Query 032311
Match_columns 143
No_of_seqs 122 out of 614
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 12:25:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032311.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032311hhsearch_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 7.8E-41 1.7E-45 238.2 11.3 123 7-136 1-132 (132)
2 KOG3444 Uncharacterized conser 100.0 6.2E-35 1.4E-39 196.7 12.2 118 1-118 1-120 (121)
3 PF04099 Sybindin: Sybindin-li 100.0 2.5E-34 5.4E-39 207.1 15.9 131 2-136 1-142 (142)
4 COG5603 TRS20 Subunit of TRAPP 100.0 3.4E-34 7.4E-39 195.9 11.9 128 1-137 1-135 (136)
5 KOG3487 TRAPP 20 K subunit [In 100.0 1.2E-33 2.6E-38 195.6 12.2 129 1-138 1-137 (139)
6 KOG3369 Transport protein part 100.0 2.9E-33 6.2E-38 203.4 12.9 102 24-136 95-197 (199)
7 COG5122 TRS23 Transport protei 100.0 5.8E-29 1.3E-33 169.5 10.2 124 2-136 3-133 (134)
8 KOG3368 Transport protein part 100.0 2.9E-27 6.2E-32 164.9 14.2 125 2-136 3-138 (140)
9 PF01217 Clat_adaptor_s: Clath 96.1 0.29 6.2E-06 34.6 13.4 96 1-111 1-96 (141)
10 KOG0861 SNARE protein YKT6, sy 93.5 2.2 4.8E-05 31.9 10.6 95 2-109 3-104 (198)
11 PF13774 Longin: Regulated-SNA 80.3 12 0.00027 23.6 6.7 47 62-110 18-64 (83)
12 PF03164 Mon1: Trafficking pro 80.2 34 0.00074 28.7 12.2 88 4-107 13-100 (415)
13 PF08800 VirE_N: VirE N-termin 56.5 27 0.00059 24.6 4.5 23 65-87 55-79 (136)
14 PF13198 DUF4014: Protein of u 51.1 11 0.00024 23.9 1.6 27 96-122 41-67 (72)
15 PF12532 DUF3732: Protein of u 48.5 29 0.00063 26.1 3.8 38 7-44 58-95 (193)
16 PF03288 Pox_D5: Poxvirus D5 p 43.1 46 0.001 21.0 3.7 34 100-136 25-59 (86)
17 PF01119 DNA_mis_repair: DNA m 42.9 21 0.00046 24.2 2.2 54 64-117 19-78 (119)
18 COG4918 Uncharacterized protei 42.0 16 0.00035 24.9 1.3 18 6-23 55-72 (114)
19 PHA01632 hypothetical protein 41.5 81 0.0018 19.1 4.3 35 78-112 14-50 (64)
20 PF10436 BCDHK_Adom3: Mitochon 41.4 57 0.0012 23.7 4.3 41 99-139 55-97 (164)
21 PF13388 DUF4106: Protein of u 41.2 51 0.0011 26.9 4.2 42 95-137 49-92 (422)
22 KOG4497 Uncharacterized conser 38.4 24 0.00052 29.3 2.1 51 31-86 170-220 (447)
23 cd03483 MutL_Trans_MLH1 MutL_T 37.0 93 0.002 21.4 4.7 51 66-116 30-85 (127)
24 cd04516 TBP_eukaryotes eukaryo 34.7 1.6E+02 0.0035 21.7 5.8 49 55-107 124-172 (174)
25 PHA00743 helix-turn-helix prot 34.5 51 0.0011 19.4 2.5 23 91-113 4-26 (51)
26 PF12423 KIF1B: Kinesin protei 33.7 22 0.00048 20.2 0.9 7 111-117 30-36 (45)
27 PF07013 DUF1314: Protein of u 33.6 20 0.00043 26.6 0.8 23 61-83 62-84 (177)
28 cd00782 MutL_Trans MutL_Trans: 32.6 1.1E+02 0.0024 20.4 4.5 53 65-117 24-82 (122)
29 cd04517 TLF TBP-like factors ( 31.1 1.6E+02 0.0035 21.7 5.3 47 55-105 125-171 (174)
30 cd03485 MutL_Trans_hPMS_1_like 30.7 1.7E+02 0.0037 20.1 5.2 43 66-110 28-78 (132)
31 PHA03371 circ protein; Provisi 29.7 24 0.00052 27.5 0.7 22 62-83 86-107 (240)
32 KOG2740 Clathrin-associated pr 28.9 29 0.00062 29.0 1.1 22 1-22 1-22 (418)
33 PF09843 DUF2070: Predicted me 28.3 2.3E+02 0.0051 20.7 5.8 71 67-137 62-146 (179)
34 PF10906 DUF2697: Protein of u 27.2 53 0.0012 20.7 1.9 19 121-139 9-27 (68)
35 PF04370 DUF508: Domain of unk 27.0 2.5E+02 0.0053 20.3 6.2 65 73-137 49-138 (156)
36 cd03484 MutL_Trans_hPMS_2_like 25.7 2.1E+02 0.0046 20.0 5.0 50 66-116 43-100 (142)
37 PF14120 YhzD: YhzD-like prote 24.9 62 0.0014 19.9 1.8 23 2-24 3-25 (61)
38 COG0125 Tmk Thymidylate kinase 24.6 1.4E+02 0.003 22.7 4.1 43 96-138 160-205 (208)
39 PRK14449 acylphosphatase; Prov 23.8 1.3E+02 0.0029 19.5 3.4 36 66-104 27-63 (90)
40 PF09441 Abp2: ARS binding pro 22.8 41 0.00088 24.9 0.8 18 101-118 13-32 (175)
41 cd00652 TBP_TLF TATA box bindi 22.2 3.2E+02 0.007 20.0 5.6 47 55-105 125-171 (174)
42 PF03558 TBSV_P22: TBSV core p 22.1 62 0.0013 23.9 1.6 14 72-85 54-67 (189)
43 COG1507 Uncharacterized conser 21.8 1E+02 0.0022 22.5 2.7 18 91-108 81-98 (167)
44 PLN00062 TATA-box-binding prot 21.6 3.4E+02 0.0074 20.1 6.1 51 56-110 125-175 (179)
45 COG3260 Ni,Fe-hydrogenase III 21.4 2E+02 0.0042 20.8 4.0 40 63-105 34-73 (148)
46 PF03928 DUF336: Domain of unk 21.2 1.1E+02 0.0023 21.2 2.7 20 3-22 26-45 (132)
47 PF06683 DUF1184: Protein of u 20.8 2.1E+02 0.0046 21.3 4.2 26 91-116 76-103 (191)
48 PF12321 DUF3634: Protein of u 20.6 1E+02 0.0022 21.2 2.4 21 67-87 60-80 (108)
49 PF12651 RHH_3: Ribbon-helix-h 20.5 83 0.0018 17.7 1.7 17 122-138 28-44 (44)
50 PF07428 Tri3: 15-O-acetyltran 20.5 1.2E+02 0.0026 25.5 3.1 45 69-116 349-398 (413)
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=7.8e-41 Score=238.22 Aligned_cols=123 Identities=46% Similarity=0.858 Sum_probs=104.1
Q ss_pred EEeCCCCeeEEecCCCch-------hHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEEEecCce
Q 032311 7 VVGHQNNPLYIQSFTEAD-------DALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKV 79 (143)
Q Consensus 7 Ii~~~~~ply~~~~~~~~-------~~l~l~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y~T~Tg~ 79 (143)
|||++|+|||+++++..+ +.+ +++++|+|||+||+++|.. +.++|||+|+++++|+||||+|+||+
T Consensus 1 IIg~~n~PLy~~~~~~~~~~~~~~~~~l-~~~~~h~sLD~iee~~~~~------~~~~yLg~l~~~~~~~vygyvT~t~~ 73 (132)
T PF04628_consen 1 IIGPNNNPLYIRSFPSEKESSSSDARHL-YQFIAHSSLDVIEEKLWKS------SSDMYLGLLDPFEDYKVYGYVTNTGI 73 (132)
T ss_dssp EE-TTS-EEEEEEE--ST-CGHHHHHHH-HHHHHHHHHHHHHHCCHCS------SSCSEEEEEEEETTEEEEEEETTT--
T ss_pred CCCCCCcceEEEecCCCcccccchHHHH-HHHHHHHHHHHHHHHHhhc------ccccccCceehhhhHHHHhhhccCce
Confidence 899999999999998662 234 9999999999999999961 25899999999999999999999999
Q ss_pred EEEEEEc--CCCcCcHHHHHHHHHHHHHHHHhhhCCCCCCCCCCcchhHHHHHHHHHHH
Q 032311 80 KFILVTT--DLDVRDADVRNFFRRFHAAYIDAVSNPFHVPGKKITSRTFAERVSTIVKS 136 (143)
Q Consensus 80 Kfvl~~~--~~~~~~~~i~~~f~~i~~~Y~~~v~NPFy~~~~~I~s~~F~~~v~~~~~~ 136 (143)
