++-.+|+++...++-|+|=+.|-- .|.++.. ..+-+.+++.+..
T Consensus 3 ~~~~~~W~~~~~~vl~lF~g~~l~~~iEdlN~lv~~~i~~~~~~~~~~~~~~dl~elL~t 62 (158)
T PF08539_consen 3 MSSDDAWNSLCAKVLPLFQGERLRLPIEDLNELVRFHIKLCIQSFPPSYFLEDLEELLTT 62 (158)
T ss_pred CchhhhHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHH
Confidence 456789999999999999999877888888777754 4555542 2233444444443
No 10
>PF14164 YqzH: YqzH-like protein
Probab=76.03 E-value=8.7 Score=23.65 Aligned_cols=36 Identities=19% Similarity=0.211 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhc
Q psy10549 39 QDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVL 74 (103)
Q Consensus 39 e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~ 74 (103)
+..|+.|...|....+.+...-=|+-.+-.||.+.+
T Consensus 28 ~~E~~~L~~~i~~~~~~~~~~Dl~eiVeDvVY~yiT 63 (64)
T PF14164_consen 28 DEEWEELCKHIQERKNEEPDEDLHEIVEDVVYDYIT 63 (64)
T ss_pred HHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhc
Confidence 456899999988888777543225555555555543
No 11
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=74.23 E-value=13 Score=23.96 Aligned_cols=38 Identities=21% Similarity=0.338 Sum_probs=30.5
Q ss_pred CCCCCCChhHHHHHH----------HHHHHHHHHHHHh-CCCCCCHHHH
Q psy10549 28 DHLMTMDEKYVQDIW----------LLLKNAIQEIQKK-NNSGLSFEEL 65 (103)
Q Consensus 28 ~~~~~~~~~~~e~~W----------~~L~~Ai~~I~~~-~~~~lsyeeL 65 (103)
+.+++..+..+...| +.+.+++.+++.- +.++++|++|
T Consensus 23 ~P~~~~HPl~~Q~~WLskeRgG~IP~~V~~sl~kL~~La~~N~v~feeL 71 (82)
T PF11020_consen 23 EPKPDHHPLQFQATWLSKERGGQIPEKVMDSLSKLYKLAKENNVSFEEL 71 (82)
T ss_pred CCCCCCCchHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHcCCCHHHH
Confidence 466777789999999 6677888888875 3478999997
No 12
>PTZ00015 histone H4; Provisional
Probab=51.07 E-value=42 Score=22.35 Aligned_cols=43 Identities=21% Similarity=0.254 Sum_probs=31.1
Q ss_pred CCCCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHhhhhccC
Q psy10549 58 SGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLETKVGVE 100 (103)
Q Consensus 58 ~~lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~~~~~~~ 100 (103)
.+++--.+.|.+-+-=..+.+++.|+.+...++.++.+++..+
T Consensus 29 ~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rda 71 (102)
T PTZ00015 29 RGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDS 71 (102)
T ss_pred cCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444445555555555677889999999999999998887654
No 13
>smart00417 H4 Histone H4.
Probab=42.61 E-value=83 Score=19.67 Aligned_cols=43 Identities=19% Similarity=0.224 Sum_probs=31.0
Q ss_pred CCCCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHhhhhccC
Q psy10549 58 SGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLETKVGVE 100 (103)
Q Consensus 58 ~~lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~~~~~~~ 100 (103)
.+++---+.|.+=+--..+.+++.|+.+...+++++..+...+
T Consensus 12 ~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rda 54 (74)
T smart00417 12 QGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDA 54 (74)
T ss_pred cCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455455555555555667889999999999999988876654
No 14
>PF03556 Cullin_binding: Cullin binding; InterPro: IPR005176 The eukaryotic defective in cullin neddylation (DCN) protein family, may contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes. These multi-protein complexes are required for polyubiquitination and subsequent degradation of target proteins by the 26S proteasome []. Proteins in the DCN family include: Yeast DCN1. Vertebrate DCN1-like protein 1. Vertebrate DCN1-like protein 2. Vertebrate DCN1-like protein 4. This entry represents a domain found within DCN family proteins. Its function is unknown but it has been suggested that it has the features of a basic helix-loop-helix leucine zipper (bHLH-ZIP) domain [].It is often found in association with a UBA-like domain (IPR009060 from INTERPRO).; PDB: 3TDI_A 2IS9_A 3O6B_E 3O2P_A 3BQ3_A 3TDZ_A 3TDU_B.
Probab=40.77 E-value=26 Score=23.53 Aligned_cols=34 Identities=21% Similarity=0.348 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHhCC-CCCCHHHHHHHHHHhhccc
Q psy10549 43 LLLKNAIQEIQKKNN-SGLSFEELYRNAYTMVLHK 76 (103)
Q Consensus 43 ~~L~~Ai~~I~~~~~-~~lsyeeLY~~VYnlC~~~ 76 (103)
+.|+..|..+-.... ..-.|.++|+-+|++|...
