Query 032720
Match_columns 135
No_of_seqs 126 out of 539
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 05:05:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032720.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032720hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04628 Sedlin_N: Sedlin, N-t 100.0 5.4E-43 1.2E-47 249.0 11.7 125 9-133 1-132 (132)
2 KOG3487 TRAPP 20 K subunit [In 100.0 2.8E-40 6E-45 229.6 11.4 133 1-135 1-137 (139)
3 COG5603 TRS20 Subunit of TRAPP 100.0 5.4E-40 1.2E-44 225.4 11.3 131 5-135 3-136 (136)
4 PF04099 Sybindin: Sybindin-li 100.0 2.8E-31 6.2E-36 191.0 15.0 129 4-133 1-142 (142)
5 KOG3444 Uncharacterized conser 100.0 9.4E-31 2E-35 177.3 10.4 108 4-115 2-120 (121)
6 KOG3369 Transport protein part 100.0 8.5E-30 1.8E-34 185.9 13.1 90 42-133 106-197 (199)
7 COG5122 TRS23 Transport protei 99.9 7E-25 1.5E-29 150.2 10.5 125 4-133 3-133 (134)
8 KOG3368 Transport protein part 99.9 3E-23 6.6E-28 145.3 13.3 128 2-132 1-137 (140)
9 PF01217 Clat_adaptor_s: Clath 95.0 0.83 1.8E-05 32.1 11.8 94 3-107 1-95 (141)
10 KOG0861 SNARE protein YKT6, sy 83.0 18 0.00038 27.2 9.6 97 3-104 2-102 (198)
11 KOG4497 Uncharacterized conser 80.8 1.8 3.9E-05 35.8 3.1 51 35-85 168-220 (447)
12 PF03164 Mon1: Trafficking pro 70.3 57 0.0012 27.3 9.5 89 6-106 13-102 (415)
13 PF08800 VirE_N: VirE N-termin 69.4 17 0.00036 25.7 5.3 24 64-87 55-80 (136)
14 PF13774 Longin: Regulated-SNA 61.9 37 0.00081 21.3 6.8 46 60-106 17-63 (83)
15 PF13388 DUF4106: Protein of u 54.8 20 0.00044 29.2 3.9 39 91-133 52-91 (422)
16 PF09843 DUF2070: Predicted me 46.5 75 0.0016 23.3 5.7 68 66-133 62-145 (179)
17 cd04517 TLF TBP-like factors ( 45.6 91 0.002 23.0 6.0 49 53-103 124-172 (174)
18 cd04516 TBP_eukaryotes eukaryo 44.0 1.1E+02 0.0023 22.7 6.1 50 54-105 124-173 (174)
19 PF13198 DUF4014: Protein of u 43.4 16 0.00035 23.3 1.4 26 94-119 42-67 (72)
20 PHA00743 helix-turn-helix prot 42.2 30 0.00065 20.5 2.3 22 89-110 5-26 (51)
21 PF12423 KIF1B: Kinesin protei 41.9 16 0.00034 20.9 1.1 24 91-114 7-36 (45)
22 COG1507 Uncharacterized conser 41.6 73 0.0016 23.3 4.7 18 88-105 81-98 (167)
23 COG4918 Uncharacterized protei 40.8 19 0.0004 24.7 1.5 17 8-24 55-71 (114)
24 cd00652 TBP_TLF TATA box bindi 34.7 1.7E+02 0.0036 21.5 5.9 47 54-102 125-171 (174)
25 PLN00062 TATA-box-binding prot 34.3 1.9E+02 0.0042 21.4 6.2 52 54-107 124-175 (179)
26 PHA01632 hypothetical protein 31.9 1.1E+02 0.0024 18.7 3.7 33 77-109 14-50 (64)
27 PF04370 DUF508: Domain of unk 30.3 2.1E+02 0.0046 20.7 5.7 62 72-133 49-137 (156)
28 PF12100 DUF3576: Domain of un 30.3 96 0.0021 21.2 3.6 49 35-83 5-67 (103)
29 PF10436 BCDHK_Adom3: Mitochon 28.2 90 0.002 22.7 3.5 39 96-134 55-95 (164)
30 KOG2635 Medium subunit of clat 27.5 4.1E+02 0.0089 23.0 7.8 96 4-113 3-109 (512)
31 COG1537 PelA Predicted RNA-bin 26.2 3.4E+02 0.0074 22.6 6.8 80 42-125 118-204 (352)
32 PRK05473 hypothetical protein; 25.9 1.4E+02 0.0029 19.8 3.6 26 89-114 17-42 (86)
33 TIGR01200 Porphyromonas gingiv 24.9 1.8E+02 0.0039 23.5 4.9 47 66-112 217-269 (292)
34 PF12651 RHH_3: Ribbon-helix-h 24.8 50 0.0011 18.7 1.3 16 119-134 28-43 (44)
35 COG1660 Predicted P-loop-conta 23.9 50 0.0011 26.5 1.6 32 104-135 186-233 (286)
36 PF06135 DUF965: Bacterial pro 23.8 1.9E+02 0.0042 18.7 4.0 27 88-114 13-39 (79)
37 PF03288 Pox_D5: Poxvirus D5 p 23.3 1.3E+02 0.0028 18.8 3.2 34 97-133 25-59 (86)
38 PF01541 GIY-YIG: GIY-YIG cata 22.4 84 0.0018 18.8 2.2 20 1-22 1-20 (80)
39 cd04518 TBP_archaea archaeal T 21.6 3.4E+02 0.0073 20.0 6.2 48 54-103 124-171 (174)
40 PF03558 TBSV_P22: TBSV core p 20.8 65 0.0014 23.9 1.5 14 70-83 53-66 (189)
41 KOG1299 Vacuolar sorting prote 20.3 87 0.0019 27.2 2.4 24 89-112 112-136 (549)
42 PF12321 DUF3634: Protein of u 20.1 1.3E+02 0.0027 20.7 2.8 67 7-87 15-81 (108)
No 1
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=100.00 E-value=5.4e-43 Score=249.05 Aligned_cols=125 Identities=46% Similarity=0.800 Sum_probs=107.3
Q ss_pred EEcCCCCeeEEEecCCCcccc--chHHHHHHHHHhcchhhhhhhcc-ccccccceeeeecceEEEEEEecCCeEEEEEec
Q 032720 9 IVSRNEIPIYEAEVGSAVKRE--DAAQLHQFILHAALDIVQDLAWT-TSAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHD 85 (135)
Q Consensus 9 Ii~~~~~ply~~~~~~~~~~~--~~~~~~~~~~~~sLD~i~~~~~~-~~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~ 85 (135)
|||++|+|||+++|++++... .....+||++|+|||+||+++|. ++++|||.|+++++|+||||+|+||+|||++++
T Consensus 1 IIg~~n~PLy~~~~~~~~~~~~~~~~~l~~~~~h~sLD~iee~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~ 80 (132)
T PF04628_consen 1 IIGPNNNPLYIRSFPSEKESSSSDARHLYQFIAHSSLDVIEEKLWKSSSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHD 80 (132)
T ss_dssp EE-TTS-EEEEEEE--ST-CGHHHHHHHHHHHHHHHHHHHHHCCHCSSSCSEEEEEEEETTEEEEEEETTT--EEEEEEC
T ss_pred CCCCCCcceEEEecCCCcccccchHHHHHHHHHHHHHHHHHHHHhhcccccccCceehhhhHHHHhhhccCceeEEEEEe
Confidence 899999999999998654322 13455899999999999999999 999999999999999999999999999999999
Q ss_pred ----CCCchhHHHHHHHHHHHHHhhhhCCCCCCCCCcCChhHHHHHHHHHHh
Q 032720 86 ----SRNDDGIKSFFQEVHELYIKILLNPLYLPGSRITSSHFDTKVRALARK 133 (135)
Q Consensus 86 ----~~~~~~i~~~f~~i~~~Y~~~v~NPFy~~~~~I~s~~F~~~v~~~~~~ 133 (135)
..++++||+||++||++|++++|||||++++||+|+.|+++|+++++|
T Consensus 81 ~~~~~~~d~~ik~fF~~vh~~Y~~~~~NPF~~~~~~I~S~~Fd~~v~~l~~k 132 (132)
T PF04628_consen 81 MSDNSIRDEDIKQFFKEVHELYVKALCNPFYQPGTPIKSPKFDSRVRALAKK 132 (132)
T ss_dssp GGG-S--HHHHHHHHHHHHHHHHHHHTSTTCGCT-HHHHHHHHHHHHHHHHH
T ss_pred cccCCcchHHHHHHHHHHHHHHHHHccCCCCCCCCCcCCHHHHHHHHHHhcC
Confidence 457999999999999999999999999999999999999999999987
No 2
>KOG3487 consensus TRAPP 20 K subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.8e-40 Score=229.57 Aligned_cols=133 Identities=57% Similarity=0.930 Sum_probs=125.3
Q ss_pred CCceEEEEEEcCCCCeeEEEecCCCc----cccchHHHHHHHHHhcchhhhhhhccccccccceeeeecceEEEEEEecC