||||+++ ....++++||+||++||++|++++|||||++++||+|+.|+++|++++++
T Consensus 74 Kfvl~~~~~~~~~~d~~ik~fF~~vh~~Y~~~~~NPF~~~~~~I~S~~Fd~~v~~l~~k 132 (132)
T PF04628_consen 74 KFVLVHDMSDNSIRDEDIKQFFKEVHELYVKALCNPFYQPGTPIKSPKFDSRVRALAKK 132 (132)
T ss_dssp EEEEEECGGG-S--HHHHHHHHHHHHHHHHHHHTSTTCGCT-HHHHHHHHHHHHHHHHH
T ss_pred eEEEEEecccCCcchHHHHHHHHHHHHHHHHHccCCCCCCCCCcCCHHHHHHHHHHhcC
Confidence 9999998 22358999999999999999999999999999999999999999999986
No 2
>KOG3444 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=6.2e-35 Score=196.74 Aligned_cols=118 Identities=57% Similarity=0.968 Sum_probs=110.3
Q ss_pred CEEEEEEEeCCCCeeEEecCCCchhHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEEEecCceE
Q 032311 1 MIACVAVVGHQNNPLYIQSFTEADDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVK 80 (143)
Q Consensus 1 mi~~l~Ii~~~~~ply~~~~~~~~~~l~l~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y~T~Tg~K 80 (143)
|+.|++|++++|+|+|++.+++.+++|++++..|+|||+|+|+.+.+.|...++++.|||+|+++++|++|||.|||.+|
T Consensus 1 m~v~~av~g~kn~~lyi~s~t~~e~~L~~~y~v~~sLDVieekvn~~gkg~~tsne~fLGLLy~ted~kvYgfvtNTkVK 80 (121)
T KOG3444|consen 1 MLVCLAVAGPKNEPLYIESITPKEKELKLHYQVHLSLDVIEEKVNDPGKGERTSNELFLGLLYPTEDYKVYGFVTNTKVK 80 (121)
T ss_pred CEEEEEEEcCCCCccEEEecCcHHHHHHhHhhhhhhHHHHHHHhcCcccCccchhhhhhcccccccceeEEEEEeccEEE
Confidence 89999999999999999999998999999999999999999999876666666789999999999999999999999999
Q ss_pred EEEEEcCC--CcCcHHHHHHHHHHHHHHHHhhhCCCCCCC
Q 032311 81 FILVTTDL--DVRDADVRNFFRRFHAAYIDAVSNPFHVPG 118 (143)
Q Consensus 81 fvl~~~~~--~~~~~~i~~~f~~i~~~Y~~~v~NPFy~~~ 118 (143)
||++++.. .++|.+||++|+.+|-+|.+..|||||-++
T Consensus 81 FIlvvdssd~avreteiRsv~r~~h~l~td~~~npfy~pg 120 (121)
T KOG3444|consen 81 FILVVDSSDYAVRETEIRSVFRILHLLYTDLSCNPFYLPG 120 (121)
T ss_pred EEEEEcCCcceehhHHHHHHHHHHHHHHHHheecceeccC
Confidence 99999765 378999999999999999999999999875
No 3
>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=100.00 E-value=2.5e-34 Score=207.05 Aligned_cols=131 Identities=21% Similarity=0.338 Sum_probs=95.6
Q ss_pred EEEEEEEeCCCCeeEEecCCCc----------hhHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEE
Q 032311 2 IACVAVVGHQNNPLYIQSFTEA----------DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVY 71 (143)
Q Consensus 2 i~~l~Ii~~~~~ply~~~~~~~----------~~~l~l~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~ 71 (143)
|++|+|+||+|++||.++|... |+.+.+..++| ||+.|..+++|.....+..+...+.. ++++.|++|
T Consensus 1 IyslyI~nr~G~lIy~~~~~~~~~~~~~~~~~ne~~ll~g~l~-sl~~i~~klsp~~~~~~~~~~~g~~~-~~T~~yklh 78 (142)
T PF04099_consen 1 IYSLYIFNRSGGLIYYREWNRSKNEGQPKLSSNEYKLLAGMLH-SLKAIASKLSPVDSKPNEPGSSGFES-FETDTYKLH 78 (142)
T ss_dssp EEEEEEE-TTS-EEEEEETSSSS--E-SSSCHHHHHHHHHHHH-HHHHHHHHT-SSSSSS-SSS--SEEE-EEESS-EEE
T ss_pred CeEEEEEeCCcceeeehhhCCCCccccCCCChhHHHHHHhhHH-HHHHHHHHhCCCCcccccccceeEEE-EEeCCEEEE
Confidence 7999999999999999999753 55677778888 99999999998532221112344544 589999999
Q ss_pred EEEecCceEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhh-hCCCCCCCCCCcchhHHHHHHHHHHH
Q 032311 72 GYLTNTKVKFILVTTDLDVRDADVRNFFRRFHAAYIDAV-SNPFHVPGKKITSRTFAERVSTIVKS 136 (143)
Q Consensus 72 ~y~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v-~NPFy~~~~~I~s~~F~~~v~~~~~~ 136 (143)
+|+|+||+|||+++|+. .......+++.+|++|++|| +||||+++|||+|+.||++|++++++
T Consensus 79 ~~eT~TGlKFvl~td~~--~~~~~~~l~~~~~~lY~dyV~KNPfy~~~~pI~~~lF~~~l~~~~~~ 142 (142)
T PF04099_consen 79 CFETPTGLKFVLITDPN--VPSLRDELLRIYYELYVDYVVKNPFYSLEMPIRCELFDTKLDQYVKS 142 (142)
T ss_dssp EEE-TTS-EEEEEE-TT--CCHCHHHHHHHHHHHHHHHHHS-TTS-TTS----HHHHHHHHHHHHC
T ss_pred EEEcCcCcEEEEEecCC--CccHHHHHHHHHHHHHHHHHhhCCCCCCCCcEehHHHHHHHHHHHhC
Confidence 99999999999999984 23556777888889999999 99999999999999999999999873
No 4
>COG5603 TRS20 Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion]
Probab=100.00 E-value=3.4e-34 Score=195.88 Aligned_cols=128 Identities=23% Similarity=0.478 Sum_probs=116.2
Q ss_pred CEEEEEEEeCCCCeeEEecCCCc-----hhHHHH--HHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEE
Q 032311 1 MIACVAVVGHQNNPLYIQSFTEA-----DDALKL--HHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGY 73 (143)
Q Consensus 1 mi~~l~Ii~~~~~ply~~~~~~~-----~~~l~l--~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y 73 (143)
|-..++|||++|+|+|+++|++. .+..++ +|++|+|||+++.+.|.. +.+|+++++.+.+.++.+|
T Consensus 1 M~~y~aIIg~KdnpVYe~e~~~~n~~~d~~~~~~ln~fiihaSlDiv~~lqwsv-------N~~Y~~~~d~f~~l~IsAY 73 (136)
T COG5603 1 MGEYLAIIGEKDNPVYEREYDPINKTSDGEYCRLLNQFIIHASLDIVVWLQWSV-------NTSYFDCLDSFGDLRISAY 73 (136)
T ss_pred CCceEEEEecCCCceeeeeecCcCcccCHHHHHHHhHHhhhhhHHHHHHHHHHh-------hhHHHHHHHhhCCeEEEEE
Confidence 56789999999999999999854 223443 599999999999999953 4799999999999999999
Q ss_pred EecCceEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhhhCCCCCCCCCCcchhHHHHHHHHHHHh
Q 032311 74 LTNTKVKFILVTTDLDVRDADVRNFFRRFHAAYIDAVSNPFHVPGKKITSRTFAERVSTIVKSF 137 (143)
Q Consensus 74 ~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v~NPFy~~~~~I~s~~F~~~v~~~~~~~ 137 (143)
++++|+||++++... ..+++|.||++||++|++.++||||++++||+|++||.+||++.+++
T Consensus 74 i~pSgmkf~~iH~n~--s~~N~rsF~qevHely~ktLmspfy~~~~pirsqafd~~Vr~~ar~~ 135 (136)
T COG5603 74 IMPSGMKFLFIHQNQ--SRKNARSFLQEVHELYAKTLMSPFYEPDEPIRSQAFDDGVREAARVC 135 (136)
T ss_pred EccCCceEEEEeccc--hhhhHHHHHHHHHHHHHHHhhCcccCCCccccchhhhhhHHHHHHhh
Confidence 999999999999875 78899999999999999999999999999999999999999999875
No 5
>KOG3487 consensus TRAPP 20 K subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.2e-33 Score=195.61 Aligned_cols=129 Identities=30% Similarity=0.529 Sum_probs=117.7
Q ss_pred CEEEEEEEeCCCCeeEEecCCCc-------hhHHHH-HHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEE
Q 032311 1 MIACVAVVGHQNNPLYIQSFTEA-------DDALKL-HHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYG 72 (143)
Q Consensus 1 mi~~l~Ii~~~~~ply~~~~~~~-------~~~l~l-~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~ 72 (143)
|-.+++|||+.++|+|+-+|+.+ ++...| +|++|+|||++||..|.. +.+|||.+++++++-|++
T Consensus 1 m~~yfaIig~~d~Pvye~e~~~~~~~~~~~~~~~~LN~FI~HAaLdiVde~~W~~-------snmYLktVDkfne~~VSA 73 (139)
T KOG3487|consen 1 MTAYFAIIGHCDNPVYEMEFGCPENSKAARDDNRHLNQFIVHAALDIVDELQWTT-------SNMYLKTVDKFNELFVSA 73 (139)
T ss_pred CceEEEEEecCCCceEEeecCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHHH-------HhhHHHHHHhhcceeEEE
Confidence 67899999999999999999843 233344 799999999999999942 479999999999999999
Q ss_pred EEecCceEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhhhCCCCCCCCCCcchhHHHHHHHHHHHhC
Q 032311 73 YLTNTKVKFILVTTDLDVRDADVRNFFRRFHAAYIDAVSNPFHVPGKKITSRTFAERVSTIVKSFG 138 (143)
Q Consensus 73 y~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v~NPFy~~~~~I~s~~F~~~v~~~~~~~~ 138 (143)
|+|++++||++++..+ .+++++.||+++|++|++.++||||++++||+|+.||.+++.+.+++-
T Consensus 74 yvTas~i~f~mlh~~~--~~~~ik~Ffqev~elyik~lmnpFy~~~dpirs~afd~kv~~~~rkhl 137 (139)
T KOG3487|consen 74 YVTASHIRFIMLHINR--ADDNIKLFFQEVHELYIKTLMNPFYEINDPIRSPAFDHKVRGLARKHL 137 (139)
T ss_pred EEccCcEEEEEEeecc--ccccHHHHHHHHHHHHHHHHhCcccccCCccccHHHHHHHHHHHHHHh
Confidence 9999999999999986 689999999999999999999999999999999999999999999873
No 6
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.9e-33 Score=203.39 Aligned_cols=102 Identities=23% Similarity=0.348 Sum_probs=93.8
Q ss_pred hhHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEEEecCceEEEEEEcCCCcCcHHHHHHHHHHH
Q 032311 24 DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVKFILVTTDLDVRDADVRNFFRRFH 103 (143)
Q Consensus 24 ~~~l~l~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~ 103 (143)
|+.+.+++++| |+++|.++++|.++++|. .+.++++|++|||+|.||+|||+++++ ....++.+|+++|
T Consensus 95 NEkL~las~fh-sl~aI~~qlsp~~ksSGi-------e~LetdtF~l~~~QTlTG~KFVvis~~---~~~~aD~lLrKiY 163 (199)
T KOG3369|consen 95 NEKLILASSFH-SLFAISTQLSPEPKSSGI-------EVLETDTFTLHIFQTLTGTKFVVIAEP---GTQGADSLLRKIY 163 (199)
T ss_pred cchhhhhhhhc-chhheeeccCCCCCCCce-------EEEEeccEEEEEEEccCCcEEEEEecC---CchhHHHHHHHHH
Confidence 56788999999 999999999999887643 345899999999999999999999998 6788999999999
Q ss_pred HHHHHhh-hCCCCCCCCCCcchhHHHHHHHHHHH
Q 032311 104 AAYIDAV-SNPFHVPGKKITSRTFAERVSTIVKS 136 (143)
Q Consensus 104 ~~Y~~~v-~NPFy~~~~~I~s~~F~~~v~~~~~~ 136 (143)
++|+||| +||||+++|||+|++||++++.++++
T Consensus 164 elYsDyvlKNPfYSlEMPIRc~lFDe~lk~~le~ 197 (199)
T KOG3369|consen 164 ELYSDYVLKNPFYSLEMPIRCELFDEKLKFLLES 197 (199)
T ss_pred HHHHHHhhcCCccCcccceeHHHhhHHHHHHHhh
Confidence 9999999 99999999999999999999999875
No 7
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=99.96 E-value=5.8e-29 Score=169.48 Aligned_cols=124 Identities=19% Similarity=0.318 Sum_probs=106.3
Q ss_pred EEEEEEEeCCCCeeEEecCCCc------hhHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEEEe
Q 032311 2 IACVAVVGHQNNPLYIQSFTEA------DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLT 75 (143)
Q Consensus 2 i~~l~Ii~~~~~ply~~~~~~~------~~~l~l~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y~T 75 (143)
+..+.||||+|++||+|+|+.. |+.|.+.+++| +..+|..++.|-++++| + ++..++++.++-|+|
T Consensus 3 ve~~~iINksGglifqref~~~et~lnsneyLiLastlh-gV~aI~tq~~p~~gssg------~-~~l~~~~f~m~I~qT 74 (134)
T COG5122 3 VEQFFIINKSGGLIFQREFGEGETELNSNEYLILASTLH-GVSAILTQTIPLPGSSG------R-LVLYFRNFVMTIFQT 74 (134)
T ss_pred eeEEEEEecCCcEEEEEeccCCccccCcccEEEEeechh-hhhhhhhhcccCCCCCc------e-EEEEeccEEEEEEEe
Confidence 4578999999999999999754 67888999999 99999999988654432 2 344789999999999
Q ss_pred cCceEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhh-hCCCCCCCCCCcchhHHHHHHHHHHH
Q 032311 76 NTKVKFILVTTDLDVRDADVRNFFRRFHAAYIDAV-SNPFHVPGKKITSRTFAERVSTIVKS 136 (143)
Q Consensus 76 ~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v-~NPFy~~~~~I~s~~F~~~v~~~~~~ 136 (143)
.||+|||++++. +..+.+-=++++|++|+||| +||||+++|||+|.+||++++++++.
T Consensus 75 ~TG~kFV~~~~k---~t~na~~ql~kiY~lYsdYV~knPfys~EMPI~c~lFde~lkrm~e~ 133 (134)
T COG5122 75 TTGTKFVFVAEK---RTVNALFQLQKIYSLYSDYVTKNPFYSPEMPIQCSLFDEHLKRMFEG 133 (134)
T ss_pred cCCcEEEEEecC---CchhHHHHHHHHHHHHHHHhhcCCCCCcccceehhhhhHHHHHHhcC
Confidence 999999999976 44455555899999999999 99999999999999999999998764
No 8
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.95 E-value=2.9e-27 Score=164.87 Aligned_cols=125 Identities=25% Similarity=0.415 Sum_probs=112.2
Q ss_pred EEEEEEEeCCCCeeEEecCCCc-------hhHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEEE
Q 032311 2 IACVAVVGHQNNPLYIQSFTEA-------DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYL 74 (143)
Q Consensus 2 i~~l~Ii~~~~~ply~~~~~~~-------~~~l~l~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y~ 74 (143)
|++++|+||+|+|||.++|..+ +++.+|.|.+-+||..+.+++++.. ..+.++. ++|+.|++|.|+
T Consensus 3 iy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d-----~k~~f~s--y~Ts~Yklhfye 75 (140)
T KOG3368|consen 3 IYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGD-----VKDGFLS--YKTSKYKLHFYE 75 (140)
T ss_pred EEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCC-----cccCeeE--EeeceeEEEEEE
Confidence 7899999999999999999865 5679999988889999999998642 2344443 689999999999
Q ss_pred ecCceEEEEEEcCCCcCcHHHHHHHHHHHH-HHHHhh-hCCCCC--CCCCCcchhHHHHHHHHHHH
Q 032311 75 TNTKVKFILVTTDLDVRDADVRNFFRRFHA-AYIDAV-SNPFHV--PGKKITSRTFAERVSTIVKS 136 (143)
Q Consensus 75 T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~-~Y~~~v-~NPFy~--~~~~I~s~~F~~~v~~~~~~ 136 (143)
||||+||||++|+ +..++|++|++||. +|+++| +||.++ +++||+|+.|...+++.++.