T Consensus 2 ~~lk~~l~~l~~~l~~d~~~F~~~Y~f~F~~~~~~ 36 (117)
T PF03556_consen 2 DKLKQKLPELRKELRSDPEYFKKFYRFTFDFAREE 36 (117)
T ss_dssp HHHHHCHHHHHHHCCHSHHHHHHHHHHHHHHHS-T
T ss_pred HHHHHHHHHHHHHHccCHHHHHHHHHHHHHHhCCc
Confidence 356777777777764 4456999999999999855
No 15
>KOG1086|consensus
Probab=40.12 E-value=79 Score=26.76 Aligned_cols=52 Identities=13% Similarity=0.277 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCC--------------CCHHHHHH-HHHHhhccccHHHHHHHHHHH
Q psy10549 37 YVQDIWLLLKNAIQEIQKKNNSG--------------LSFEELYR-NAYTMVLHKHGERLYSGLKEV 88 (103)
Q Consensus 37 ~~e~~W~~L~~Ai~~I~~~~~~~--------------lsyeeLY~-~VYnlC~~~~g~~LY~~lk~~ 88 (103)
.-|+-|+-|..-++.|+..-.+. ..+|.||. +|-.+|.+.-|++..+++-.|
T Consensus 21 ~~eedw~ai~~fceqinkdp~gp~lAv~LlaHKiqSPqe~EAl~altvLe~cmkncGekfH~evgkf 87 (594)
T KOG1086|consen 21 NDEEDWKAIDGFCEQINKDPEGPLLAVRLLAHKIQSPQEWEALQALTVLEYCMKNCGEKFHEEVGKF 87 (594)
T ss_pred chHHHHHHHHHHHHHHhcCCCCchhHHHHHHhhcCChhHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 36788999999888888764322 24999998 788999999999988887665
No 16
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=39.59 E-value=73 Score=20.41 Aligned_cols=43 Identities=16% Similarity=0.227 Sum_probs=31.2
Q ss_pred CCCCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHhhhhccC
Q psy10549 58 SGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLETKVGVE 100 (103)
Q Consensus 58 ~~lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~~~~~~~ 100 (103)
.+++---+.|.+-+--..+.+.+.|+.+.+.++.++.++...+
T Consensus 12 ~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~da 54 (85)
T cd00076 12 KGITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDA 54 (85)
T ss_pred ccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555556665555667889999999999999988877654
No 17
>PF08066 PMC2NT: PMC2NT (NUC016) domain; InterPro: IPR012588 Exosomes are nano-compartments that function in the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA) [, ]. Exosomes occur in both archaea and eukaryotes, and have a similar overall structure to each other and to bacterial/organelle PNPases (polynucleotide phosphorylases; 2.7.7.8 from EC) [], consisting of a barrel structure composed of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. There are two types of exosomes in eukaryotes, cytoplasmic exosomes that are responsible for 3'-5' exoribonuclease degradation of mRNAs, and nuclear exosomes that degrade pre-mRNAs (such as nonsense transcripts) and degrade rRNAs, snRNAs and snoRNAs. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. There are several accessory proteins that help degrade, unwind or polyadenylate RNA substrate before they enter the exosome. This entry represents the N-terminal domain of Rrp6 (exosome component 10 in humans), a nuclear exosome accessory factor that interacts with the bottom of the hexameric PH-ring opposite the cap. Rrp6 functions as a hydrolytic exonuclease, and is homologous to RNase-D in Escherichia coli. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0006396 RNA processing, 0000176 nuclear exosome (RNase complex)
Probab=39.21 E-value=39 Score=21.44 Aligned_cols=23 Identities=17% Similarity=0.280 Sum_probs=20.2
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhC
Q psy10549 34 DEKYVQDIWLLLKNAIQEIQKKN 56 (103)
Q Consensus 34 ~~~~~e~~W~~L~~Ai~~I~~~~ 56 (103)
+..+.++.|+.+-++++.|+++-
T Consensus 59 ~~~d~d~~~~~vvd~~D~LlEk~ 81 (91)
T PF08066_consen 59 DVDDVDERWDSVVDVNDSLLEKA 81 (91)
T ss_pred ccccHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999873
No 18
>PF13202 EF-hand_5: EF hand; PDB: 3DD4_A 2Q4U_A 2BE4_A 1UHJ_B 1UHI_A 1UHH_B 1EJ3_B 1UHK_A 2ZFD_A 1UHN_A ....
Probab=38.57 E-value=34 Score=16.55 Aligned_cols=24 Identities=38% Similarity=0.595 Sum_probs=15.5
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHH
Q psy10549 45 LKNAIQEIQKKNNSGLSFEELYRN 68 (103)
Q Consensus 45 L~~Ai~~I~~~~~~~lsyeeLY~~ 68 (103)
|+.++..+=....+.+|++|+.+.
T Consensus 1 l~~~F~~~D~d~DG~is~~E~~~~ 24 (25)
T PF13202_consen 1 LKDAFQQFDTDGDGKISFEEFQRL 24 (25)
T ss_dssp HHHHHHHHTTTSSSEEEHHHHHHH
T ss_pred CHHHHHHHcCCCCCcCCHHHHHHH
Confidence 344555555556677888888764
No 19
>PF08511 COQ9: COQ9; InterPro: IPR013718 COQ9 is an enzyme that is required for the biosynthesis of coenzyme Q []. It may either catalyse a reaction in the coenzyme Q biosynthetic pathway or have a regulatory role. ; PDB: 3NI7_B.