Q 032720 1 MATTACFIIVSRNEIPIYEAEVGSAV----KREDAAQLHQFILHAALDIVQDLAWTTSAMFLKAIDRFNDLVVSVYVTAG 76 (135)
Q Consensus 1 m~~i~~l~Ii~~~~~ply~~~~~~~~----~~~~~~~~~~~~~~~sLD~i~~~~~~~~~~ylg~l~~~~~~~v~~y~T~t 76 (135)
|++ |++|||+.+.|+|+-+|+.++ .++++..++||++|||||++||.+|.++++|||.+|+++++-|++|+|++
T Consensus 1 m~~--yfaIig~~d~Pvye~e~~~~~~~~~~~~~~~~LN~FI~HAaLdiVde~~W~~snmYLktVDkfne~~VSAyvTas 78 (139)
T KOG3487|consen 1 MTA--YFAIIGHCDNPVYEMEFGCPENSKAARDDNRHLNQFIVHAALDIVDELQWTTSNMYLKTVDKFNELFVSAYVTAS 78 (139)
T ss_pred Cce--EEEEEecCCCceEEeecCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHhhcceeEEEEEccC
Confidence 445 999999999999999998443 25567899999999999999999999999999999999999999999999
Q ss_pred CeEEEEEecCCCchhHHHHHHHHHHHHHhhhhCCCCCCCCCcCChhHHHHHHHHHHhhC
Q 032720 77 HTRFMLLHDSRNDDGIKSFFQEVHELYIKILLNPLYLPGSRITSSHFDTKVRALARKYL 135 (135)
Q Consensus 77 g~Kfvl~~~~~~~~~i~~~f~~i~~~Y~~~v~NPFy~~~~~I~s~~F~~~v~~~~~~~~ 135 (135)
++||++++..+.+++++.||+++|++|++.+|||||++++||+|+.||.+++.+++|||
T Consensus 79 ~i~f~mlh~~~~~~~ik~Ffqev~elyik~lmnpFy~~~dpirs~afd~kv~~~~rkhl 137 (139)
T KOG3487|consen 79 HIRFIMLHINRADDNIKLFFQEVHELYIKTLMNPFYEINDPIRSPAFDHKVRGLARKHL 137 (139)
T ss_pred cEEEEEEeeccccccHHHHHHHHHHHHHHHHhCcccccCCccccHHHHHHHHHHHHHHh
Confidence 99999999988899999999999999999999999999999999999999999999997
No 3
>COG5603 TRS20 Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion]
Probab=100.00 E-value=5.4e-40 Score=225.44 Aligned_cols=131 Identities=37% Similarity=0.684 Sum_probs=122.3
Q ss_pred EEEEEEcCCCCeeEEEecCCCc---cccchHHHHHHHHHhcchhhhhhhccccccccceeeeecceEEEEEEecCCeEEE
Q 032720 5 ACFIIVSRNEIPIYEAEVGSAV---KREDAAQLHQFILHAALDIVQDLAWTTSAMFLKAIDRFNDLVVSVYVTAGHTRFM 81 (135)
Q Consensus 5 ~~l~Ii~~~~~ply~~~~~~~~---~~~~~~~~~~~~~~~sLD~i~~~~~~~~~~ylg~l~~~~~~~v~~y~T~tg~Kfv 81 (135)
.+++|||++|+|+|+++|+..+ ..+...+++||++|||||++++++|..+.+|+++++.+.+..++||++|+|+||+
T Consensus 3 ~y~aIIg~KdnpVYe~e~~~~n~~~d~~~~~~ln~fiihaSlDiv~~lqwsvN~~Y~~~~d~f~~l~IsAYi~pSgmkf~ 82 (136)
T COG5603 3 EYLAIIGEKDNPVYEREYDPINKTSDGEYCRLLNQFIIHASLDIVVWLQWSVNTSYFDCLDSFGDLRISAYIMPSGMKFL 82 (136)
T ss_pred ceEEEEecCCCceeeeeecCcCcccCHHHHHHHhHHhhhhhHHHHHHHHHHhhhHHHHHHHhhCCeEEEEEEccCCceEE
Confidence 4899999999999999998432 2344568899999999999999999999999999999999999999999999999
Q ss_pred EEecCCCchhHHHHHHHHHHHHHhhhhCCCCCCCCCcCChhHHHHHHHHHHhhC
Q 032720 82 LLHDSRNDDGIKSFFQEVHELYIKILLNPLYLPGSRITSSHFDTKVRALARKYL 135 (135)
Q Consensus 82 l~~~~~~~~~i~~~f~~i~~~Y~~~v~NPFy~~~~~I~s~~F~~~v~~~~~~~~ 135 (135)
+++.++.++++|.||++||++|++.+|||||++++||+|++||.+|+++++++|
T Consensus 83 ~iH~n~s~~N~rsF~qevHely~ktLmspfy~~~~pirsqafd~~Vr~~ar~~L 136 (136)
T COG5603 83 FIHQNQSRKNARSFLQEVHELYAKTLMSPFYEPDEPIRSQAFDDGVREAARVCL 136 (136)
T ss_pred EEeccchhhhHHHHHHHHHHHHHHHhhCcccCCCccccchhhhhhHHHHHHhhC
Confidence 999887789999999999999999999999999999999999999999999987
No 4
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. Syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin []. ; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005801 cis-Golgi network; PDB: 3CUE_C 2J3T_C 2ZMV_B 2JSN_A.
Probab=99.98 E-value=2.8e-31 Score=191.03 Aligned_cols=129 Identities=17% Similarity=0.185 Sum_probs=93.8
Q ss_pred eEEEEEEcCCCCeeEEEecCCCc-----cccchHHHHHHHHHhcchhhhhhhcccc-------ccccceeeeecceEEEE
Q 032720 4 TACFIIVSRNEIPIYEAEVGSAV-----KREDAAQLHQFILHAALDIVQDLAWTTS-------AMFLKAIDRFNDLVVSV 71 (135)
Q Consensus 4 i~~l~Ii~~~~~ply~~~~~~~~-----~~~~~~~~~~~~~~~sLD~i~~~~~~~~-------~~ylg~l~~~~~~~v~~ 71 (135)
|++++|+||+|++||.++|.... +..+++...-+.+..||..+..+++|.+ ...+.. ..++.|++|+
T Consensus 1 IyslyI~nr~G~lIy~~~~~~~~~~~~~~~~~ne~~ll~g~l~sl~~i~~klsp~~~~~~~~~~~g~~~-~~T~~yklh~ 79 (142)
T PF04099_consen 1 IYSLYIFNRSGGLIYYREWNRSKNEGQPKLSSNEYKLLAGMLHSLKAIASKLSPVDSKPNEPGSSGFES-FETDTYKLHC 79 (142)
T ss_dssp EEEEEEE-TTS-EEEEEETSSSS--E-SSSCHHHHHHHHHHHHHHHHHHHHT-SSSSSS-SSS--SEEE-EEESS-EEEE
T ss_pred CeEEEEEeCCcceeeehhhCCCCccccCCCChhHHHHHHhhHHHHHHHHHHhCCCCcccccccceeEEE-EEeCCEEEEE
Confidence 68999999999999999998643 2334444444566569999999998821 123333 3389999999
Q ss_pred EEecCCeEEEEEecCCCchhHHHHHHHHHHHHHhhhh-CCCCCCCCCcCChhHHHHHHHHHHh
Q 032720 72 YVTAGHTRFMLLHDSRNDDGIKSFFQEVHELYIKILL-NPLYLPGSRITSSHFDTKVRALARK 133 (135)
Q Consensus 72 y~T~tg~Kfvl~~~~~~~~~i~~~f~~i~~~Y~~~v~-NPFy~~~~~I~s~~F~~~v~~~~~~ 133 (135)
|+|+||+|||+++|++.......+++.+|++|+++|+ ||||.+||||+|+.||++|++++++
T Consensus 80 ~eT~TGlKFvl~td~~~~~~~~~l~~~~~~lY~dyV~KNPfy~~~~pI~~~lF~~~l~~~~~~ 142 (142)
T PF04099_consen 80 FETPTGLKFVLITDPNVPSLRDELLRIYYELYVDYVVKNPFYSLEMPIRCELFDTKLDQYVKS 142 (142)
T ss_dssp EE-TTS-EEEEEE-TTCCHCHHHHHHHHHHHHHHHHHS-TTS-TTS----HHHHHHHHHHHHC
T ss_pred EEcCcCcEEEEEecCCCccHHHHHHHHHHHHHHHHHhhCCCCCCCCcEehHHHHHHHHHHHhC
Confidence 9999999999999987657788899999999999986 9999999999999999999999874
No 5
>KOG3444 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.97 E-value=9.4e-31 Score=177.33 Aligned_cols=108 Identities=26% Similarity=0.535 Sum_probs=99.0
Q ss_pred eEEEEEEcCCCCeeEEEecCCCccccchHHHHHHHHHhcchhhhhhhcc-------ccccccceeeeecceEEEEEEecC
Q 032720 4 TACFIIVSRNEIPIYEAEVGSAVKREDAAQLHQFILHAALDIVQDLAWT-------TSAMFLKAIDRFNDLVVSVYVTAG 76 (135)
Q Consensus 4 i~~l~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~~~~~sLD~i~~~~~~-------~~~~ylg~l~~~~~~~v~~y~T~t 76 (135)
++|++++|++|+|+|++++.. .++++..|+..|+|||+|+|+.+. +++.|||.++++++|++|||.|+|
T Consensus 2 ~v~~av~g~kn~~lyi~s~t~----~e~~L~~~y~v~~sLDVieekvn~~gkg~~tsne~fLGLLy~ted~kvYgfvtNT 77 (121)
T KOG3444|consen 2 LVCLAVAGPKNEPLYIESITP----KEKELKLHYQVHLSLDVIEEKVNDPGKGERTSNELFLGLLYPTEDYKVYGFVTNT 77 (121)
T ss_pred EEEEEEEcCCCCccEEEecCc----HHHHHHhHhhhhhhHHHHHHHhcCcccCccchhhhhhcccccccceeEEEEEecc
Confidence 579999999999999999853 367888899999999999999842 467899999999999999999999
Q ss_pred CeEEEEEecCC----CchhHHHHHHHHHHHHHhhhhCCCCCCC
Q 032720 77 HTRFMLLHDSR----NDDGIKSFFQEVHELYIKILLNPLYLPG 115 (135)
Q Consensus 77 g~Kfvl~~~~~----~~~~i~~~f~~i~~~Y~~~v~NPFy~~~ 115 (135)