T Consensus 76 Tptglk~vl~Tdp---k~~~ir~vLq~IYs~lyVE~Vvknpl~~~~~~~~i~~E~fr~~ld~~vrs 138 (140)
T KOG3368|consen 76 TPTGLKFVLNTDP---KAGSIRDVLQYIYSHLYVEYVVKNPLYTYDPGSPIRSELFRKILDRFVRS 138 (140)
T ss_pred cCCCcEEEEecCC---CcccHHHHHHHHHHHHHHHHHHcCcccccCCCCccchHHHHHHHHhhhcc
Confidence 9999999999998 88999999999996 999999 999999 89999999999999998873
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=96.13 E-value=0.29 Score=34.60 Aligned_cols=96 Identities=14% Similarity=0.304 Sum_probs=59.5
Q ss_pred CEEEEEEEeCCCCeeEEecCCCchhHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEEEecCceE
Q 032311 1 MIACVAVVGHQNNPLYIQSFTEADDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVK 80 (143)
Q Consensus 1 mi~~l~Ii~~~~~ply~~~~~~~~~~l~l~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y~T~Tg~K 80 (143)
||.++.|+|++|++++.|-|...+..-+ +-....-......+ . +. . ..+...+++++ .|....++-
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~-~~~~~~~~~~~~~~---~--~~---~----~~i~~~~~~~~-vy~~~~dl~ 66 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEER-QKLFEKFIKKKSSR---N--SK---Q----SPIFEHDNYRI-VYKRYSDLY 66 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHH-HHHHHHHHHHHHTS---S--SS---S----TSEEEETTEEE-EEEEETTEE
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHH-HHHHHHHHHHHHhc---c--cc---c----ceeeeccccee-eeEeeccEE
Confidence 9999999999999999998854322111 11222111222211 1 10 0 12334556554 787888999
Q ss_pred EEEEEcCCCcCcHHHHHHHHHHHHHHHHhhh
Q 032311 81 FILVTTDLDVRDADVRNFFRRFHAAYIDAVS 111 (143)
Q Consensus 81 fvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v~ 111 (143)
|+++++.. .++-.+-++++.+.+++-++..
T Consensus 67 ~~~v~~~~-eNel~~~e~l~~~v~~l~~~~~ 96 (141)
T PF01217_consen 67 FVVVGDEN-ENELLLLEFLHRLVEVLDDYFG 96 (141)
T ss_dssp EEEEESST-SBHHHHHHHHHHHHHHHHHHHS
T ss_pred EEEEeecc-cchHHHHHHHHHhhhhhhhhhc
Confidence 99999852 2344567788888888888765
No 10
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.50 E-value=2.2 Score=31.90 Aligned_cols=95 Identities=13% Similarity=0.135 Sum_probs=57.7
Q ss_pred EEEEEEEeCCCCeeEE--ecCCCc-----hhHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEEE
Q 032311 2 IACVAVVGHQNNPLYI--QSFTEA-----DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYL 74 (143)
Q Consensus 2 i~~l~Ii~~~~~ply~--~~~~~~-----~~~l~l~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y~ 74 (143)
|+++.|+.+.....-+ ..+.-. ...-.-.|+.+ .-..+.++..+..++ + .+.++|.+|+|+
T Consensus 3 i~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F-~sktvaeRt~~g~rq----------s-vk~~~Y~~h~yv 70 (198)
T KOG0861|consen 3 IYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTF-ISKTVAERTGPGQRQ----------S-VKHEEYLVHVYV 70 (198)
T ss_pred eEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHH-HHHHHHHhcCccccc----------c-cccceeEEEEEE
Confidence 7888998884433222 211111 11112245555 445667766654322 2 367799999999
Q ss_pred ecCceEEEEEEcCCCcCcHHHHHHHHHHHHHHHHh
Q 032311 75 TNTKVKFILVTTDLDVRDADVRNFFRRFHAAYIDA 109 (143)
Q Consensus 75 T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~ 109 (143)
-+.|+--|+++|+. +..-..-.++.+|-+-|..-
T Consensus 71 rndgL~~V~~~D~e-YP~rvA~tLL~kvld~~~~k 104 (198)
T KOG0861|consen 71 RNDGLCGVLIADDE-YPVRVAFTLLNKVLDEFTTK 104 (198)
T ss_pred ecCCeeEEEEecCc-CchhHHHHHHHHHHHHHhhc
Confidence 99999999999963 33444566777777777443
No 11
>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=80.25 E-value=12 Score=23.63 Aligned_cols=47 Identities=13% Similarity=0.280 Sum_probs=36.5
Q ss_pred ceecCCeEEEEEEecCceEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhh
Q 032311 62 LYPTENYKVYGYLTNTKVKFILVTTDLDVRDADVRNFFRRFHAAYIDAV 110 (143)
Q Consensus 62 l~~~~~~~v~~y~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v 110 (143)
.++.+++.+|.+. ..|+-++++++. .......=.||++|++.|....
T Consensus 18 s~~~~~~~fh~~~-~~~i~~~citd~-~~~~r~aF~fL~~i~~~F~~~~ 64 (83)
T PF13774_consen 18 SYESGNYVFHYLV-EDGIAYLCITDK-SYPKRVAFAFLEEIKQEFIQTY 64 (83)
T ss_dssp EEEETTEEEEEEE-ETTEEEEEEEET-TS-HHHHHHHHHHHHHHHHHHC
T ss_pred EEEECCEEEEEEE-cCCeEEEEEEcC-CCCcchHHHHHHHHHHHHHHHc
Confidence 3567888888888 999999999996 3345556778899998887753
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=80.19 E-value=34 Score=28.72 Aligned_cols=88 Identities=9% Similarity=0.254 Sum_probs=50.3
Q ss_pred EEEEEeCCCCeeEEecCCCchhHHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEEEecCceEEEE
Q 032311 4 CVAVVGHQNNPLYIQSFTEADDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVKFIL 83 (143)
Q Consensus 4 ~l~Ii~~~~~ply~~~~~~~~~~l~l~~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y~T~Tg~Kfvl 83 (143)
-+.|++..|.|||.+ +++++.-.-+..++++=+..+++. ..-|..+ ..++.++. |..-+.+-+|.
T Consensus 13 h~fIlS~AGKPIysr-~G~e~~l~~~~g~~~aiiS~~~~~------------~d~l~~i-~~~~~~iv-fl~r~pl~lv~ 77 (415)
T PF03164_consen 13 HFFILSSAGKPIYSR-YGDEDKLSSLMGVIQAIISFFQSN------------GDELRSI-RAGDHRIV-FLNRGPLILVA 77 (415)
T ss_pred eEEEECCCCceeEEe-cCChHHHHHHHHHHHHHHHHHHhC------------CCcEEEE-EeCCEEEE-EEecCCEEEEE
Confidence 478999999999998 565332233333444333333321 1113233 34555555 55577777777
Q ss_pred EEcCCCcCcHHHHHHHHHHHHHHH
Q 032311 84 VTTDLDVRDADVRNFFRRFHAAYI 107 (143)
Q Consensus 84 ~~~~~~~~~~~i~~~f~~i~~~Y~ 107 (143)
++... -.+..++.-|+-+|..-+
T Consensus 78 vS~~~-e~~~~l~~qL~~ly~qil 100 (415)
T PF03164_consen 78 VSKTG-ESESQLRKQLDYLYSQIL 100 (415)
T ss_pred EcCCc-CCHHHHHHHHHHHHHHHH
Confidence 77642 135567777777775443
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=56.53 E-value=27 Score=24.58 Aligned_cols=23 Identities=17% Similarity=0.352 Sum_probs=18.1
Q ss_pred cCCeEEEEEEecCc--eEEEEEEcC
Q 032311 65 TENYKVYGYLTNTK--VKFILVTTD 87 (143)
Q Consensus 65 ~~~~~v~~y~T~Tg--~Kfvl~~~~ 87 (143)
.+.+.+.+|+|++| +|+++-++.
T Consensus 55 ~~p~t~~~f~SpSG~GvKi~v~~~~ 79 (136)
T PF08800_consen 55 EDPYTLAAFVSPSGRGVKIIVPFDY 79 (136)
T ss_pred cCCcEEEEEEcCCCCeEEEEEEecC
Confidence 45577999998886 899998864
No 14
>PF13198 DUF4014: Protein of unknown function (DUF4014)
Probab=51.07 E-value=11 Score=23.86 Aligned_cols=27 Identities=26% Similarity=0.373 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHhhhCCCCCCCCCCc
Q 032311 96 RNFFRRFHAAYIDAVSNPFHVPGKKIT 122 (143)
Q Consensus 96 ~~~f~~i~~~Y~~~v~NPFy~~~~~I~ 122 (143)
-..++.+.+.|.+.++|||-.++..|.
T Consensus 41 ~~~~E~l~e~Y~~~~w~~F~~Lhnkin 67 (72)
T PF13198_consen 41 GKIIEPLFELYKDWFWNPFNALHNKIN 67 (72)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHhcccc
Confidence 336788999999999999987766653
No 15
>PF12532 DUF3732: Protein of unknown function (DUF3732); InterPro: IPR022205 This domain family is found in bacteria and eukaryotes, and is typically between 180 and 198 amino acids in length. There is a conserved DQP sequence motif.
Probab=48.54 E-value=29 Score=26.09 Aligned_cols=38 Identities=16% Similarity=0.246 Sum_probs=34.3
Q ss_pred EEeCCCCeeEEecCCCchhHHHHHHHHHHHHHHHHhhc
Q 032311 7 VVGHQNNPLYIQSFTEADDALKLHHIVHCSLDVVDERV 44 (143)
Q Consensus 7 Ii~~~~~ply~~~~~~~~~~l~l~~~~~~sLd~i~~~~ 44 (143)
+.++.+.++|.++.+++++.|-+|..++.||+-+-.+.