Probab=36.16 E-value=36 Score=21.50 Aligned_cols=21 Identities=19% Similarity=0.474 Sum_probs=16.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHh
Q psy10549 35 EKYVQDIWLLLKNAIQEIQKK 55 (103)
Q Consensus 35 ~~~~e~~W~~L~~Ai~~I~~~ 55 (103)
..+++++|.+|+.-|+.+.+-
T Consensus 54 S~~~~~T~~Fl~rri~~v~~~ 74 (79)
T PF08511_consen 54 SPDFEDTWAFLDRRIDDVMQF 74 (79)
T ss_dssp SGGGHHHHHHHHHHHHHH---
T ss_pred CCCHHHHHHHHHHHHHhhhcc
Confidence 468899999999999988653
No 20
>PF03387 Herpes_UL46: Herpesvirus UL46 protein; InterPro: IPR005051 The UL46 protein (VP11/12) is produced in the late phase of Herpes virus infection in a manner highly dependent on viral DNA synthesis, and is mainly distributed at the edge of the nucleus in the cytoplasm. It is a tegument phosphoprotein reported to modulate the activity of UL48 (anti-TNF) protein.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=35.92 E-value=57 Score=27.13 Aligned_cols=35 Identities=17% Similarity=0.013 Sum_probs=29.0
Q ss_pred CCceeecCCCCCCChhHHHHHHHHHHHHHHHHHHh
Q psy10549 21 NGHRTSRDHLMTMDEKYVQDIWLLLKNAIQEIQKK 55 (103)
Q Consensus 21 ~~kl~ik~~~~~~~~~~~e~~W~~L~~Ai~~I~~~ 55 (103)
.|.|+=+||+-..+...+...|..|++|++.|.+-
T Consensus 147 ~k~L~k~PFk~~~~n~~Y~~~~~~Lr~a~~~iqkY 181 (444)
T PF03387_consen 147 RKPLSKAPFKHKKDNAAYLACVAELRDAFHFIQKY 181 (444)
T ss_pred CCccccCcccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 45677778986677788899999999999999873
No 21
>PRK06922 hypothetical protein; Provisional
Probab=33.77 E-value=1.1e+02 Score=26.94 Aligned_cols=64 Identities=20% Similarity=0.307 Sum_probs=47.3
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHhhh
Q psy10549 31 MTMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLETK 96 (103)
Q Consensus 31 ~~~~~~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~~~ 96 (103)
+.+.+-+||+-|..+--+-+.|-......+|||-|-...|-=--...--.+|. |..|+.||.+.
T Consensus 258 ~a~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ 321 (677)
T PRK06922 258 PSMHALSFEDIWTVFVMLKNEIGTRKVQHIHFEKLMQQLHYDFKGEKKDNVYR--KRVIEKYLREY 321 (677)
T ss_pred hhhhhcCHHHHHHHHHHHHHhcCccccceeehHHHHHHHHHhhcCcchhhHHH--HHHHHHHHHHh
Confidence 34556688999999988888877777788899999888876555556667886 45566666654
No 22
>PLN00035 histone H4; Provisional
Probab=33.00 E-value=1.1e+02 Score=20.41 Aligned_cols=41 Identities=15% Similarity=0.146 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHhhhhccC
Q psy10549 60 LSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLETKVGVE 100 (103)
Q Consensus 60 lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~~~~~~~ 100 (103)
++---+.|.+-+-=..+.+++.|+.+.+.++.++..++...
T Consensus 30 ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~da 70 (103)
T PLN00035 30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDA 70 (103)
T ss_pred CCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555556665555677889999999999999988877654
No 23
>PF12583 TPPII_N: Tripeptidyl peptidase II N terminal; InterPro: IPR022232 This entry represents a region of approximately 190 amino acids in length and is found in association with PF00082 from PFAM. The members are serine peptidases belonging to MEROPS peptidase family S8A, tripeptidyl peptidase II (TPPII), clan SB. They are a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. ; PDB: 3LXU_X.
Probab=32.43 E-value=75 Score=22.38 Aligned_cols=47 Identities=23% Similarity=0.290 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHhhh
Q psy10549 37 YVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLETK 96 (103)
Q Consensus 37 ~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~~~ 96 (103)
.--..|+...++++.+....-..+..+ +++.||..|++..-.||..+
T Consensus 67 k~ktk~DeY~EaLRDfq~~~iaKle~e-------------~Ae~vY~el~~~~P~HLpaH 113 (139)
T PF12583_consen 67 KDKTKWDEYSEALRDFQCSWIAKLEPE-------------NAEQVYEELLEAHPDHLPAH 113 (139)
T ss_dssp -----HHHHHHHHHHHHHHHHTTS-HH-------------HHHHHHHHHHHH-TT-THHH
T ss_pred cccccHHHHHHHHHHHHHHHHHhhCHH-------------HHHHHHHHHHHHCcchHHHH
Confidence 345678888888887766643444332 45888888888877777644
No 24
>PHA03195 tegument protein VP11/12; Provisional
Probab=31.34 E-value=76 Score=27.76 Aligned_cols=35 Identities=11% Similarity=-0.031 Sum_probs=28.3
Q ss_pred CCceeecCCCCCCChhHHHHHHHHHHHHHHHHHHh
Q psy10549 21 NGHRTSRDHLMTMDEKYVQDIWLLLKNAIQEIQKK 55 (103)
Q Consensus 21 ~~kl~ik~~~~~~~~~~~e~~W~~L~~Ai~~I~~~ 55 (103)
.|.|+=+|||-.-+...+...|..|++|++.|.+-
T Consensus 154 ~K~LsK~PFK~k~~Na~Y~a~~aeLRda~~~IQkY 188 (746)
T PHA03195 154 KKRLSKNPFKHKGPNVGYKSNLEDLRSAFTKIEKY 188 (746)
T ss_pred cCccccCccccccchHHHHHHHHHHHHHHHHHHHH
Confidence 46666668996666678889999999999999873
No 25
>PF00557 Peptidase_M24: Metallopeptidase family M24 This Prosite entry corresponds to sub-family M24B This Prosite entry corresponds to sub-families M24A and M24C; InterPro: IPR000994 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry contains proteins that belong to MEROPS peptidase family M24 (clan MG), which share a common structural-fold, the "pita-bread" fold. The fold contains both alpha helices and an anti-parallel beta sheet within two structurally similar domains that are thought to be derived from an ancient gene duplication. The active site, where conserved, is located between the two domains. The fold is common to methionine aminopeptidase (3.4.11.18 from EC), aminopeptidase P (3.4.11.9 from EC), prolidase (3.4.13.9 from EC), agropine synthase and creatinase (3.5.3.3 from EC). Though many of these peptidases require a divalent cation, creatinase is not a metal-dependent enzyme [, , ]. The entry also contains proteins that have lost catalytic activity, for example Spt16, which is a component of the FACT complex. The crystal structure of the N-terminal domain of Spt16, determined to 2.1A, reveals an aminopeptidase P fold whose enzymatic activity has been lost. This fold binds directly to histones H3-H4 through a interaction with their globular core domains, as well as with their N-terminal tails []. The FACT complex is a stable heterodimer in Saccharomyces cerevisiae (Baker's yeast) comprising Spt16p (P32558 from SWISSPROT, IPR013953 from INTERPRO) and Pob3p (Q04636 from SWISSPROT, IPR000969 from INTERPRO). The complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin []; it also facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, , ]. ; GO: 0009987 cellular process; PDB: 4A6V_B 4A6W_A 3CTZ_A 3IG4_B 2B3H_A 2NQ6_A 2NQ7_A 2GZ5_A 2G6P_A 2B3L_A ....