.+|||+++|.+ +|.+||++|+..|-+|++..|||||-|+
T Consensus 78 kVKFIlvvdssd~avreteiRsv~r~~h~l~td~~~npfy~pg 120 (121)
T KOG3444|consen 78 KVKFILVVDSSDYAVRETEIRSVFRILHLLYTDLSCNPFYLPG 120 (121)
T ss_pred EEEEEEEEcCCcceehhHHHHHHHHHHHHHHHHheecceeccC
Confidence 99999999865 5899999999999999999999999876
No 6
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=8.5e-30 Score=185.94 Aligned_cols=90 Identities=20% Similarity=0.376 Sum_probs=80.6
Q ss_pred cchhhhhhhccccc-cccceeeeecceEEEEEEecCCeEEEEEecCCCchhHHHHHHHHHHHHHhhhh-CCCCCCCCCcC
Q 032720 42 ALDIVQDLAWTTSA-MFLKAIDRFNDLVVSVYVTAGHTRFMLLHDSRNDDGIKSFFQEVHELYIKILL-NPLYLPGSRIT 119 (135)
Q Consensus 42 sLD~i~~~~~~~~~-~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~~~~~~~i~~~f~~i~~~Y~~~v~-NPFy~~~~~I~ 119 (135)
|+++|.+++++-+. ..+..++ +++|+++||+|.||+|||+++++. ...++.++++||++|+||++ ||||+++||||
T Consensus 106 sl~aI~~qlsp~~ksSGie~Le-tdtF~l~~~QTlTG~KFVvis~~~-~~~aD~lLrKiYelYsDyvlKNPfYSlEMPIR 183 (199)
T KOG3369|consen 106 SLFAISTQLSPEPKSSGIEVLE-TDTFTLHIFQTLTGTKFVVIAEPG-TQGADSLLRKIYELYSDYVLKNPFYSLEMPIR 183 (199)
T ss_pred chhheeeccCCCCCCCceEEEE-eccEEEEEEEccCCcEEEEEecCC-chhHHHHHHHHHHHHHHHhhcCCccCccccee
Confidence 88999999987554 3455555 899999999999999999999975 68999999999999999997 99999999999
Q ss_pred ChhHHHHHHHHHHh
Q 032720 120 SSHFDTKVRALARK 133 (135)
Q Consensus 120 s~~F~~~v~~~~~~ 133 (135)
|++||++++.++.+
T Consensus 184 c~lFDe~lk~~le~ 197 (199)
T KOG3369|consen 184 CELFDEKLKFLLES 197 (199)
T ss_pred HHHhhHHHHHHHhh
Confidence 99999999998865
No 7
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=99.92 E-value=7e-25 Score=150.24 Aligned_cols=125 Identities=18% Similarity=0.349 Sum_probs=93.1
Q ss_pred eEEEEEEcCCCCeeEEEecCCCccccchHHHHHHHHHh----cchhhhhhhccccc-cccceeeeecceEEEEEEecCCe
Q 032720 4 TACFIIVSRNEIPIYEAEVGSAVKREDAAQLHQFILHA----ALDIVQDLAWTTSA-MFLKAIDRFNDLVVSVYVTAGHT 78 (135)
Q Consensus 4 i~~l~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~~~~~----sLD~i~~~~~~~~~-~ylg~l~~~~~~~v~~y~T~tg~ 78 (135)
+=.+.||||+|++||+|+|++.. .+...+++++.+ +..+|..+..+-+. ..+.+++ ++.+.++.|+|.||+
T Consensus 3 ve~~~iINksGglifqref~~~e---t~lnsneyLiLastlhgV~aI~tq~~p~~gssg~~~l~-~~~f~m~I~qT~TG~ 78 (134)
T COG5122 3 VEQFFIINKSGGLIFQREFGEGE---TELNSNEYLILASTLHGVSAILTQTIPLPGSSGRLVLY-FRNFVMTIFQTTTGT 78 (134)
T ss_pred eeEEEEEecCCcEEEEEeccCCc---cccCcccEEEEeechhhhhhhhhhcccCCCCCceEEEE-eccEEEEEEEecCCc
Confidence 45689999999999999997532 111223343333 34566666655322 2233444 899999999999999
Q ss_pred EEEEEecCCCchhHHHHHHHHHHHHHhhhh-CCCCCCCCCcCChhHHHHHHHHHHh
Q 032720 79 RFMLLHDSRNDDGIKSFFQEVHELYIKILL-NPLYLPGSRITSSHFDTKVRALARK 133 (135)
Q Consensus 79 Kfvl~~~~~~~~~i~~~f~~i~~~Y~~~v~-NPFy~~~~~I~s~~F~~~v~~~~~~ 133 (135)
|||++++.+. .+.+--++++|.+|+|||+ ||||+++|||+|.+||+++++++..
T Consensus 79 kFV~~~~k~t-~na~~ql~kiY~lYsdYV~knPfys~EMPI~c~lFde~lkrm~e~ 133 (134)
T COG5122 79 KFVFVAEKRT-VNALFQLQKIYSLYSDYVTKNPFYSPEMPIQCSLFDEHLKRMFEG 133 (134)
T ss_pred EEEEEecCCc-hhHHHHHHHHHHHHHHHhhcCCCCCcccceehhhhhHHHHHHhcC
Confidence 9999997553 3344447889999999997 9999999999999999999998754
No 8
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.91 E-value=3e-23 Score=145.29 Aligned_cols=128 Identities=22% Similarity=0.309 Sum_probs=108.7
Q ss_pred CceEEEEEEcCCCCeeEEEecCCCc---cccchHHHHHHHHHhcchhhhhhhccc--cccccceeeeecceEEEEEEecC
Q 032720 2 ATTACFIIVSRNEIPIYEAEVGSAV---KREDAAQLHQFILHAALDIVQDLAWTT--SAMFLKAIDRFNDLVVSVYVTAG 76 (135)
Q Consensus 2 ~~i~~l~Ii~~~~~ply~~~~~~~~---~~~~~~~~~~~~~~~sLD~i~~~~~~~--~~~ylg~l~~~~~~~v~~y~T~t 76 (135)
++|+.++|.+|+|.+||.++|..+. ...+++...-|.+..||.-+.+++++. .+.+ .-++|+.|+++.|+|||
T Consensus 1 Mtiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~k~~f--~sy~Ts~YklhfyeTpt 78 (140)
T KOG3368|consen 1 MTIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDVKDGF--LSYKTSKYKLHFYETPT 78 (140)
T ss_pred CeEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCcccCe--eEEeeceeEEEEEEcCC
Confidence 4789999999999999999997432 122333444488888999999999875 3443 34568999999999999
Q ss_pred CeEEEEEecCCCchhHHHHHHHHHH-HHHhhhh-CCCCC--CCCCcCChhHHHHHHHHHH
Q 032720 77 HTRFMLLHDSRNDDGIKSFFQEVHE-LYIKILL-NPLYL--PGSRITSSHFDTKVRALAR 132 (135)
Q Consensus 77 g~Kfvl~~~~~~~~~i~~~f~~i~~-~Y~~~v~-NPFy~--~~~~I~s~~F~~~v~~~~~ 132 (135)
|+|||+++|++ ...+|++++.||. +|+++|. ||.++ +++||+|+.|.+++++.++
T Consensus 79 glk~vl~Tdpk-~~~ir~vLq~IYs~lyVE~Vvknpl~~~~~~~~i~~E~fr~~ld~~vr 137 (140)
T KOG3368|consen 79 GLKFVLNTDPK-AGSIRDVLQYIYSHLYVEYVVKNPLYTYDPGSPIRSELFRKILDRFVR 137 (140)
T ss_pred CcEEEEecCCC-cccHHHHHHHHHHHHHHHHHHcCcccccCCCCccchHHHHHHHHhhhc
Confidence 99999999985 7899999999998 9999985 99999 9999999999999999886
No 9
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=94.98 E-value=0.83 Score=32.15 Aligned_cols=94 Identities=15% Similarity=0.216 Sum_probs=54.8
Q ss_pred ceEEEEEEcCCCCeeEEEecCCCccccchHHHHHHHHHhcchhhhhhhccccccccceeeeecceEEEEEEecCCeEEEE
Q 032720 3 TTACFIIVSRNEIPIYEAEVGSAVKREDAAQLHQFILHAALDIVQDLAWTTSAMFLKAIDRFNDLVVSVYVTAGHTRFML 82 (135)
Q Consensus 3 ~i~~l~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~~~~~sLD~i~~~~~~~~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl 82 (135)
+|-++.|+|++|++++.|-|...+....+.....+. ......+++. ..+...+++++ .|.--+++-|++
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~--------~~~~~~~~~~--~~i~~~~~~~~-vy~~~~dl~~~~ 69 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFI--------KKKSSRNSKQ--SPIFEHDNYRI-VYKRYSDLYFVV 69 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHH--------HHHHTSSSSS--TSEEEETTEEE-EEEEETTEEEEE
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHH--------HHHHhccccc--ceeeeccccee-eeEeeccEEEEE
Confidence 467999999999999999995432211111111111 1111111111 22223455554 777889999999
Q ss_pred EecCC-CchhHHHHHHHHHHHHHhhh
Q 032720 83 LHDSR-NDDGIKSFFQEVHELYIKIL 107 (135)
Q Consensus 83 ~~~~~-~~~~i~~~f~~i~~~Y~~~v 107 (135)
+++.. ++-.+-++++.+.++.-++.