T Consensus 58 ~~~~~~~~~~L~~~GSgaNwl~~Hla~fLaLH~~f~~~ 95 (193)
T PF12532_consen 58 VFDRKNRPIPLREMGSGANWLAYHLALFLALHEFFAKN 95 (193)
T ss_pred EecCCCCeEeHHhcCChHHHHHHHHHHHHHHHHHHHhc
Confidence 58899999999999999999999999999999887665
No 16
>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=43.07 E-value=46 Score=20.95 Aligned_cols=34 Identities=15% Similarity=0.335 Sum_probs=24.1
Q ss_pred HHHHHHHHHhh-hCCCCCCCCCCcchhHHHHHHHHHHH
Q 032311 100 RRFHAAYIDAV-SNPFHVPGKKITSRTFAERVSTIVKS 136 (143)
Q Consensus 100 ~~i~~~Y~~~v-~NPFy~~~~~I~s~~F~~~v~~~~~~ 136 (143)
..||++|..+. .|=... ++....|.+++++++..
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 57888888887 776543 68999999999999866
No 17
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=42.92 E-value=21 Score=24.22 Aligned_cols=54 Identities=11% Similarity=0.226 Sum_probs=28.4
Q ss_pred ecCCeEEEEEEecCc------eEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhhhCCCCCC
Q 032311 64 PTENYKVYGYLTNTK------VKFILVTTDLDVRDADVRNFFRRFHAAYIDAVSNPFHVP 117 (143)
Q Consensus 64 ~~~~~~v~~y~T~Tg------~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v~NPFy~~ 117 (143)
..+++++.||.+..+ -...+..+.++++...+....+++|+-+...-..|++-+
T Consensus 19 ~~~~~~i~G~is~p~~~~~~~~~q~ifVN~R~V~~~~l~~~I~~~y~~~~~~~~~P~~vL 78 (119)
T PF01119_consen 19 EDEDFSIEGYISKPDVSRSSRDRQFIFVNGRPVENKALSKAINEAYRERLPKGRYPIFVL 78 (119)
T ss_dssp EECCEEEEEEEE-SSCSBSSCTCEEEEETTEEE--HHHHHHHHHHHHCTTCTTSB-EEEE
T ss_pred cCCCEEEEEEEECchhccCCCCcEEEEeCCCeEeChHHHHHHHHHHhhcccCCCCceEEE
Confidence 456799999987552 244445555555555555555554442223336676653
No 18
>COG4918 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.02 E-value=16 Score=24.94 Aligned_cols=18 Identities=22% Similarity=0.530 Sum_probs=15.7
Q ss_pred EEEeCCCCeeEEecCCCc
Q 032311 6 AVVGHQNNPLYIQSFTEA 23 (143)
Q Consensus 6 ~Ii~~~~~ply~~~~~~~ 23 (143)
.+|+.++.|||+++|++-
T Consensus 55 ~~idsn~gPiyik~~~~~ 72 (114)
T COG4918 55 ASIDSNFGPIYIKDYGSY 72 (114)
T ss_pred cccccCCCcEEEEeccee
Confidence 478999999999999865
No 19
>PHA01632 hypothetical protein
Probab=41.51 E-value=81 Score=19.14 Aligned_cols=35 Identities=11% Similarity=0.410 Sum_probs=26.9
Q ss_pred ceEEEEEEcCC--CcCcHHHHHHHHHHHHHHHHhhhC
Q 032311 78 KVKFILVTTDL--DVRDADVRNFFRRFHAAYIDAVSN 112 (143)
Q Consensus 78 g~Kfvl~~~~~--~~~~~~i~~~f~~i~~~Y~~~v~N 112 (143)
.+|+-++.+.. .+.++++|.++-++-.-|...+-|
T Consensus 14 hikiyilieqvp~kpteeelrkvlpkilkdyanmie~ 50 (64)
T PHA01632 14 HIKIYILIEQVPQKPTEEELRKVLPKILKDYANMIEN 50 (64)
T ss_pred EEEEEEehhhcCCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 35666666643 257899999999999999998855
No 20
>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=41.35 E-value=57 Score=23.73 Aligned_cols=41 Identities=15% Similarity=0.246 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhh--hCCCCCCCCCCcchhHHHHHHHHHHHhCC
Q 032311 99 FRRFHAAYIDAV--SNPFHVPGKKITSRTFAERVSTIVKSFGL 139 (143)
Q Consensus 99 f~~i~~~Y~~~v--~NPFy~~~~~I~s~~F~~~v~~~~~~~~~ 139 (143)
.++||+.|.+.. .-.|-.+.+.=+...|.+.++.+.++++.
T Consensus 55 i~~V~~~Y~~sF~~L~~~~~~~~~~~~~~F~~~l~~i~~~H~~ 97 (164)
T PF10436_consen 55 IQQVYEWYLQSFEELRSFPPPKTLEDNEKFTELLERILDRHSD 97 (164)
T ss_dssp HHHHHHHHHHHHHHHHTTSTTTSCCHHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhcc
Confidence 667777777765 44454455555689999999999988754
No 21
>PF13388 DUF4106: Protein of unknown function (DUF4106)
Probab=41.23 E-value=51 Score=26.92 Aligned_cols=42 Identities=21% Similarity=0.381 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHH-HHhh-hCCCCCCCCCCcchhHHHHHHHHHHHh
Q 032311 95 VRNFFRRFHAAY-IDAV-SNPFHVPGKKITSRTFAERVSTIVKSF 137 (143)
Q Consensus 95 i~~~f~~i~~~Y-~~~v-~NPFy~~~~~I~s~~F~~~v~~~~~~~ 137 (143)
+..-|+..+++. .+.. -|-|. .+..++|+.||+.+|+.++..
T Consensus 49 mnadfknafealhskvklvndfs-sgkklksegfdkelrevaqnm 92 (422)
T PF13388_consen 49 MNADFKNAFEALHSKVKLVNDFS-SGKKLKSEGFDKELREVAQNM 92 (422)
T ss_pred hcchHHHHHHHHHhhhhhhcccc-cccccccchhhHHHHHHHHHH
Confidence 444455555433 2333 78886 588999999999999988765
No 22
>KOG4497 consensus Uncharacterized conserved protein WDR8, contains WD repeats [General function prediction only]
Probab=38.45 E-value=24 Score=29.32 Aligned_cols=51 Identities=24% Similarity=0.292 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHhhcCCCCCCCCCCcccccccceecCCeEEEEEEecCceEEEEEEc
Q 032311 31 HIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVKFILVTT 86 (143)
Q Consensus 31 ~~~~~sLd~i~~~~~~~~~~~~~~~~~ylg~l~~~~~~~v~~y~T~Tg~Kfvl~~~ 86 (143)
.+-|+.+|.+|..=... + ++++.|-..+..=+|+||+|+-.+|+|||--..
T Consensus 170 ll~~f~~dT~DltgieW--s---Pdg~~laVwd~~Leykv~aYe~~lG~k~v~wsP 220 (447)
T KOG4497|consen 170 LLKEFKLDTIDLTGIEW--S---PDGNWLAVWDNVLEYKVYAYERGLGLKFVEWSP 220 (447)
T ss_pred HHHhcCCCcccccCceE--C---CCCcEEEEecchhhheeeeeeeccceeEEEecc
Confidence 45566777766422211 1 245777777777799999999999999987443
No 23
>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.
Probab=36.96 E-value=93 Score=21.41 Aligned_cols=51 Identities=27% Similarity=0.425 Sum_probs=29.1
Q ss_pred CCeEEEEEEec-----CceEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhhhCCCCC
Q 032311 66 ENYKVYGYLTN-----TKVKFILVTTDLDVRDADVRNFFRRFHAAYIDAVSNPFHV 116 (143)
Q Consensus 66 ~~~~v~~y~T~-----Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v~NPFy~ 116 (143)
+.+++.||.+. +.-+..+....+++++..+.....+.|.-|.---.-||+-
T Consensus 30 ~~~~i~G~is~p~~~~~~~~q~~fVNgR~V~~~~l~~aI~~~Y~~~l~~~~~P~~~ 85 (127)
T cd03483 30 LGFKVKGLISNANYSKKKIIFILFINNRLVECSALRRAIENVYANYLPKGAHPFVY 85 (127)
T ss_pred CcEEEEEEEcCchhcCCCceEEEEEcCCEecCHHHHHHHHHHHHHhCcCCCccEEE
Confidence 46999999743 2334555556666666555554444444443333567774
No 24
>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=34.66 E-value=1.6e+02 Score=21.70 Aligned_cols=49 Identities=18% Similarity=0.252 Sum_probs=34.0
Q ss_pred cccccccceecCCeEEEEEEecCceEEEEEEcCCCcCcHHHHHHHHHHHHHHH
Q 032311 55 NETFLGLLYPTENYKVYGYLTNTKVKFILVTTDLDVRDADVRNFFRRFHAAYI 107 (143)
Q Consensus 55 ~~~ylg~l~~~~~~~v~~y~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~ 107 (143)
++.|=|++++..+-++-.-+=.||- |+++..+ +.++++..++.|+..-.