Probab=29.91 E-value=1.9e+02 Score=20.04 Aligned_cols=42 Identities=7% Similarity=0.133 Sum_probs=33.8
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhcc
Q psy10549 34 DEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLH 75 (103)
Q Consensus 34 ~~~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~ 75 (103)
++....+.|+.+..+.+.++..-..+.+..++|..+.+.+..
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~pG~~~~~v~~~~~~~~~~ 141 (207)
T PF00557_consen 100 PTPEQRRAYEAAREALEAAIEALRPGVTGSDVYEAVREVLEE 141 (207)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHH-STTSBHHHHHHHHHHHHHH
T ss_pred ecccccchhhhhHHHHHhHhhhcccccccchhhHHHHHHHHh
Confidence 556788899999999999998877888899988888876643
No 26
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=28.13 E-value=1.4e+02 Score=17.75 Aligned_cols=35 Identities=23% Similarity=0.285 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhccccH
Q psy10549 43 LLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHG 78 (103)
Q Consensus 43 ~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~~~g 78 (103)
..++.||-.|+..+ ..+++.+|...|...+.+.+.
T Consensus 7 ~~I~AaIVrimK~~-k~~~~~~L~~~v~~~l~~~f~ 41 (68)
T PF10557_consen 7 YQIDAAIVRIMKQE-KKLSHDELINEVIEELKKRFP 41 (68)
T ss_dssp HHHHHHHHHHHHHS-SEEEHHHHHHHHHHHTTTTS-
T ss_pred hhhhhheehhhhhc-CceeHHHHHHHHHHHhcCCcC
Confidence 45889999999987 668999999999999976544
No 27
>cd01066 APP_MetAP A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation.
Probab=28.05 E-value=1.9e+02 Score=19.43 Aligned_cols=42 Identities=12% Similarity=0.166 Sum_probs=34.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhccc
Q psy10549 35 EKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHK 76 (103)
Q Consensus 35 ~~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~~ 76 (103)
+....+.|+.+..+++.+...-..+.++.++|..+.++....
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~i~pG~~~~ei~~~~~~~~~~~ 142 (207)
T cd01066 101 SDEQRELYEAVREAQEAALAALRPGVTAEEVDAAAREVLEEH 142 (207)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHc
Confidence 456778889999999888888777889999999998877654
No 28
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=26.28 E-value=87 Score=18.58 Aligned_cols=29 Identities=17% Similarity=0.329 Sum_probs=20.6
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHHhh
Q psy10549 45 LKNAIQEIQKKNNSGLSFEELYRNAYTMV 73 (103)
Q Consensus 45 L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC 73 (103)
+.+|...|++....+++|.+++..+-+.=
T Consensus 3 ~~eaa~~vL~~~~~pm~~~eI~~~i~~~~ 31 (72)
T PF05066_consen 3 FKEAAYEVLEEAGRPMTFKEIWEEIQERG 31 (72)
T ss_dssp HHHHHHHHHHHH-S-EEHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHHHhC
Confidence 34566677777778999999999888653
No 29
>PF10808 DUF2542: Protein of unknown function (DUF2542) ; InterPro: IPR020155 This entry represents transmembrane proteins with no known function.; GO: 0016021 integral to membrane
Probab=25.62 E-value=1.1e+02 Score=19.57 Aligned_cols=33 Identities=18% Similarity=0.340 Sum_probs=23.0
Q ss_pred HHHHHHHHHHH-HHHHHHHhCCCCC------------CHHHHHHHH
Q psy10549 37 YVQDIWLLLKN-AIQEIQKKNNSGL------------SFEELYRNA 69 (103)
Q Consensus 37 ~~e~~W~~L~~-Ai~~I~~~~~~~l------------syeeLY~~V 69 (103)
.|-+.|+-+++ |+|++.++...++ ||+-+|-.+
T Consensus 19 ~fREa~KgwRsGaVdK~vkna~ePvyi~R~~~P~~ywsYi~~Y~G~ 64 (79)
T PF10808_consen 19 CFREAWKGWRSGAVDKIVKNAQEPVYIYRAKNPGQYWSYIFAYFGC 64 (79)
T ss_pred HHHHHHHHHhhcchHHHhcCCCCcEEEEecCCcchhHHHHHHHHHH
Confidence 57889999995 4888887643332 577777643
No 30
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=25.28 E-value=2.2e+02 Score=19.70 Aligned_cols=20 Identities=10% Similarity=0.054 Sum_probs=8.0
Q ss_pred HHHHHHHhhccc-cHHHHHHH
Q psy10549 65 LYRNAYTMVLHK-HGERLYSG 84 (103)
Q Consensus 65 LY~~VYnlC~~~-~g~~LY~~ 84 (103)
+|+.++.++.+. .++++++.