T Consensus 70 v~~~~eNel~~~e~l~~~v~~l~~~~ 95 (141)
T PF01217_consen 70 VGDENENELLLLEFLHRLVEVLDDYF 95 (141)
T ss_dssp EESSTSBHHHHHHHHHHHHHHHHHHH
T ss_pred EeecccchHHHHHHHHHhhhhhhhhh
Confidence 99854 23355667777777666654
No 10
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.96 E-value=18 Score=27.25 Aligned_cols=97 Identities=8% Similarity=0.112 Sum_probs=55.6
Q ss_pred ceEEEEEEcCCCCe--eEEEecCCCcccc-chHHHHHHHHHhcchhhhhhhccccccccceeeeecceEEEEEEecCCeE
Q 032720 3 TTACFIIVSRNEIP--IYEAEVGSAVKRE-DAAQLHQFILHAALDIVQDLAWTTSAMFLKAIDRFNDLVVSVYVTAGHTR 79 (135)
Q Consensus 3 ~i~~l~Ii~~~~~p--ly~~~~~~~~~~~-~~~~~~~~~~~~sLD~i~~~~~~~~~~ylg~l~~~~~~~v~~y~T~tg~K 79 (135)
-|+++.|+...... |.-..++-+.+.- +.....+|+.+.|=-+.+ +. +.+..+-.+.++|.+|+|+-+.|+-
T Consensus 2 ki~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F~sktvae-Rt----~~g~rqsvk~~~Y~~h~yvrndgL~ 76 (198)
T KOG0861|consen 2 KIYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTFISKTVAE-RT----GPGQRQSVKHEEYLVHVYVRNDGLC 76 (198)
T ss_pred ceEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHHHHHHHHH-hc----CcccccccccceeEEEEEEecCCee
Confidence 47888888874333 3332222111100 001133577764433333 22 2233344446899999999999999
Q ss_pred EEEEecCCC-chhHHHHHHHHHHHHH
Q 032720 80 FMLLHDSRN-DDGIKSFFQEVHELYI 104 (135)
Q Consensus 80 fvl~~~~~~-~~~i~~~f~~i~~~Y~ 104 (135)
=|+++|..- ....-.++++|-+.|.
T Consensus 77 ~V~~~D~eYP~rvA~tLL~kvld~~~ 102 (198)
T KOG0861|consen 77 GVLIADDEYPVRVAFTLLNKVLDEFT 102 (198)
T ss_pred EEEEecCcCchhHHHHHHHHHHHHHh
Confidence 999999641 2334567788887775
No 11
>KOG4497 consensus Uncharacterized conserved protein WDR8, contains WD repeats [General function prediction only]
Probab=80.76 E-value=1.8 Score=35.78 Aligned_cols=51 Identities=16% Similarity=0.232 Sum_probs=40.7
Q ss_pred HHHHHHhcchhhhhh--hccccccccceeeeecceEEEEEEecCCeEEEEEec
Q 032720 35 HQFILHAALDIVQDL--AWTTSAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHD 85 (135)
Q Consensus 35 ~~~~~~~sLD~i~~~--~~~~~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~ 85 (135)
.+.+-++.+|-+|.. -|...+..|...+..=+|+||+|+-.+|+||+--..
T Consensus 168 W~ll~~f~~dT~DltgieWsPdg~~laVwd~~Leykv~aYe~~lG~k~v~wsP 220 (447)
T KOG4497|consen 168 WILLKEFKLDTIDLTGIEWSPDGNWLAVWDNVLEYKVYAYERGLGLKFVEWSP 220 (447)
T ss_pred HHHHHhcCCCcccccCceECCCCcEEEEecchhhheeeeeeeccceeEEEecc
Confidence 345667788888744 366777889898988899999999999999987443
No 12
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=70.34 E-value=57 Score=27.35 Aligned_cols=89 Identities=13% Similarity=0.251 Sum_probs=45.1
Q ss_pred EEEEEcCCCCeeEEEecCCCccccchHHHHHHHHHhcchhhhhhhccccccccceeeeecceEEEEEEecCCeEEEEEec
Q 032720 6 CFIIVSRNEIPIYEAEVGSAVKREDAAQLHQFILHAALDIVQDLAWTTSAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHD 85 (135)
Q Consensus 6 ~l~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~~~~~sLD~i~~~~~~~~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~ 85 (135)
-+.|+..+|+|||.+. ++ ++...--+.+ +.++-.-.....+ -|..+. .++.++. |...+.+-+|.++.
T Consensus 13 h~fIlS~AGKPIysr~-G~-----e~~l~~~~g~---~~aiiS~~~~~~d-~l~~i~-~~~~~iv-fl~r~pl~lv~vS~ 80 (415)
T PF03164_consen 13 HFFILSSAGKPIYSRY-GD-----EDKLSSLMGV---IQAIISFFQSNGD-ELRSIR-AGDHRIV-FLNRGPLILVAVSK 80 (415)
T ss_pred eEEEECCCCceeEEec-CC-----hHHHHHHHHH---HHHHHHHHHhCCC-cEEEEE-eCCEEEE-EEecCCEEEEEEcC
Confidence 4789999999999985 32 2222221222 2222221111112 233333 3444444 44566666666665
Q ss_pred CC-CchhHHHHHHHHHHHHHhh
Q 032720 86 SR-NDDGIKSFFQEVHELYIKI 106 (135)
Q Consensus 86 ~~-~~~~i~~~f~~i~~~Y~~~ 106 (135)
.. .+..++.-++-+|..-+-.
T Consensus 81 ~~e~~~~l~~qL~~ly~qils~ 102 (415)
T PF03164_consen 81 TGESESQLRKQLDYLYSQILSI 102 (415)
T ss_pred CcCCHHHHHHHHHHHHHHHHHh
Confidence 43 2345666666666544433
No 13
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=69.36 E-value=17 Score=25.66 Aligned_cols=24 Identities=8% Similarity=0.243 Sum_probs=18.4
Q ss_pred ecceEEEEEEecCC--eEEEEEecCC
Q 032720 64 FNDLVVSVYVTAGH--TRFMLLHDSR 87 (135)
Q Consensus 64 ~~~~~v~~y~T~tg--~Kfvl~~~~~ 87 (135)
.+.+.+.+|+|++| +|+++-.+..
T Consensus 55 ~~p~t~~~f~SpSG~GvKi~v~~~~~ 80 (136)
T PF08800_consen 55 EDPYTLAAFVSPSGRGVKIIVPFDYP 80 (136)
T ss_pred cCCcEEEEEEcCCCCeEEEEEEecCC
Confidence 35577899999875 9999877643
No 14
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=61.87 E-value=37 Score=21.30 Aligned_cols=46 Identities=13% Similarity=0.229 Sum_probs=34.1
Q ss_pred eeeeecceEEEEEEecCCeEEEEEecCC-CchhHHHHHHHHHHHHHhh
Q 032720 60 AIDRFNDLVVSVYVTAGHTRFMLLHDSR-NDDGIKSFFQEVHELYIKI 106 (135)
Q Consensus 60 ~l~~~~~~~v~~y~T~tg~Kfvl~~~~~-~~~~i~~~f~~i~~~Y~~~ 106 (135)
.....+++..|.+. ..|+-++.++|.. .....=.|+++|++.|...