T Consensus 124 PE~fPgliyr~~~pk~~~liF~sGk--vvitGak--s~~~~~~a~~~i~p~L~ 172 (174)
T cd04516 124 PELFPGLIYRMVKPKIVLLIFVSGK--IVLTGAK--SREEIYQAFENIYPILL 172 (174)
T ss_pred CccCceEEEEecCCcEEEEEeCCCE--EEEEecC--CHHHHHHHHHHHHHHHh
Confidence 3567778888888777777777774 3344333 77889998999886544
No 25
>PHA00743 helix-turn-helix protein
Probab=34.53 E-value=51 Score=19.44 Aligned_cols=23 Identities=30% Similarity=0.512 Sum_probs=19.8
Q ss_pred CcHHHHHHHHHHHHHHHHhhhCC
Q 032311 91 RDADVRNFFRRFHAAYIDAVSNP 113 (143)
Q Consensus 91 ~~~~i~~~f~~i~~~Y~~~v~NP 113 (143)
-|+++|.++.-||+.=+|.+.+-
T Consensus 4 LD~~iReLLs~iheIKID~i~~~ 26 (51)
T PHA00743 4 LDEDVRELLSIIHEIKIDIITQS 26 (51)
T ss_pred hHHHHHHHHHHHHHHhhhhhccc
Confidence 37899999999999999999443
No 26
>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=33.67 E-value=22 Score=20.17 Aligned_cols=7 Identities=43% Similarity=0.989 Sum_probs=6.0
Q ss_pred hCCCCCC
Q 032311 111 SNPFHVP 117 (143)
Q Consensus 111 ~NPFy~~ 117 (143)
.+|||++
T Consensus 30 ~DPF~e~ 36 (45)
T PF12423_consen 30 DDPFYEP 36 (45)
T ss_pred CCCCCCC
Confidence 8999986
No 27
>PF07013 DUF1314: Protein of unknown function (DUF1314); InterPro: IPR010741 This family consists of several alphaherpesvirus proteins of around 200 residues in length. They belong to the varicellovirus ORF2 family and their function is unknown.
Probab=33.65 E-value=20 Score=26.63 Aligned_cols=23 Identities=35% Similarity=0.696 Sum_probs=19.6
Q ss_pred cceecCCeEEEEEEecCceEEEE
Q 032311 61 LLYPTENYKVYGYLTNTKVKFIL 83 (143)
Q Consensus 61 ~l~~~~~~~v~~y~T~Tg~Kfvl 83 (143)
.|+...+..||||+-.||+-|+.
T Consensus 62 ~iy~~~~~~vyGyE~~tgLH~La 84 (177)
T PF07013_consen 62 VIYLSRNGSVYGYENGTGLHFLA 84 (177)
T ss_pred EEEEccCCeEEeecCCcchhhhh
Confidence 45678889999999999998764
No 28
>cd00782 MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot synd
Probab=32.64 E-value=1.1e+02 Score=20.42 Aligned_cols=53 Identities=17% Similarity=0.344 Sum_probs=31.2
Q ss_pred cCCeEEEEEEecCce------EEEEEEcCCCcCcHHHHHHHHHHHHHHHHhhhCCCCCC
Q 032311 65 TENYKVYGYLTNTKV------KFILVTTDLDVRDADVRNFFRRFHAAYIDAVSNPFHVP 117 (143)
Q Consensus 65 ~~~~~v~~y~T~Tg~------Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v~NPFy~~ 117 (143)
.+.+++.||.+.-+. ...+..+.+++....+.....++|.-|...-..|++-+
T Consensus 24 ~~~~~i~G~is~~~~~~~~~~~q~~fVN~R~v~~~~l~~ai~~~y~~~~~~~~~P~~~L 82 (122)
T cd00782 24 SGDFRISGYISKPDFGRSSKDRQFLFVNGRPVRDKLLSKAINEAYRSYLPKGRYPVFVL 82 (122)
T ss_pred CCCEEEEEEEECchhhcCCCccEEEEECCeEecCHHHHHHHHHHHHHhCcCCCCcEEEE
Confidence 456999999866552 23334444555655666655555555554346777654
No 29
>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=31.10 E-value=1.6e+02 Score=21.67 Aligned_cols=47 Identities=19% Similarity=0.165 Sum_probs=34.4
Q ss_pred cccccccceecCCeEEEEEEecCceEEEEEEcCCCcCcHHHHHHHHHHHHH
Q 032311 55 NETFLGLLYPTENYKVYGYLTNTKVKFILVTTDLDVRDADVRNFFRRFHAA 105 (143)
Q Consensus 55 ~~~ylg~l~~~~~~~v~~y~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~ 105 (143)
++.|=|++++..+-++-+.+=+||- |+++..+ +.++++..++.++..
T Consensus 125 PE~fPgliyr~~~p~~t~lIF~sGk--ivitGak--s~~~~~~a~~~i~pi 171 (174)
T cd04517 125 PELHPGVVYRITGPRATLSIFSTGS--VTVTGAR--SMEDVREAVEKIYPI 171 (174)
T ss_pred CccCCEEEEEECCCcEEEEEeCCCE--EEEEecC--CHHHHHHHHHHHHHH
Confidence 3577788888888788887878875 3344443 678899999998864
No 30
>cd03485 MutL_Trans_hPMS_1_like MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition.
Probab=30.72 E-value=1.7e+02 Score=20.14 Aligned_cols=43 Identities=12% Similarity=0.103 Sum_probs=23.2
Q ss_pred CCeEEEEEEecCc--------eEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhh
Q 032311 66 ENYKVYGYLTNTK--------VKFILVTTDLDVRDADVRNFFRRFHAAYIDAV 110 (143)
Q Consensus 66 ~~~~v~~y~T~Tg--------~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v 110 (143)
+++++.||.+.-+ -.-.+..+.++++. -+.+.+.|.++|-.++
T Consensus 28 ~~~~i~G~is~p~~~~~~~~~~~q~~fVN~R~v~~--~~~l~k~i~~~y~~~~ 78 (132)
T cd03485 28 PQISLEGFLPKPGSDVSKTKSDGKFISVNSRPVSL--GKDIGKLLRQYYSSAY 78 (132)
T ss_pred CcEEEEEEECCCCcCCCcccCCcEEEEECCeeccc--chHHHHHHHHHHHHHh
Confidence 4699999986641 12233444455554 1344445555555544
No 31
>PHA03371 circ protein; Provisional
Probab=29.75 E-value=24 Score=27.50 Aligned_cols=22 Identities=36% Similarity=0.700 Sum_probs=18.7
Q ss_pred ceecCCeEEEEEEecCceEEEE
Q 032311 62 LYPTENYKVYGYLTNTKVKFIL 83 (143)
Q Consensus 62 l~~~~~~~v~~y~T~Tg~Kfvl 83 (143)
|+...+.+||||+-.||+.|+.
T Consensus 86 iyl~r~~sVyGYE~gtGLH~LA 107 (240)
T PHA03371 86 IYLSRNGSVYGYENGTGLHFLA 107 (240)
T ss_pred EEEccCCeEEeecCCcchhhhH
Confidence 4567789999999999998875
No 32
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.88 E-value=29 Score=29.03 Aligned_cols=22 Identities=14% Similarity=0.261 Sum_probs=20.3
Q ss_pred CEEEEEEEeCCCCeeEEecCCC
Q 032311 1 MIACVAVVGHQNNPLYIQSFTE 22 (143)
Q Consensus 1 mi~~l~Ii~~~~~ply~~~~~~ 22 (143)
|+.|++++|.+|..++++.|..
T Consensus 1 mi~siflidtsg~l~lek~~~g 22 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKG 22 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCC
Confidence 8999999999999999998863
No 33
>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=28.28 E-value=2.3e+02 Score=20.69 Aligned_cols=71 Identities=10% Similarity=0.154 Sum_probs=42.7
Q ss_pred CeEEEEEEecCceEEEEEEcCCCcCc---HHHHHHHHHH---------HHHHHHhh--hCCCCCCCCCCcchhHHHHHHH
Q 032311 67 NYKVYGYLTNTKVKFILVTTDLDVRD---ADVRNFFRRF---------HAAYIDAV--SNPFHVPGKKITSRTFAERVST 132 (143)
Q Consensus 67 ~~~v~~y~T~Tg~Kfvl~~~~~~~~~---~~i~~~f~~i---------~~~Y~~~v--~NPFy~~~~~I~s~~F~~~v~~ 132 (143)
.-+++..++..+-.++++.|..++.. +.|++.|.++ -..++..+ .|+.++.+..+.++.+++.++.