T Consensus 43 l~~~~~~~~~~~~dAeDivQe 63 (194)
T PRK09646 43 VYGLVRRVLRDPGYSEETTQE 63 (194)
T ss_pred HHHHHHHHhCCHHHHHHHHHH
Confidence 344444444332 34444443
No 31
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=25.15 E-value=1.8e+02 Score=20.35 Aligned_cols=49 Identities=8% Similarity=0.044 Sum_probs=30.7
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHhh
Q psy10549 47 NAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLET 95 (103)
Q Consensus 47 ~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~~ 95 (103)
.+|-.++......+|-++||..+-..-.+--=..+|+-|..+.+..|..
T Consensus 29 ~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~ 77 (169)
T PRK11639 29 LEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVH 77 (169)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEE
Confidence 3444555555567788888877766544333466787777777666543
No 32
>cd01092 APP-like Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline.
Probab=25.10 E-value=2.4e+02 Score=19.46 Aligned_cols=41 Identities=17% Similarity=0.250 Sum_probs=33.6
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhc
Q psy10549 34 DEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVL 74 (103)
Q Consensus 34 ~~~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~ 74 (103)
++....+.|+...++.+.+......+.++.++|..+.+...
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~pG~~~~di~~~~~~~~~ 141 (208)
T cd01092 101 PSDELKEIYEIVLEAQQAAIKAVKPGVTAKEVDKAARDVIE 141 (208)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHH
Confidence 35677789999999999998887788899999988876543
No 33
>PF05814 DUF843: Baculovirus protein of unknown function (DUF843); InterPro: IPR008561 This family consists of several unidentified baculovirus proteins of around 85 residues long with no known function.
Probab=24.92 E-value=74 Score=20.51 Aligned_cols=16 Identities=38% Similarity=0.376 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHhCCC
Q psy10549 43 LLLKNAIQEIQKKNNS 58 (103)
Q Consensus 43 ~~L~~Ai~~I~~~~~~ 58 (103)
..|++|+|+|.+++++
T Consensus 67 ~~ln~afDAiLNKN~S 82 (83)
T PF05814_consen 67 RDLNDAFDAILNKNTS 82 (83)
T ss_pred HHHHHHHHHHHhccCC
Confidence 5689999999999864
No 34
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=24.69 E-value=1.7e+02 Score=17.65 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=16.4
Q ss_pred CHHHHHHHHHHhhcccc-HHHHHHHHHHH
Q psy10549 61 SFEELYRNAYTMVLHKH-GERLYSGLKEV 88 (103)
Q Consensus 61 syeeLY~~VYnlC~~~~-g~~LY~~lk~~ 88 (103)
+|.+.+..+|++...++ +.++...+.+.
T Consensus 19 ~~~~~~~~~~~l~~~G~s~~~Il~~l~~~ 47 (89)
T PF08542_consen 19 DFKEARKKLYELLVEGYSASDILKQLHEV 47 (89)
T ss_dssp CHHHHHHHHHHHHHTT--HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 57778888888777763 23344433333
No 35
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=24.60 E-value=55 Score=19.65 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=13.5
Q ss_pred cHHHHHHHHHHHHHHH
Q psy10549 77 HGERLYSGLKEVVTAH 92 (103)
Q Consensus 77 ~g~~LY~~lk~~i~~~ 92 (103)
..+.||+.++.||+.|
T Consensus 6 iPe~L~~~m~~fie~h 21 (57)
T PF10929_consen 6 IPEDLHQAMKDFIETH 21 (57)
T ss_pred ccHHHHHHHHHHHHcC
Confidence 3578999999999887
No 36
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=24.07 E-value=2.6e+02 Score=19.50 Aligned_cols=14 Identities=14% Similarity=0.370 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHh
Q psy10549 81 LYSGLKEVVTAHLE 94 (103)
Q Consensus 81 LY~~lk~~i~~~l~ 94 (103)
||.-.+..+-+|+.
T Consensus 65 L~~Ia~n~~~d~~R 78 (187)
T PRK12516 65 LFTILRNEFYSQMR 78 (187)
T ss_pred HHHHHHHHHHHHHH
Confidence 44444444444444
No 37
>PHA03193 tegument protein VP11/12; Provisional
Probab=24.02 E-value=1.3e+02 Score=25.79 Aligned_cols=36 Identities=19% Similarity=0.328 Sum_probs=28.5
Q ss_pred CCCceeecCCCCCCChhHHHHHHHHHHHHHHHHHHh
Q psy10549 20 SNGHRTSRDHLMTMDEKYVQDIWLLLKNAIQEIQKK 55 (103)
Q Consensus 20 ~~~kl~ik~~~~~~~~~~~e~~W~~L~~Ai~~I~~~ 55 (103)
..|.|+=+|||-..+...+...|..|+++++.|.+-
T Consensus 171 ~~K~Lsk~PFK~k~~Na~Y~~~~aeLRda~~~IQkY 206 (594)
T PHA03193 171 NRNALTKKPFQLAKDNALFLKCWAEIRDALEFIQKY 206 (594)
T ss_pred cCCccccCCcccccchHHHHHHHHHHHHHHHHHHHH
Confidence 355566667986666678889999999999999873
No 38
>PF07034 ORC3_N: Origin recognition complex (ORC) subunit 3 N-terminus; InterPro: IPR020795 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex
Probab=23.80 E-value=1.3e+02 Score=23.41 Aligned_cols=37 Identities=30% Similarity=0.425 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhh
Q psy10549 36 KYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMV 73 (103)
Q Consensus 36 ~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC 73 (103)
.-++..|+.++..|+.|++..+..+ |.+|-+-|-+-.