T Consensus 17 ~s~~~~~~~fh~~~-~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~ 63 (83)
T PF13774_consen 17 MSYESGNYVFHYLV-EDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQT 63 (83)
T ss_dssp EEEEETTEEEEEEE-ETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHH
T ss_pred EEEEECCEEEEEEE-cCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHH
Confidence 44446788888888 9999999999975 2344556778888888754
No 15
>PF13388 DUF4106: Protein of unknown function (DUF4106)
Probab=54.83 E-value=20 Score=29.20 Aligned_cols=39 Identities=31% Similarity=0.638 Sum_probs=27.6
Q ss_pred hHHHHHHHHHHHHHhh-hhCCCCCCCCCcCChhHHHHHHHHHHh
Q 032720 91 GIKSFFQEVHELYIKI-LLNPLYLPGSRITSSHFDTKVRALARK 133 (135)
Q Consensus 91 ~i~~~f~~i~~~Y~~~-v~NPFy~~~~~I~s~~F~~~v~~~~~~ 133 (135)
+.++-|+.+|. +. +.|-|. .+..++|+.||+.+++.++.
T Consensus 52 dfknafealhs---kvklvndfs-sgkklksegfdkelrevaqn 91 (422)
T PF13388_consen 52 DFKNAFEALHS---KVKLVNDFS-SGKKLKSEGFDKELREVAQN 91 (422)
T ss_pred hHHHHHHHHHh---hhhhhcccc-cccccccchhhHHHHHHHHH
Confidence 34444554443 33 349886 58899999999999998874
No 16
>PF09843 DUF2070: Predicted membrane protein (DUF2070); InterPro: IPR019204 This domain of unknown function is found in various bacterial and archael hypothetical proteins, as well as in prokaryotic polyketide synthase.
Probab=46.46 E-value=75 Score=23.32 Aligned_cols=68 Identities=18% Similarity=0.233 Sum_probs=42.8
Q ss_pred ceEEEEEEecCCeEEEEEecCCC-----chhHHHHHHHH---------HHHHHhhhh--CCCCCCCCCcCChhHHHHHHH
Q 032720 66 DLVVSVYVTAGHTRFMLLHDSRN-----DDGIKSFFQEV---------HELYIKILL--NPLYLPGSRITSSHFDTKVRA 129 (135)
Q Consensus 66 ~~~v~~y~T~tg~Kfvl~~~~~~-----~~~i~~~f~~i---------~~~Y~~~v~--NPFy~~~~~I~s~~F~~~v~~ 129 (135)
.-+++..++..+-.+++..|.++ .+.|++.+.++ -..++..++ |+.+..+..+.++.+.+.+++
T Consensus 62 gi~~~~v~~~g~~~~lv~~DsNNm~~~lr~~i~~~~~~~~d~~ev~TTDtH~~~~~~~g~~y~~vG~~~~~~~i~~~~~~ 141 (179)
T PF09843_consen 62 GISALVVEVGGQRSALVLADSNNMEPGLREKIREALGDVVDEVEVMTTDTHFVNGESGGNGYWPVGPLIPPREIIESRRE 141 (179)
T ss_pred ccEEEEEEeCCcEEEEEEEECCCCCHHHHHHHHHHHhhhcceeEEecCcccEEccEECCccceeccccCCHHHHHHHHHH
Confidence 44566666666666777777653 24455555555 444555554 644555667788888888888
Q ss_pred HHHh
Q 032720 130 LARK 133 (135)
Q Consensus 130 ~~~~ 133 (135)
.+++
T Consensus 142 ~~~~ 145 (179)
T PF09843_consen 142 AVSE 145 (179)
T ss_pred HHHH
Confidence 7765
No 17
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=45.64 E-value=91 Score=22.97 Aligned_cols=49 Identities=4% Similarity=0.150 Sum_probs=38.1
Q ss_pred ccccccceeeeecceEEEEEEecCCeEEEEEecCCCchhHHHHHHHHHHHH
Q 032720 53 TSAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHDSRNDDGIKSFFQEVHELY 103 (135)
Q Consensus 53 ~~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~~~~~~~i~~~f~~i~~~Y 103 (135)
.++.|=|.+++..+-++-+.+=+||- |+++..++.++++..++.++..-
T Consensus 124 ePE~fPgliyr~~~p~~t~lIF~sGk--ivitGaks~~~~~~a~~~i~pil 172 (174)
T cd04517 124 EPELHPGVVYRITGPRATLSIFSTGS--VTVTGARSMEDVREAVEKIYPIV 172 (174)
T ss_pred CCccCCEEEEEECCCcEEEEEeCCCE--EEEEecCCHHHHHHHHHHHHHHH
Confidence 36778899999998888888888884 44444456788999999888653
No 18
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=43.97 E-value=1.1e+02 Score=22.66 Aligned_cols=50 Identities=12% Similarity=0.286 Sum_probs=37.5
Q ss_pred cccccceeeeecceEEEEEEecCCeEEEEEecCCCchhHHHHHHHHHHHHHh
Q 032720 54 SAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHDSRNDDGIKSFFQEVHELYIK 105 (135)
Q Consensus 54 ~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~~~~~~~i~~~f~~i~~~Y~~ 105 (135)
++.|=|.+++..+-++-..+=.||= |+++..++.++++.-++.|+..-.+
T Consensus 124 PE~fPgliyr~~~pk~~~liF~sGk--vvitGaks~~~~~~a~~~i~p~L~~ 173 (174)
T cd04516 124 PELFPGLIYRMVKPKIVLLIFVSGK--IVLTGAKSREEIYQAFENIYPILLQ 173 (174)
T ss_pred CccCceEEEEecCCcEEEEEeCCCE--EEEEecCCHHHHHHHHHHHHHHHhh
Confidence 6678899999988888888888883 4444445678889888888865443
No 19
>PF13198 DUF4014: Protein of unknown function (DUF4014)
Probab=43.37 E-value=16 Score=23.27 Aligned_cols=26 Identities=23% Similarity=0.430 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhhhhCCCCCCCCCcC
Q 032720 94 SFFQEVHELYIKILLNPLYLPGSRIT 119 (135)
Q Consensus 94 ~~f~~i~~~Y~~~v~NPFy~~~~~I~ 119 (135)
..++.+.+.|.+.+.|||-.++..|.
T Consensus 42 ~~~E~l~e~Y~~~~w~~F~~Lhnkin 67 (72)
T PF13198_consen 42 KIIEPLFELYKDWFWNPFNALHNKIN 67 (72)
T ss_pred HHHHHHHHHHHHHHHHhHHHHhcccc
Confidence 37788999999999999987766553
No 20
>PHA00743 helix-turn-helix protein
Probab=42.16 E-value=30 Score=20.51 Aligned_cols=22 Identities=23% Similarity=0.599 Sum_probs=19.8
Q ss_pred chhHHHHHHHHHHHHHhhhhCC
Q 032720 89 DDGIKSFFQEVHELYIKILLNP 110 (135)
Q Consensus 89 ~~~i~~~f~~i~~~Y~~~v~NP 110 (135)
|+++|.++.-||+.=+|.+.+-
T Consensus 5 D~~iReLLs~iheIKID~i~~~ 26 (51)
T PHA00743 5 DEDVRELLSIIHEIKIDIITQS 26 (51)
T ss_pred HHHHHHHHHHHHHHhhhhhccc
Confidence 6899999999999999999744
No 21
>PF12423 KIF1B: Kinesin protein 1B; InterPro: IPR022140 This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00225 from PFAM, PF00498 from PFAM. KIF1B is an anterograde motor for transport of mitochondria in axons of neuronal cells.