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 34556666666666677777653222 2344444444 33344444 6655666777788888888888
Q ss_pred HHHHh
Q 032311 133 IVKSF 137 (143)
Q Consensus 133 ~~~~~ 137 (143)
.++..
T Consensus 142 ~~~~A 146 (179)
T PF09843_consen 142 AVSEA 146 (179)
T ss_pred HHHHH
Confidence 87764
No 34
>PF10906 DUF2697: Protein of unknown function (DUF2697); InterPro: IPR020301 This entry contains proteins with no known function.
Probab=27.21 E-value=53 Score=20.66 Aligned_cols=19 Identities=21% Similarity=0.128 Sum_probs=17.3
Q ss_pred CcchhHHHHHHHHHHHhCC
Q 032311 121 ITSRTFAERVSTIVKSFGL 139 (143)
Q Consensus 121 I~s~~F~~~v~~~~~~~~~ 139 (143)
++|+.|-+-|+.+.++.|+
T Consensus 9 l~SpgFhrfVR~Ih~kVN~ 27 (68)
T PF10906_consen 9 LDSPGFHRFVRRIHAKVNG 27 (68)
T ss_pred HcChhHHHHHHHHHHHHhC
Confidence 6899999999999999876
No 35
>PF04370 DUF508: Domain of unknown function (DUF508) ; InterPro: IPR007465 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=27.00 E-value=2.5e+02 Score=20.32 Aligned_cols=65 Identities=22% Similarity=0.369 Sum_probs=43.3
Q ss_pred EEecCceEEEEEEcCC------------CcCcHHHHHHHHHHHHHHHHhhh-CCCCC-----CC-------CCCcchhHH
Q 032311 73 YLTNTKVKFILVTTDL------------DVRDADVRNFFRRFHAAYIDAVS-NPFHV-----PG-------KKITSRTFA 127 (143)
Q Consensus 73 y~T~Tg~Kfvl~~~~~------------~~~~~~i~~~f~~i~~~Y~~~v~-NPFy~-----~~-------~~I~s~~F~ 127 (143)
|+|.-.+||||++-+. -..|-.+..+.-..|+++.+-+. +-|.+ .+ .|+-..-..
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 7888889999999652 12344566666677888888873 33322 12 477777777
Q ss_pred HHHHHHHHHh
Q 032311 128 ERVSTIVKSF 137 (143)
Q Consensus 128 ~~v~~~~~~~ 137 (143)
+.+.++++..
T Consensus 129 KtLAqLA~t~ 138 (156)
T PF04370_consen 129 KTLAQLAATN 138 (156)
T ss_pred HHHHHHhccC
Confidence 7777777643
No 36
>cd03484 MutL_Trans_hPMS_2_like MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2). hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome.
Probab=25.66 E-value=2.1e+02 Score=20.02 Aligned_cols=50 Identities=14% Similarity=0.289 Sum_probs=28.9
Q ss_pred CCeEEEEEEecC--------ceEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhhhCCCCC
Q 032311 66 ENYKVYGYLTNT--------KVKFILVTTDLDVRDADVRNFFRRFHAAYIDAVSNPFHV 116 (143)
Q Consensus 66 ~~~~v~~y~T~T--------g~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v~NPFy~ 116 (143)
.++++.||.+.- .-+..+..+.+++....+.....+.|.-|. .-+-||+-
T Consensus 43 ~~~~i~G~is~p~~~~~r~~~~~q~~fVN~R~V~~~~l~~aI~~~y~~~~-~~~~P~~v 100 (142)
T cd03484 43 SEVKITGYISKPSHGCGRSSSDRQFFYINGRPVDLKKVAKLINEVYKSFN-SRQYPFFI 100 (142)
T ss_pred CcEEEEEEECCCcccCCCCCCCcEEEEECCeecCCHHHHHHHHHHHHHhc-CcCCcEEE
Confidence 469999998665 223455556565665554444444444433 12677773
No 37
>PF14120 YhzD: YhzD-like protein
Probab=24.91 E-value=62 Score=19.89 Aligned_cols=23 Identities=13% Similarity=0.213 Sum_probs=20.4
Q ss_pred EEEEEEEeCCCCeeEEecCCCch
Q 032311 2 IACVAVVGHQNNPLYIQSFTEAD 24 (143)
Q Consensus 2 i~~l~Ii~~~~~ply~~~~~~~~ 24 (143)
.|.+.++.++|.-|+...|..++
T Consensus 3 ~Y~lTaFe~~Ge~lldE~feA~~ 25 (61)
T PF14120_consen 3 TYFLTAFEKSGEKLLDETFEAAN 25 (61)
T ss_pred ceEEEEECCCCchhhhcceecCC
Confidence 68999999999999999998763
No 38
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=24.63 E-value=1.4e+02 Score=22.66 Aligned_cols=43 Identities=16% Similarity=0.250 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHhh-hCC--CCCCCCCCcchhHHHHHHHHHHHhC
Q 032311 96 RNFFRRFHAAYIDAV-SNP--FHVPGKKITSRTFAERVSTIVKSFG 138 (143)
Q Consensus 96 ~~~f~~i~~~Y~~~v-~NP--Fy~~~~~I~s~~F~~~v~~~~~~~~ 138 (143)
..|++++++.|.+.. +.| |...+..-.-+...+.+.+.+..+.
T Consensus 160 ~~f~~kvr~~Y~~la~~~~~r~~vIda~~~~e~v~~~i~~~l~~~l 205 (208)
T COG0125 160 DEFLEKVREGYLELAAKFPERIIVIDASRPLEEVHEEILKILKERL 205 (208)
T ss_pred HHHHHHHHHHHHHHHhhCCCeEEEEECCCCHHHHHHHHHHHHHHhh
Confidence 368999999999999 998 7655544444566666666666553
No 39
>PRK14449 acylphosphatase; Provisional
Probab=23.76 E-value=1.3e+02 Score=19.46 Aligned_cols=36 Identities=11% Similarity=0.248 Sum_probs=23.4
Q ss_pred CCeEEEEEEecCce-EEEEEEcCCCcCcHHHHHHHHHHHH
Q 032311 66 ENYKVYGYLTNTKV-KFILVTTDLDVRDADVRNFFRRFHA 104 (143)
Q Consensus 66 ~~~~v~~y~T~Tg~-Kfvl~~~~~~~~~~~i~~~f~~i~~ 104 (143)
..+.+.||+.|..= ..-+.... +++.+.+|++.+.+
T Consensus 27 ~~lgl~G~V~N~~dG~Vei~~~G---~~~~v~~f~~~l~~ 63 (90)
T PRK14449 27 VSLGITGYAENLYDGSVEVVAEG---DEENIKELINFIKT 63 (90)
T ss_pred HHcCCEEEEEECCCCeEEEEEEe---CHHHHHHHHHHHhh
Confidence 45778899866553 23333443 56778888888864
No 40
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=22.84 E-value=41 Score=24.87 Aligned_cols=18 Identities=22% Similarity=0.333 Sum_probs=15.1
Q ss_pred HHHHHHHHhh--hCCCCCCC
Q 032311 101 RFHAAYIDAV--SNPFHVPG 118 (143)
Q Consensus 101 ~i~~~Y~~~v--~NPFy~~~ 118 (143)
.|-++|+.++ |||-+.++
T Consensus 13 ti~dAYv~FilyCNP~vP~~ 32 (175)
T PF09441_consen 13 TIDDAYVAFILYCNPAVPLD 32 (175)
T ss_pred chhhhhheeeeecCCCCCCC
Confidence 5668999988 99999766
No 41
>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=22.20 E-value=3.2e+02 Score=20.00 Aligned_cols=47 Identities=21% Similarity=0.271 Sum_probs=33.5
Q ss_pred cccccccceecCCeEEEEEEecCceEEEEEEcCCCcCcHHHHHHHHHHHHH
Q 032311 55 NETFLGLLYPTENYKVYGYLTNTKVKFILVTTDLDVRDADVRNFFRRFHAA 105 (143)
Q Consensus 55 ~~~ylg~l~~~~~~~v~~y~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~ 105 (143)
++.|=|++++..+-++.+.+=.||- |+++..+ +.++++..++.++..