T Consensus 33 ~~y~~~W~~~~~~Iq~il~~~n~~~-f~~l~~Fi~~~~ 69 (330)
T PF07034_consen 33 EAYQKLWSKIESRIQEILRELNSKL-FDDLVDFIRNSH 69 (330)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhc
Confidence 3589999999999999999863332 555555444443
No 39
>PF07340 Herpes_IE1: Cytomegalovirus IE1 protein; InterPro: IPR010855 Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present []. The IE1 protein from cytomegalovirus is also known as UL123.; GO: 0050792 regulation of viral reproduction, 0042025 host cell nucleus
Probab=23.52 E-value=4.1e+02 Score=21.84 Aligned_cols=38 Identities=21% Similarity=0.098 Sum_probs=23.0
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhh
Q psy10549 36 KYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMV 73 (103)
Q Consensus 36 ~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC 73 (103)
..|++.|.-+++||+.+-.-...-..---+.+++|++|
T Consensus 118 ~~F~~i~~~l~n~~~lL~k~~epf~dmK~I~~t~~~~~ 155 (392)
T PF07340_consen 118 GKFNDIQGGLQNAIDLLNKVMEPFEDMKCILQTMNDMY 155 (392)
T ss_pred HHHHHHHHHHHHHHHHHHhhhccccccccHHHHHHHHc
Confidence 46899999999999866554321112223455555555
No 40
>KOG3533|consensus
Probab=22.50 E-value=4.4e+02 Score=26.10 Aligned_cols=80 Identities=15% Similarity=0.199 Sum_probs=50.4
Q ss_pred ccCCCCCCCceeecCCCCCCChhHHHHHHHHHHHHHHHHHH---hCC----CCCC-----------HHHHHHHHHHhhcc
Q psy10549 14 KSSLVKSNGHRTSRDHLMTMDEKYVQDIWLLLKNAIQEIQK---KNN----SGLS-----------FEELYRNAYTMVLH 75 (103)
Q Consensus 14 ~~~~~~~~~kl~ik~~~~~~~~~~~e~~W~~L~~Ai~~I~~---~~~----~~ls-----------yeeLY~~VYnlC~~ 75 (103)
.+++.+|+..+.|--++|+.+....-..=++|.+-+.-+.. ... .-+. |..++|.+|.+ -
T Consensus 505 t~~~nn~q~vL~i~~~kPnRdRQKLmREQniLkQvF~iLkaPF~~~t~g~Gp~lrleeLsDqrnap~k~mfrLCYrv--L 582 (2706)
T KOG3533|consen 505 TNSSNNGQDVLKISDFKPNRDRQKLLREQNILKQVFLLLKAPFLPRTTGLGPLLRLEELSDQRNAPFKTMFRLCYRV--L 582 (2706)
T ss_pred ccCCcCCCcceeeeccCCchHHHHHHHHHHHHHHHHHHhcCcCccccCCCCceeeHHhhcCccccHHHHHHHHHHHH--H
Confidence 46677899999998888888766655555555554432221 111 1112 55555555543 3
Q ss_pred ccHHHHHHHHHHHHHHHHhh
Q psy10549 76 KHGERLYSGLKEVVTAHLET 95 (103)
Q Consensus 76 ~~g~~LY~~lk~~i~~~l~~ 95 (103)
+++++=|.+=++||.++...
T Consensus 583 r~SQqdYRKNQEyiAk~Fg~ 602 (2706)
T KOG3533|consen 583 RHSQQDYRKNQEYIAKKFGE 602 (2706)
T ss_pred HHhHHHHhhhHHHHHHHHHH
Confidence 47888899999999988653
No 41
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=22.21 E-value=1.9e+02 Score=17.30 Aligned_cols=38 Identities=16% Similarity=0.062 Sum_probs=27.0
Q ss_pred HHHHHHHHHhhccccHHHHHHHHHHHHHHHHhhhhccC
Q psy10549 63 EELYRNAYTMVLHKHGERLYSGLKEVVTAHLETKVGVE 100 (103)
Q Consensus 63 eeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~~~~~~~ 100 (103)
..+.+.+-+.-..+.+++.|..|.+.++.++.++.++.
T Consensus 6 ~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A 43 (65)
T smart00803 6 ETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEA 43 (65)
T ss_pred HHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555566788888888888888888877654
No 42
>PF03613 EIID-AGA: PTS system mannose/fructose/sorbose family IID component; InterPro: IPR004704 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IID subunits of this family of PTS transporters.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane
Probab=22.05 E-value=3.5e+02 Score=20.75 Aligned_cols=37 Identities=22% Similarity=0.431 Sum_probs=31.1
Q ss_pred CCCCHHHHHHHHHHhhccccHHHHH---HHHHHHHHHHHh
Q psy10549 58 SGLSFEELYRNAYTMVLHKHGERLY---SGLKEVVTAHLE 94 (103)
Q Consensus 58 ~~lsyeeLY~~VYnlC~~~~g~~LY---~~lk~~i~~~l~ 94 (103)
...+||.+-..-|-++.-+--++|| +.+++.+++|++
T Consensus 20 ~~~nyErmq~~gf~~~m~P~lkklY~~~e~~~~al~rh~~ 59 (264)
T PF03613_consen 20 ASWNYERMQGLGFAYSMLPALKKLYKDKEELKEALKRHME 59 (264)
T ss_pred CCCCHHHHHhHhHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 6778999999999999999899999 467777888864
No 43
>PF11123 DNA_Packaging_2: DNA packaging protein ; InterPro: IPR024345 This entry represents Gp18 (gene 18 product), also known as DNA maturase A, from T7-like bacteriophages. In Bacteriophage T3, this protein is required for DNA packaging and functions in a complex with Gp19 [].