Probab=41.91 E-value=16 Score=20.87 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=12.8
Q ss_pred hHHHHHHHH----HHHHHhhh--hCCCCCC
Q 032720 91 GIKSFFQEV----HELYIKIL--LNPLYLP 114 (135)
Q Consensus 91 ~i~~~f~~i----~~~Y~~~v--~NPFy~~ 114 (135)
.+|++++.. ...+.+.. .+|||++
T Consensus 7 ~MRemYq~~~~~~~~~~~~~~~~~DPF~e~ 36 (45)
T PF12423_consen 7 DMREMYQQYKENDFPEYDQHFKEDDPFYEP 36 (45)
T ss_pred HHHHHHHHHHhcCCccccccCCCCCCCCCC
Confidence 344444444 33333333 4999986
No 22
>COG1507 Uncharacterized conserved protein [Function unknown]
Probab=41.56 E-value=73 Score=23.34 Aligned_cols=18 Identities=33% Similarity=0.912 Sum_probs=16.4
Q ss_pred CchhHHHHHHHHHHHHHh
Q 032720 88 NDDGIKSFFQEVHELYIK 105 (135)
Q Consensus 88 ~~~~i~~~f~~i~~~Y~~ 105 (135)
.|++++++|++.|+.|++
T Consensus 81 ~d~eL~~~~~raHe~~lk 98 (167)
T COG1507 81 QDEELRAFYRRAHESYLK 98 (167)
T ss_pred ccHHHHHHHHHHHHHHHH
Confidence 488999999999999986
No 23
>COG4918 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.79 E-value=19 Score=24.71 Aligned_cols=17 Identities=35% Similarity=0.450 Sum_probs=14.7
Q ss_pred EEEcCCCCeeEEEecCC
Q 032720 8 IIVSRNEIPIYEAEVGS 24 (135)
Q Consensus 8 ~Ii~~~~~ply~~~~~~ 24 (135)
.+|..+++|||+++|++
T Consensus 55 ~~idsn~gPiyik~~~~ 71 (114)
T COG4918 55 ASIDSNFGPIYIKDYGS 71 (114)
T ss_pred cccccCCCcEEEEecce
Confidence 46889999999999964
No 24
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=34.73 E-value=1.7e+02 Score=21.53 Aligned_cols=47 Identities=11% Similarity=0.274 Sum_probs=36.9
Q ss_pred cccccceeeeecceEEEEEEecCCeEEEEEecCCCchhHHHHHHHHHHH
Q 032720 54 SAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHDSRNDDGIKSFFQEVHEL 102 (135)
Q Consensus 54 ~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~~~~~~~i~~~f~~i~~~ 102 (135)
++.|=|.+++..+-++.+.+=+||= |+++..+++++++.-++.++..
T Consensus 125 Pe~fpgli~r~~~pk~t~lIF~sGk--vvitGaks~~~~~~a~~~i~~~ 171 (174)
T cd00652 125 PELFPGLIYRMDEPKVVLLIFVSGK--IVITGAKSREDIYEAVEKIYPI 171 (174)
T ss_pred CccCceEEEEecCCcEEEEEEcCCE--EEEEecCCHHHHHHHHHHHHHH
Confidence 6678899999888888888888884 4445545678899988888865
No 25
>PLN00062 TATA-box-binding protein; Provisional
Probab=34.28 E-value=1.9e+02 Score=21.41 Aligned_cols=52 Identities=10% Similarity=0.240 Sum_probs=39.5
Q ss_pred cccccceeeeecceEEEEEEecCCeEEEEEecCCCchhHHHHHHHHHHHHHhhh
Q 032720 54 SAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHDSRNDDGIKSFFQEVHELYIKIL 107 (135)
Q Consensus 54 ~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~~~~~~~i~~~f~~i~~~Y~~~v 107 (135)
++.|=|.+++..+-++-..+=.||= |+++..++.++++.-++.|+..-.++-
T Consensus 124 PE~fPgliyr~~~pk~~~liF~sGk--vvitGaks~~~~~~ai~~i~p~L~~~~ 175 (179)
T PLN00062 124 PELFPGLIYRMKQPKIVLLIFVSGK--IVITGAKVREEIYTAFENIYPVLTEFR 175 (179)
T ss_pred cccCceEEEEeCCCcEEEEEeCCCE--EEEEecCCHHHHHHHHHHHHHHHHHhc
Confidence 5677889999888888888888883 444544567889999999998766553
No 26
>PHA01632 hypothetical protein
Probab=31.90 E-value=1.1e+02 Score=18.69 Aligned_cols=33 Identities=12% Similarity=0.423 Sum_probs=26.0
Q ss_pred CeEEEEEecC----CCchhHHHHHHHHHHHHHhhhhC
Q 032720 77 HTRFMLLHDS----RNDDGIKSFFQEVHELYIKILLN 109 (135)
Q Consensus 77 g~Kfvl~~~~----~~~~~i~~~f~~i~~~Y~~~v~N 109 (135)
.+|+-++.++ +.++++|..+-++-.-|++.+-|
T Consensus 14 hikiyilieqvp~kpteeelrkvlpkilkdyanmie~ 50 (64)
T PHA01632 14 HIKIYILIEQVPQKPTEEELRKVLPKILKDYANMIEN 50 (64)
T ss_pred EEEEEEehhhcCCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 3677666653 36899999999999999988754
No 27
>PF04370 DUF508: Domain of unknown function (DUF508) ; InterPro: IPR007465 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=30.30 E-value=2.1e+02 Score=20.68 Aligned_cols=62 Identities=24% Similarity=0.347 Sum_probs=42.4
Q ss_pred EEecCCeEEEEEecCC--------------CchhHHHHHHHHHHHHHhhhh-CCCCC-----C-------CCCcCChhHH
Q 032720 72 YVTAGHTRFMLLHDSR--------------NDDGIKSFFQEVHELYIKILL-NPLYL-----P-------GSRITSSHFD 124 (135)
Q Consensus 72 y~T~tg~Kfvl~~~~~--------------~~~~i~~~f~~i~~~Y~~~v~-NPFy~-----~-------~~~I~s~~F~ 124 (135)
|+|.-.+|||+++-+. .|--+....-..|+++.+-+. +-|.. . ..|+..+...
T Consensus 49 ~V~MVhVKFilLh~Dv~kRrvQS~F~DEF~SDc~LqdVi~nF~qlc~RqLr~~~f~PRlsYCIGeln~~nSKPv~~~Dl~ 128 (156)
T PF04370_consen 49 YVTMVHVKFILLHRDVFKRRVQSCFTDEFPSDCLLQDVIINFHQLCSRQLRNQEFNPRLSYCIGELNYKNSKPVLKSDLG 128 (156)
T ss_pred EEEEEEEEEEEEehHHHHHHHHHhhcccCcccCcHHHHHHHHHHHHHHHHhccccCcceeeeeccccccCCCcchHHHHH
Confidence 7888889999998642 244566666677888888876 33321 1 3467777778
Q ss_pred HHHHHHHHh
Q 032720 125 TKVRALARK 133 (135)
Q Consensus 125 ~~v~~~~~~ 133 (135)
+.+.++++.
T Consensus 129 KtLAqLA~t 137 (156)
T PF04370_consen 129 KTLAQLAAT 137 (156)
T ss_pred HHHHHHhcc
Confidence 888887753
No 28
>PF12100 DUF3576: Domain of unknown function (DUF3576); InterPro: IPR021959 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 100 amino acids in length. This domain has a single completely conserved residue G that may be functionally important.
Probab=30.26 E-value=96 Score=21.17 Aligned_cols=49 Identities=18% Similarity=0.296 Sum_probs=31.7
Q ss_pred HHHHHHhcchhhhhhhccccccccceeee---------ecceEEEEEEe-----cCCeEEEEE
Q 032720 35 HQFILHAALDIVQDLAWTTSAMFLKAIDR---------FNDLVVSVYVT-----AGHTRFMLL 83 (135)
Q Consensus 35 ~~~~~~~sLD~i~~~~~~~~~~ylg~l~~---------~~~~~v~~y~T-----~tg~Kfvl~ 83 (135)
+.|+.-||||.++-.--.+.+.+-|.|-+ .+.|++..|+. ..++|.-+.
T Consensus 5 N~yLWrASLdtLsFmPl~saD~~gGVI~TdWY~~p~~~~er~k~tv~Ild~~Lradal~V~vf 67 (103)
T PF12100_consen 5 NAYLWRASLDTLSFMPLASADPFGGVIVTDWYSPPPGPNERFKATVYILDRALRADALRVSVF 67 (103)
T ss_pred hHHHHHHHHHHHhhcchhhcCCCCCEEEeccccCCCCCCeeEEEEEEEECccccCCceEEEEE
Confidence 45888899999985544455555555543 24588888876 445566553
No 29
>PF10436 BCDHK_Adom3: Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase; InterPro: IPR018955 Catabolism and synthesis of leucine, isoleucine and valine are finely balanced, allowing the body to make the most of dietary input but removing excesses to prevent toxic build-up of their corresponding keto-acids. Regulating the activity of the branched-chain alpha-ketoacid dehydrogenase (BCDH) complex is the primary means by which these processes are coordinated. BCDH kinase regulates BCDH by phosphorylation, thereby inactivating it when synthesis is required. Pyruvate dehydrogenase kinase inhibits the pyruvate dehydrogenase complex by phosphorylation of the E1 alpha subunit, thus contributing to the regulation of glucose metabolism. It is also involved in telomere maintenance. This entry is associated with IPR003594 from INTERPRO which is found towards the C terminus. ; PDB: 1GKX_A 1GJV_A 1GKZ_A 1JM6_B 3CRL_B 3CRK_B 1Y8O_A 2PNR_A 1Y8P_A 1Y8N_A ....