T Consensus 125 Pe~fpgli~r~~~pk~t~lIF~sGk--vvitGak--s~~~~~~a~~~i~~~ 171 (174)
T cd00652 125 PELFPGLIYRMDEPKVVLLIFVSGK--IVITGAK--SREDIYEAVEKIYPI 171 (174)
T ss_pred CccCceEEEEecCCcEEEEEEcCCE--EEEEecC--CHHHHHHHHHHHHHH
Confidence 3567778888888777777777774 3344443 678888888888864
No 42
>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=22.06 E-value=62 Score=23.94 Aligned_cols=14 Identities=36% Similarity=0.864 Sum_probs=12.5
Q ss_pred EEEecCceEEEEEE
Q 032311 72 GYLTNTKVKFILVT 85 (143)
Q Consensus 72 ~y~T~Tg~Kfvl~~ 85 (143)
||.|++++||+++-
T Consensus 54 gY~t~~~Vr~~itP 67 (189)
T PF03558_consen 54 GYITIRDVRFVITP 67 (189)
T ss_pred ceeeceeeEEEEee
Confidence 79999999999954
No 43
>COG1507 Uncharacterized conserved protein [Function unknown]
Probab=21.81 E-value=1e+02 Score=22.50 Aligned_cols=18 Identities=39% Similarity=0.971 Sum_probs=16.4
Q ss_pred CcHHHHHHHHHHHHHHHH
Q 032311 91 RDADVRNFFRRFHAAYID 108 (143)
Q Consensus 91 ~~~~i~~~f~~i~~~Y~~ 108 (143)
+|+++++++++.|+-|++
T Consensus 81 ~d~eL~~~~~raHe~~lk 98 (167)
T COG1507 81 QDEELRAFYRRAHESYLK 98 (167)
T ss_pred ccHHHHHHHHHHHHHHHH
Confidence 678999999999999986
No 44
>PLN00062 TATA-box-binding protein; Provisional
Probab=21.64 E-value=3.4e+02 Score=20.09 Aligned_cols=51 Identities=18% Similarity=0.236 Sum_probs=36.0
Q ss_pred ccccccceecCCeEEEEEEecCceEEEEEEcCCCcCcHHHHHHHHHHHHHHHHhh
Q 032311 56 ETFLGLLYPTENYKVYGYLTNTKVKFILVTTDLDVRDADVRNFFRRFHAAYIDAV 110 (143)
Q Consensus 56 ~~ylg~l~~~~~~~v~~y~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~Y~~~v 110 (143)
+.|=|++++..+-++-.-+=.||- |+++..+ +.++++..++.|+..-.++-
T Consensus 125 E~fPgliyr~~~pk~~~liF~sGk--vvitGak--s~~~~~~ai~~i~p~L~~~~ 175 (179)
T PLN00062 125 ELFPGLIYRMKQPKIVLLIFVSGK--IVITGAK--VREEIYTAFENIYPVLTEFR 175 (179)
T ss_pred ccCceEEEEeCCCcEEEEEeCCCE--EEEEecC--CHHHHHHHHHHHHHHHHHhc
Confidence 566677788777777777767773 3344443 78889999999997766654
No 45
>COG3260 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]
Probab=21.42 E-value=2e+02 Score=20.84 Aligned_cols=40 Identities=18% Similarity=0.252 Sum_probs=33.0
Q ss_pred eecCCeEEEEEEecCceEEEEEEcCCCcCcHHHHHHHHHHHHH
Q 032311 63 YPTENYKVYGYLTNTKVKFILVTTDLDVRDADVRNFFRRFHAA 105 (143)
Q Consensus 63 ~~~~~~~v~~y~T~Tg~Kfvl~~~~~~~~~~~i~~~f~~i~~~ 105 (143)
+..+.|-++.--+|-.--.+|+|.. -...++.-++++|++
T Consensus 34 YDaErfgI~~v~sPRhADiLlVTG~---vT~~~~e~lkk~Yea 73 (148)
T COG3260 34 YDAERFGIKVVNSPRHADILLVTGA---VTRQMREPLKKAYEA 73 (148)
T ss_pred cchHHheeEEeCCCccccEEEEecc---ccHHHHHHHHHHHHh
Confidence 4467788888889999999999987 567788888888875
No 46
>PF03928 DUF336: Domain of unknown function (DUF336); InterPro: IPR005624 This entry contains uncharacterised proteins, including GlcG P45504 from SWISSPROT. The alignment contains many conserved motifs that are suggestive of cofactor binding and enzymatic activity.; PDB: 2A2L_D 3FPW_A 3FPV_E.
Probab=21.17 E-value=1.1e+02 Score=21.16 Aligned_cols=20 Identities=20% Similarity=0.223 Sum_probs=14.6
Q ss_pred EEEEEEeCCCCeeEEecCCC
Q 032311 3 ACVAVVGHQNNPLYIQSFTE 22 (143)
Q Consensus 3 ~~l~Ii~~~~~ply~~~~~~ 22 (143)
.+++|++++|.+++...-+.
T Consensus 26 v~iaVvd~~G~~~~~~r~dg 45 (132)
T PF03928_consen 26 VSIAVVDAGGHLLAFARMDG 45 (132)
T ss_dssp -EEEEEETTS-EEEEEE-TT
T ss_pred eEEEEEECCCCEEEEEecCC
Confidence 48999999999999875543
No 47
>PF06683 DUF1184: Protein of unknown function (DUF1184); InterPro: IPR009568 This family contains a number of hypothetical proteins of unknown function from Arabidopsis thaliana.
Probab=20.81 E-value=2.1e+02 Score=21.34 Aligned_cols=26 Identities=19% Similarity=0.263 Sum_probs=21.8
Q ss_pred CcHHHHHHHHHHHHHHHHhh--hCCCCC
Q 032311 91 RDADVRNFFRRFHAAYIDAV--SNPFHV 116 (143)
Q Consensus 91 ~~~~i~~~f~~i~~~Y~~~v--~NPFy~ 116 (143)
.+..++.++.-+|-.|..|+ +|--|+
T Consensus 76 ~~pVv~rLl~Vm~YV~~tyIKPKNgVyq 103 (191)
T PF06683_consen 76 PDPVVERLLRVMHYVFSTYIKPKNGVYQ 103 (191)
T ss_pred CchHHHHHHHhhhhhhhcccCCCccccc
Confidence 45678888999999999998 898887
No 48
>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=20.64 E-value=1e+02 Score=21.20 Aligned_cols=21 Identities=10% Similarity=0.037 Sum_probs=16.8
Q ss_pred CeEEEEEEecCceEEEEEEcC
Q 032311 67 NYKVYGYLTNTKVKFILVTTD 87 (143)
Q Consensus 67 ~~~v~~y~T~Tg~Kfvl~~~~ 87 (143)
.-+|.+|.+.+|+|.++--+-
T Consensus 60 ~G~ik~~r~~~g~rL~fS~~i 80 (108)
T PF12321_consen 60 RGTIKVYRQRGGVRLHFSRSI 80 (108)
T ss_pred cEEEEEEEeCCceEEEEeCCC
Confidence 567889999999998776553
No 49
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=20.53 E-value=83 Score=17.67 Aligned_cols=17 Identities=12% Similarity=0.331 Sum_probs=14.5
Q ss_pred cchhHHHHHHHHHHHhC
Q 032311 122 TSRTFAERVSTIVKSFG 138 (143)
Q Consensus 122 ~s~~F~~~v~~~~~~~~ 138 (143)
+|+.+++.|+.++++|.
T Consensus 28 ~S~Ll~eAle~~l~ky~ 44 (44)
T PF12651_consen 28 KSKLLREALEDYLEKYE 44 (44)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 68899999999998874
No 50
>PF07428 Tri3: 15-O-acetyltransferase Tri3; InterPro: IPR009992 This family represents a conserved region approximately 400 residues long within 15-O-acetyltransferase (Tri3), which seems to be restricted to ascomycete fungi. In Fusarium sporotrichioides, this is required for acetylation of the C-15 hydroxyl group of trichothecenes in the biosynthesis of T-2 toxin [].; PDB: 3FP0_A 3FOT_A.
Probab=20.51 E-value=1.2e+02 Score=25.47 Aligned_cols=45 Identities=24% Similarity=0.380 Sum_probs=25.3
Q ss_pred EEEEEEecCceEEEEEEcCCCcCcHHH-----HHHHHHHHHHHHHhhhCCCCC
Q 032311 69 KVYGYLTNTKVKFILVTTDLDVRDADV-----RNFFRRFHAAYIDAVSNPFHV 116 (143)
Q Consensus 69 ~v~~y~T~Tg~Kfvl~~~~~~~~~~~i-----~~~f~~i~~~Y~~~v~NPFy~ 116 (143)
...|.+--.++|=+.+.+. +++++ .+-++.+.+.|=.++.|||..
T Consensus 349 qt~a~V~~eniks~~v~~~---d~k~~~~~~l~~a~~~~k~~yd~~l~np~~~ 398 (413)
T PF07428_consen 349 QTAAVVRFENIKSIAVSDA---DDKDIQVKALEQACRDVKKSYDQWLSNPFQL 398 (413)
T ss_dssp EEEEEEEE--GGGG---TT---S-HHHHHHHHHHHHHHHHHHHHHHHT-TTHH
T ss_pred hccceEEEccchheecccc---ccccccHHHHHHHHHHHHHHHHHHhcChhhh
Confidence 3344555556665666654 44444 455788889999999999953
Done!