Probab=21.66 E-value=77 Score=20.29 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=15.3
Q ss_pred ccHHHHHHHHHHHHHHHHh
Q psy10549 76 KHGERLYSGLKEVVTAHLE 94 (103)
Q Consensus 76 ~~g~~LY~~lk~~i~~~l~ 94 (103)
+..++||+-+..++++|=-
T Consensus 28 kRsPQLYnAI~k~L~RHkF 46 (82)
T PF11123_consen 28 KRSPQLYNAIGKLLDRHKF 46 (82)
T ss_pred hcChHHHHHHHHHHHHccc
Confidence 4778899999999988843
No 44
>PRK05572 sporulation sigma factor SigF; Validated
Probab=21.63 E-value=3.3e+02 Score=19.91 Aligned_cols=25 Identities=8% Similarity=0.105 Sum_probs=12.5
Q ss_pred CCCChhHHHHHHHHHH----HHHHHHHHh
Q psy10549 31 MTMDEKYVQDIWLLLK----NAIQEIQKK 55 (103)
Q Consensus 31 ~~~~~~~~e~~W~~L~----~Ai~~I~~~ 55 (103)
|.+......+.+..+. .|++.++..
T Consensus 12 ~~l~~~~~~~li~~~~~gd~~a~~~L~~~ 40 (252)
T PRK05572 12 PQLKDEENKELIKKSQDGDQEARDTLVEK 40 (252)
T ss_pred CCCCHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 5666555555554443 344444443
No 45
>cd03735 SOCS_SOCS1 SOCS (suppressors of cytokine signaling) box of SOCS1-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS1, like CIS1 and SOCS3, is involved in the down-regulation of the JAK/STAT pathway. SOCS1 has a dual function as a direct potent JAK kinase inhibitor and as a component of an E3 ubiquitin-ligase complex recruiting substrates to the protein degradation machinery.
Probab=21.49 E-value=1.1e+02 Score=17.22 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=21.5
Q ss_pred CHHHHHHHHHHhhccccH-H--HHHHHHHHHHHHH
Q psy10549 61 SFEELYRNAYTMVLHKHG-E--RLYSGLKEVVTAH 92 (103)
Q Consensus 61 syeeLY~~VYnlC~~~~g-~--~LY~~lk~~i~~~ 92 (103)
|.|+|=|..=|-|+.+.+ + .|=..+|+|+.+|
T Consensus 5 sLQhLCR~tI~~~~~~~~i~~lpLP~~LKdyL~~y 39 (43)
T cd03735 5 PLQELCRKSIVATFGRENLARIPLNPVLKDYLKSF 39 (43)
T ss_pred CHHHHHHHHHHHhcCccccccCcCCHHHHHHHHhC
Confidence 577888887777776543 2 3337778777765
No 46
>KOG3189|consensus
Probab=21.45 E-value=1.1e+02 Score=23.44 Aligned_cols=24 Identities=17% Similarity=-0.065 Sum_probs=21.8
Q ss_pred cHHHHHHHHHHHHHHHHhhhhccC
Q psy10549 77 HGERLYSGLKEVVTAHLETKVGVE 100 (103)
Q Consensus 77 ~g~~LY~~lk~~i~~~l~~~~~~~ 100 (103)
.|++.|++|..++-.|+..+-+|-
T Consensus 96 LGee~~q~liNF~LrYlsdidlPi 119 (252)
T KOG3189|consen 96 LGEEKLQELINFCLRYLSDIDLPI 119 (252)
T ss_pred HhHHHHHHHHHHHHHHHHhcCCcc
Confidence 699999999999999999887774
No 47
>PRK05716 methionine aminopeptidase; Validated
Probab=21.18 E-value=3.2e+02 Score=19.70 Aligned_cols=41 Identities=7% Similarity=-0.051 Sum_probs=34.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhcc
Q psy10549 35 EKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLH 75 (103)
Q Consensus 35 ~~~~e~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~ 75 (103)
+....+.|+.+.++.+.++..-..+.++.++|+.+.++...
T Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~pG~~~~dv~~~~~~~~~~ 157 (252)
T PRK05716 117 SPEDKRLCEVTKEALYLGIAAVKPGARLGDIGHAIQKYAEA 157 (252)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence 45667889999999999888877888999999999888755
No 48
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=21.08 E-value=2.6e+02 Score=18.46 Aligned_cols=58 Identities=21% Similarity=0.223 Sum_probs=30.2
Q ss_pred ccccccCCCCCCCceeecCCCCCCChhHHHHHHHHHHHHHHHHHHhCCC-CCCHHHHHHHHHHhhccccHHHHHHHH
Q psy10549 10 TDAVKSSLVKSNGHRTSRDHLMTMDEKYVQDIWLLLKNAIQEIQKKNNS-GLSFEELYRNAYTMVLHKHGERLYSGL 85 (103)
Q Consensus 10 ~~~~~~~~~~~~~kl~ik~~~~~~~~~~~e~~W~~L~~Ai~~I~~~~~~-~lsyeeLY~~VYnlC~~~~g~~LY~~l 85 (103)
+|+.+.+.+.+...+.-++.| +..+.+++.-|.+.+. .. ..+|+|+.+....-|-+.+
T Consensus 8 sd~~~~s~~~t~~~~~~~plR------------dsV~~~L~~Y~~~L~G~~v------~~lY~mVL~evE~PLL~~v 66 (98)
T COG2901 8 SDVLTVSTPNSQDQITQKPLR------------DSVKQALKNYFADLNGQDV------NDLYEMVLAEVEQPLLDMV 66 (98)
T ss_pred ccceeccccccCCccccccHH------------HHHHHHHHHHHHHcCCCCh------hhHHHHHHHHHHhHHHHHH
Confidence 566666666666666655533 2344556666666532 22 3355555544444443333
No 49
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=21.04 E-value=98 Score=19.39 Aligned_cols=54 Identities=11% Similarity=0.105 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHh
Q psy10549 40 DIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLE 94 (103)
Q Consensus 40 ~~W~~L~~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~~~g~~LY~~lk~~i~~~l~ 94 (103)
..|.-|+-|++.=..+..+.---..|...|.+++.+..+.. -+.|.++|.+.+.