Probab=28.23 E-value=90 Score=22.65 Aligned_cols=39 Identities=15% Similarity=0.252 Sum_probs=26.9
Q ss_pred HHHHHHHHHhhhh--CCCCCCCCCcCChhHHHHHHHHHHhh
Q 032720 96 FQEVHELYIKILL--NPLYLPGSRITSSHFDTKVRALARKY 134 (135)
Q Consensus 96 f~~i~~~Y~~~v~--NPFy~~~~~I~s~~F~~~v~~~~~~~ 134 (135)
.++||+.|.+... -.|-.+.+.=....|.+.++++.+++
T Consensus 55 i~~V~~~Y~~sF~~L~~~~~~~~~~~~~~F~~~l~~i~~~H 95 (164)
T PF10436_consen 55 IQQVYEWYLQSFEELRSFPPPKTLEDNEKFTELLERILDRH 95 (164)
T ss_dssp HHHHHHHHHHHHHHHHTTSTTTSCCHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHh
Confidence 5567777777652 44544555555789999999988875
No 30
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.47 E-value=4.1e+02 Score=23.03 Aligned_cols=96 Identities=20% Similarity=0.175 Sum_probs=59.7
Q ss_pred eEEEEEEcCCCCeeEEEecCCCccccchHHHHHHHHHhcchhhhhhhccc-cccccceeeeecceEEEEEEecCCeEEEE
Q 032720 4 TACFIIVSRNEIPIYEAEVGSAVKREDAAQLHQFILHAALDIVQDLAWTT-SAMFLKAIDRFNDLVVSVYVTAGHTRFML 82 (135)
Q Consensus 4 i~~l~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~~~~~sLD~i~~~~~~~-~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl 82 (135)
+...+|+.+.|++|..|.|-.- ...-+-+ =|..|-..+... ...|+ ..+.-=|.|+--..+=+||
T Consensus 3 vlaa~i~t~~Gk~ivsRqf~~M--------sr~RIEg-Ll~aFpkLv~~~~qhT~v-----Et~~VRYVYqP~d~lY~vL 68 (512)
T KOG2635|consen 3 VLAASINTKTGKAIVSRQFREM--------SRSRIEG-LLAAFPKLVSAGKQHTFV-----ETDSVRYVYQPLDNLYIVL 68 (512)
T ss_pred EEEEEEeecCCceeeehHhHhh--------hHHHHHH-HHHHhHHhhccCCCccEE-----ecccEEEEEEecccEEEEE
Confidence 4577899999999999988421 1111111 112222222211 12232 2345558999999999999
Q ss_pred EecCC----CchhHHHHHHHHHHHHHhhh-----h-CCCCC
Q 032720 83 LHDSR----NDDGIKSFFQEVHELYIKIL-----L-NPLYL 113 (135)
Q Consensus 83 ~~~~~----~~~~i~~~f~~i~~~Y~~~v-----~-NPFy~ 113 (135)
+|... .|-+.-.+|.++--.|++.+ + |-|+-
T Consensus 69 ITtk~SNIleDl~TL~Lfskvipey~~slde~eI~~~~Fel 109 (512)
T KOG2635|consen 69 ITTKQSNILEDLETLRLFSKVIPEYCSSLDEKEILENAFEL 109 (512)
T ss_pred EeccccchhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhh
Confidence 99864 36677888999988888753 3 66654
No 31
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=26.25 E-value=3.4e+02 Score=22.55 Aligned_cols=80 Identities=11% Similarity=0.069 Sum_probs=47.0
Q ss_pred cchhhhhhhccccccccceeeeecceEEEEEEecCCeEEEEEecCC----CchhHH---HHHHHHHHHHHhhhhCCCCCC
Q 032720 42 ALDIVQDLAWTTSAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHDSR----NDDGIK---SFFQEVHELYIKILLNPLYLP 114 (135)
Q Consensus 42 sLD~i~~~~~~~~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~~~----~~~~i~---~~f~~i~~~Y~~~v~NPFy~~ 114 (135)
+|+.+.+...++..+=...+---++...-|.+|..|++++.-...+ .++..+ .||.+|.+.--++. ||..-
T Consensus 118 ~lerLkeA~~~~~~~~~~~v~~degea~i~iv~~ygi~~~~~i~~~~~gK~~~~~~~~~k~~~~i~~~~~~~~-~~~~i- 195 (352)
T COG1537 118 QLERLKEAVEASKRPEVAIVVVDEGEAAIAIVRDYGIIILGKIRSGIPGKREGDIRAERKFFDEIAKALKEYA-NLDII- 195 (352)
T ss_pred HHHHHHHHhhcccCCceEEEEEecCceEEEEEeccceEEEEEEeccCCCCcccchhhHHHHHHHHHHHHHHhh-CCCeE-
Confidence 4555555554422211112222467888899999999999876543 234444 88888887777665 55532
Q ss_pred CCCcCChhHHH
Q 032720 115 GSRITSSHFDT 125 (135)
Q Consensus 115 ~~~I~s~~F~~ 125 (135)
.+-.|.|.+
T Consensus 196 --IvaGPGF~k 204 (352)
T COG1537 196 --IVAGPGFAK 204 (352)
T ss_pred --EEeCCchHH
Confidence 344555543
No 32
>PRK05473 hypothetical protein; Provisional
Probab=25.88 E-value=1.4e+02 Score=19.77 Aligned_cols=26 Identities=12% Similarity=0.172 Sum_probs=19.9
Q ss_pred chhHHHHHHHHHHHHHhhhhCCCCCC
Q 032720 89 DDGIKSFFQEVHELYIKILLNPLYLP 114 (135)
Q Consensus 89 ~~~i~~~f~~i~~~Y~~~v~NPFy~~ 114 (135)
..++++.++.||++-..==-||-.++
T Consensus 17 ~~~v~eiL~~Vy~AL~EKGYNPinQi 42 (86)
T PRK05473 17 KKDVREILTTVYDALEEKGYNPINQI 42 (86)
T ss_pred HHHHHHHHHHHHHHHHHcCCChHHHH
Confidence 46899999999999875444776663
No 33
>TIGR01200 Porphyromonas gingivalis paralogous family TIGR01200. No identifiable homologs outside Porphyromonas gingivalis.
Probab=24.91 E-value=1.8e+02 Score=23.50 Aligned_cols=47 Identities=9% Similarity=0.117 Sum_probs=31.4
Q ss_pred ceEEEEEEecCCeEEEEEecCC-----CchhHHHHHHHHHHHHHhhhhC-CCC
Q 032720 66 DLVVSVYVTAGHTRFMLLHDSR-----NDDGIKSFFQEVHELYIKILLN-PLY 112 (135)
Q Consensus 66 ~~~v~~y~T~tg~Kfvl~~~~~-----~~~~i~~~f~~i~~~Y~~~v~N-PFy 112 (135)
.|.+.|-+..++..=|++.+.. ..++.|..++++||.|...++| |-.
T Consensus 217 ~f~~~gi~~~~~~~PI~~~~~~ye~~~~ree~rk~~r~~~e~~~~~~~~~~~~ 269 (292)
T TIGR01200 217 VFELNGMQEITFPSPIYLVNTPYEKLYSREESRKEIRNIYENYYEEIDNQKIF 269 (292)
T ss_pred EEEEeeeEeccCCCceEEcCCCccccccHHHHHHHHHHHHHHHHhhhccCcce
Confidence 3556666554544434444432 2467999999999999999887 543
No 34
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=24.76 E-value=50 Score=18.66 Aligned_cols=16 Identities=19% Similarity=0.289 Sum_probs=13.7
Q ss_pred CChhHHHHHHHHHHhh
Q 032720 119 TSSHFDTKVRALARKY 134 (135)
Q Consensus 119 ~s~~F~~~v~~~~~~~ 134 (135)
+|..++++|+.+.++|
T Consensus 28 ~S~Ll~eAle~~l~ky 43 (44)
T PF12651_consen 28 KSKLLREALEDYLEKY 43 (44)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 5689999999998887
No 35
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=23.93 E-value=50 Score=26.48 Aligned_cols=32 Identities=31% Similarity=0.541 Sum_probs=22.8
Q ss_pred HhhhhCCCCCCC--------CCc--------CChhHHHHHHHHHHhhC
Q 032720 104 IKILLNPLYLPG--------SRI--------TSSHFDTKVRALARKYL 135 (135)
Q Consensus 104 ~~~v~NPFy~~~--------~~I--------~s~~F~~~v~~~~~~~~ 135 (135)
++++-||+|.++ .|+ .++.|..++..++..||
T Consensus 186 VRfLPNP~y~peLRp~tG~d~~V~dYv~~~~e~~ef~~~l~~~l~~~L 233 (286)
T COG1660 186 VRFLPNPHYDPELRPLTGLDKPVADYVMSQPEVEEFYEKLRDLLEFWL 233 (286)
T ss_pred ecccCCCccccccCcCCCCChhHHHHHHcChHHHHHHHHHHHHHHHHh
Confidence 344569999873 233 56788888888888775
No 36
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=23.84 E-value=1.9e+02 Score=18.73 Aligned_cols=27 Identities=15% Similarity=0.210 Sum_probs=21.1
Q ss_pred CchhHHHHHHHHHHHHHhhhhCCCCCC
Q 032720 88 NDDGIKSFFQEVHELYIKILLNPLYLP 114 (135)
Q Consensus 88 ~~~~i~~~f~~i~~~Y~~~v~NPFy~~ 114 (135)
.+..+++.++.||++--+-=-||-.++
T Consensus 13 ~~~~~~~iL~~Vy~AL~EKGYnPinQi 39 (79)
T PF06135_consen 13 KEKEIREILKQVYAALEEKGYNPINQI 39 (79)
T ss_pred chhhHHHHHHHHHHHHHHcCCChHHHH
Confidence 357899999999999776545887664
No 37
>PF03288 Pox_D5: Poxvirus D5 protein-like; InterPro: IPR004968 This domain is found at the C terminus of phage P4 alpha protein and related proteins. Phage P4 DNA replication depends on the product of the alpha gene, which has origin recognition ability, DNA helicase activity, and DNA primase activity. The structure of the protein can be summarised as follows: The N terminus provides the primase activity, the central region is the helicase/nucleoside triphosphatase domain and the ori DNA recognition resides in the C-terminal 1/3 of the protein []. The domain is also found at the C terminus of a number of proteins from orthopox viruses including vaccinia virus D5. D5 encodes a 90kDa protein that is transiently expressed at early times after infection. It has an nucleoside triphosphatase activity which is independent of common nucleic acid cofactors and it can hydrolyse all the common ribo- and deoxyribonucleoside triphosphates to diphosphates in the presence of a divalent cation [].; PDB: 1KA8_E.