T Consensus 11 ~~WtaL~lAVen~wGG~~s~~K~~~l~~~i~~~f~~~~~~~-~~~le~~L~~~m~ 64 (82)
T PF10273_consen 11 NRWTALQLAVENGWGGPDSQEKADWLAEVIVDWFTENKDPD-ADDLEDFLEDIMD 64 (82)
T ss_pred hcCHHHHHHHHhccCCccHHHHHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHH
Confidence 45888888876433332222225677788888887764443 3335555555443
No 50
>KOG0819|consensus
Probab=20.86 E-value=1.9e+02 Score=23.16 Aligned_cols=27 Identities=26% Similarity=0.363 Sum_probs=22.3
Q ss_pred CHHHHHHHHHHhhccc---cHHHHHHHHHH
Q psy10549 61 SFEELYRNAYTMVLHK---HGERLYSGLKE 87 (103)
Q Consensus 61 syeeLY~~VYnlC~~~---~g~~LY~~lk~ 87 (103)
.|++++.++-.++.++ +++.||.-.+.
T Consensus 233 d~~~~llaiv~c~~n~~~yFA~~L~~amkg 262 (321)
T KOG0819|consen 233 DFEKLLLAIVKCIRNPPAYFAERLRKAMKG 262 (321)
T ss_pred hHHHHHHHHHHHHcCHHHHHHHHHHHHHhc
Confidence 6999999999999887 67888876553
No 51
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=20.61 E-value=2.2e+02 Score=19.45 Aligned_cols=25 Identities=20% Similarity=0.252 Sum_probs=12.9
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHHHHhhccc
Q psy10549 47 NAIQEIQKKNNSGLSFEELYRNAYTMVLHK 76 (103)
Q Consensus 47 ~Ai~~I~~~~~~~lsyeeLY~~VYnlC~~~ 76 (103)
.|+..+|... +..+|+.++.++.+.
T Consensus 23 ~a~~~l~~~~-----~~~l~~~~~~~~~~~ 47 (182)
T PRK12537 23 RALQALYQQE-----SARLLGVARRIVRDR 47 (182)
T ss_pred HHHHHHHHHH-----HHHHHHHHHHHhCCH
Confidence 4455555443 445556666555443
No 52
>PRK15331 chaperone protein SicA; Provisional
Probab=20.50 E-value=1.4e+02 Score=21.45 Aligned_cols=25 Identities=24% Similarity=0.430 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHhhccc---cHHHHHHHH
Q psy10549 61 SFEELYRNAYTMVLHK---HGERLYSGL 85 (103)
Q Consensus 61 syeeLY~~VYnlC~~~---~g~~LY~~l 85 (103)
..+.+|+..|++=.++ -++.+|.-|
T Consensus 36 ~le~iY~~Ay~~y~~Gk~~eA~~~F~~L 63 (165)
T PRK15331 36 MMDGLYAHAYEFYNQGRLDEAETFFRFL 63 (165)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 4999999999987776 345555544
No 53
>TIGR02396 diverge_rpsU rpsU-divergently transcribed protein. This uncharacterized protein is found in a number of Alphaproteobacteria and, with N-terminal regions long enough to be transit peptides, in eukaryotes. This phylogeny suggests mitochondrial derivation. In several Alphaproteobacteria, the gene for this protein is encoded divergently from rpsU, the gene for ribosomal protein S21. S21 is unusual in being encoded outside the usual long ribosomal protein operons, but rather in contexts that suggest regulation of the initiation of protein translation.
Probab=20.45 E-value=1e+02 Score=22.07 Aligned_cols=21 Identities=24% Similarity=0.427 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHh
Q psy10549 35 EKYVQDIWLLLKNAIQEIQKK 55 (103)
Q Consensus 35 ~~~~e~~W~~L~~Ai~~I~~~ 55 (103)
..++.++|.+|+..|+.+.+-
T Consensus 157 S~~~~~T~~FLdrri~~v~~~ 177 (184)
T TIGR02396 157 SEGFEDTWSFLDSRIDNAVKL 177 (184)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 578999999999999887653
No 54
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=20.35 E-value=1.3e+02 Score=15.00 Aligned_cols=27 Identities=30% Similarity=0.458 Sum_probs=16.5
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHH
Q psy10549 45 LKNAIQEIQKKNNSGLSFEELYRNAYT 71 (103)
Q Consensus 45 L~~Ai~~I~~~~~~~lsyeeLY~~VYn 71 (103)
++.+++.+=....+.++|+|+=+.+-+
T Consensus 2 ~~~~F~~~D~d~dG~I~~~Ef~~~~~~ 28 (29)
T PF00036_consen 2 LKEAFREFDKDGDGKIDFEEFKEMMKK 28 (29)
T ss_dssp HHHHHHHHSTTSSSEEEHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCCcCCHHHHHHHHHh
Confidence 445555544555677888887665543
No 55
>PF07655 Secretin_N_2: Secretin N-terminal domain; InterPro: IPR011514 This is a short domain found in bacterial type II/III secretory system proteins. The architecture of these proteins suggests that this family may be functionally analogous to IPR005644 from INTERPRO.; GO: 0009297 pilus assembly, 0019867 outer membrane
Probab=20.14 E-value=87 Score=20.11 Aligned_cols=15 Identities=33% Similarity=0.596 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHH
Q psy10549 40 DIWLLLKNAIQEIQK 54 (103)
Q Consensus 40 ~~W~~L~~Ai~~I~~ 54 (103)
+-|+.|+.+|..|..
T Consensus 70 dfW~~L~~~l~~ilg 84 (98)
T PF07655_consen 70 DFWEDLQKTLQAILG 84 (98)
T ss_pred chHHHHHHHHHHHhC
Confidence 459999999999995
Done!