Probab=23.26 E-value=1.3e+02 Score=18.80 Aligned_cols=34 Identities=9% Similarity=0.183 Sum_probs=22.4
Q ss_pred HHHHHHHHhhhh-CCCCCCCCCcCChhHHHHHHHHHHh
Q 032720 97 QEVHELYIKILL-NPLYLPGSRITSSHFDTKVRALARK 133 (135)
Q Consensus 97 ~~i~~~Y~~~v~-NPFy~~~~~I~s~~F~~~v~~~~~~ 133 (135)
..+|++|..+.. |=... ++....|.+++++.+..
T Consensus 25 ~~lY~~Y~~wc~~ng~~~---~ls~~~F~~~L~~~~~~ 59 (86)
T PF03288_consen 25 KDLYDAYKEWCEENGYKP---PLSKRKFGKELKQYFPE 59 (86)
T ss_dssp TBHHHHHHHHHHHTT-S-------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCc---ccCHHHHHHHHHHHhhh
Confidence 567888888764 54432 68999999999998754
No 38
>PF01541 GIY-YIG: GIY-YIG catalytic domain; InterPro: IPR000305 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. It is found in the amino terminal region of excinuclease abc subunit c (uvrC), Bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage.; GO: 0004518 nuclease activity, 0006281 DNA repair, 0005622 intracellular; PDB: 1YWL_A 1YD6_D 1YD5_A 1YD1_A 1YCZ_A 1YD0_A 1YD3_A 1YD4_A 1YD2_A 1LN0_A ....
Probab=22.38 E-value=84 Score=18.82 Aligned_cols=20 Identities=10% Similarity=0.087 Sum_probs=13.7
Q ss_pred CCceEEEEEEcCCCCeeEEEec
Q 032720 1 MATTACFIIVSRNEIPIYEAEV 22 (135)
Q Consensus 1 m~~i~~l~Ii~~~~~ply~~~~ 22 (135)
|.+||++ .+.+++.+|+-.-
T Consensus 1 k~gIY~i--~~~~~~~~YIG~t 20 (80)
T PF01541_consen 1 KYGIYII--YNKDNKKIYIGST 20 (80)
T ss_dssp -EEEEEE--EETTTEEEEEEEE
T ss_pred CcEEEEE--EECCCCEEEEEEE
Confidence 3455544 3789999999866
No 39
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=21.63 E-value=3.4e+02 Score=19.98 Aligned_cols=48 Identities=10% Similarity=0.234 Sum_probs=36.0
Q ss_pred cccccceeeeecceEEEEEEecCCeEEEEEecCCCchhHHHHHHHHHHHH
Q 032720 54 SAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHDSRNDDGIKSFFQEVHELY 103 (135)
Q Consensus 54 ~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~~~~~~~i~~~f~~i~~~Y 103 (135)
++.|=|.+++..+-++-+.+=.||= |+++..++.++++.-+++++..-
T Consensus 124 Pe~fpglvyR~~~pk~~~lIF~SGK--vvitGaks~~~~~~a~~~i~~~l 171 (174)
T cd04518 124 PEQFPGLVYRLDEPKVVLLLFSSGK--MVITGAKSEEDAKRAVEKLLSRL 171 (174)
T ss_pred cccCceEEEEecCCcEEEEEeCCCE--EEEEecCCHHHHHHHHHHHHHHH
Confidence 5667789999888888888888883 44454456788888888887654
No 40
>PF03558 TBSV_P22: TBSV core protein P21/P22; InterPro: IPR005332 Two small nested genes (p19 and p22) are located near the 3' end of the genome of tomato bushy stunt virus (TBSV) - the p19 gene encodes a soluble protein, whereas the p22 gene specifies a membrane-associated protein. p22 is required for cell-to-cell movement in all plants tested [].; GO: 0019028 viral capsid
Probab=20.78 E-value=65 Score=23.88 Aligned_cols=14 Identities=29% Similarity=0.570 Sum_probs=12.5
Q ss_pred EEEEecCCeEEEEE
Q 032720 70 SVYVTAGHTRFMLL 83 (135)
Q Consensus 70 ~~y~T~tg~Kfvl~ 83 (135)
-||.|++++||+++
T Consensus 53 ggY~t~~~Vr~~it 66 (189)
T PF03558_consen 53 GGYITIRDVRFVIT 66 (189)
T ss_pred cceeeceeeEEEEe
Confidence 37999999999995
No 41
>KOG1299 consensus Vacuolar sorting protein VPS45/Stt10 (Sec1 family) [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.34 E-value=87 Score=27.23 Aligned_cols=24 Identities=25% Similarity=0.528 Sum_probs=19.1
Q ss_pred chhHHHHHHHHHHHHHhhhh-CCCC
Q 032720 89 DDGIKSFFQEVHELYIKILL-NPLY 112 (135)
Q Consensus 89 ~~~i~~~f~~i~~~Y~~~v~-NPFy 112 (135)
+.+-.+.-++|+|.|.|+++ ||+.
T Consensus 112 esD~~E~V~eVqE~y~Df~~~n~~L 136 (549)
T KOG1299|consen 112 ESDEQEVVREVQEIYLDFFKVNPDL 136 (549)
T ss_pred hcchHHHHHHHHHHHHhhhccCCce
Confidence 34456677899999999997 9975
No 42
>PF12321 DUF3634: Protein of unknown function (DUF3634); InterPro: IPR022090 This family of proteins is found in bacteria. Proteins in this family are typically between 103 and 114 amino acids in length.
Probab=20.08 E-value=1.3e+02 Score=20.74 Aligned_cols=67 Identities=21% Similarity=0.344 Sum_probs=37.3
Q ss_pred EEEEcCCCCeeEEEecCCCccccchHHHHHHHHHhcchhhhhhhccccccccceeeeecceEEEEEEecCCeEEEEEecC
Q 032720 7 FIIVSRNEIPIYEAEVGSAVKREDAAQLHQFILHAALDIVQDLAWTTSAMFLKAIDRFNDLVVSVYVTAGHTRFMLLHDS 86 (135)
Q Consensus 7 l~Ii~~~~~ply~~~~~~~~~~~~~~~~~~~~~~~sLD~i~~~~~~~~~~ylg~l~~~~~~~v~~y~T~tg~Kfvl~~~~ 86 (135)
+..+++.+.|+|.-.|............-+-..|..-|+-. -+++ +-.|-+|.+.+|+|.++--+-
T Consensus 15 Lv~~~r~~~~vf~i~f~dG~l~~~KG~iP~~F~~~c~dIa~-------------~~~~-~G~ik~~r~~~g~rL~fS~~i 80 (108)
T PF12321_consen 15 LVFVDRRGLPVFEIHFKDGRLRVHKGHIPPGFLHNCRDIAR-------------RYPF-RGTIKVYRQRGGVRLHFSRSI 80 (108)
T ss_pred HHHccccCceEEEEEEECCcEEEEcCCCChHHHHHHHHHHH-------------hCCC-cEEEEEEEeCCceEEEEeCCC
Confidence 34568888999999996432100001111122222222221 1123 457889999999998887765
Q ss_pred C
Q 032720 87 R 87 (135)
Q Consensus 87 ~ 87 (135)
+
T Consensus 81 p 81 (108)
T PF12321_consen 81 P 81 (108)
T ss_pred C
Confidence 4
Done!