Query 033894
Match_columns 109
No_of_seqs 106 out of 427
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 07:30:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033894.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033894hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01217 Clat_adaptor_s: Clath 100.0 7.1E-32 1.5E-36 190.5 14.3 104 1-105 1-139 (141)
2 COG5030 APS2 Clathrin adaptor 100.0 3.3E-31 7.2E-36 189.4 10.9 101 1-102 1-136 (152)
3 KOG0936 Clathrin adaptor compl 100.0 3.1E-30 6.7E-35 187.3 11.0 106 1-107 1-147 (182)
4 KOG3343 Vesicle coat complex C 100.0 4.6E-30 1E-34 186.9 9.7 97 9-105 51-147 (175)
5 KOG0934 Clathrin adaptor compl 99.9 1.8E-28 3.9E-33 174.8 5.4 101 1-102 1-136 (145)
6 KOG0935 Clathrin adaptor compl 99.9 1.6E-27 3.4E-32 167.5 8.5 102 1-103 1-138 (143)
7 COG5541 RET3 Vesicle coat comp 99.9 3.5E-22 7.6E-27 145.8 7.6 99 9-108 58-156 (187)
8 KOG2740 Clathrin-associated pr 98.9 9.4E-09 2E-13 83.7 7.6 104 1-107 1-139 (418)
9 KOG0938 Adaptor complexes medi 98.8 6.9E-08 1.5E-12 78.5 10.9 103 1-104 1-135 (446)
10 KOG0937 Adaptor complexes medi 97.9 0.00024 5.2E-09 59.1 10.9 90 14-104 47-136 (424)
11 PF15001 AP-5_subunit_s1: AP-5 96.7 0.022 4.8E-07 43.0 9.4 79 19-97 103-181 (189)
12 KOG2635 Medium subunit of clat 96.2 0.048 1E-06 46.1 9.3 86 14-100 48-133 (512)
13 COG2093 DNA-directed RNA polym 65.4 5.7 0.00012 25.1 2.0 24 86-109 34-59 (64)
14 PF05184 SapB_1: Saposin-like 61.4 17 0.00036 19.5 3.3 32 46-77 4-35 (39)
15 PF10788 DUF2603: Protein of u 53.3 31 0.00068 24.8 4.4 65 45-109 57-133 (137)
16 PF08923 MAPKK1_Int: Mitogen-a 52.4 76 0.0017 22.0 7.9 46 14-59 70-115 (119)
17 smart00836 DALR_1 DALR anticod 50.6 70 0.0015 21.0 5.8 62 39-101 35-97 (122)
18 PF03164 Mon1: Trafficking pro 41.9 2E+02 0.0044 23.8 9.5 37 19-55 62-98 (415)
19 cd07956 Anticodon_Ia_Arg Antic 40.4 1.2E+02 0.0025 21.1 5.7 63 39-102 70-132 (156)
20 PF13812 PPR_3: Pentatricopept 31.0 44 0.00096 16.4 1.7 17 72-88 16-32 (34)
21 PF13456 RVT_3: Reverse transc 29.2 71 0.0015 19.1 2.7 21 85-105 21-41 (87)
22 PF08866 DUF1831: Putative ami 26.3 62 0.0013 22.5 2.2 18 73-90 94-111 (112)
23 COG2047 Uncharacterized protei 26.3 2.8E+02 0.0061 21.9 6.1 52 6-58 59-114 (258)
24 PF08784 RPA_C: Replication pr 25.9 71 0.0015 20.7 2.4 46 47-92 47-98 (102)
25 TIGR03882 cyclo_dehyd_2 bacter 25.2 2.8E+02 0.0061 20.4 7.4 41 53-93 32-78 (193)
26 PF01535 PPR: PPR repeat; Int 22.8 77 0.0017 15.0 1.7 18 71-88 14-31 (31)
27 PF04504 DUF573: Protein of un 21.8 2.5E+02 0.0054 18.6 4.7 15 38-52 8-22 (98)
28 KOG1511 Mevalonate kinase MVK/ 21.6 82 0.0018 26.4 2.4 27 1-28 1-27 (397)
29 PF01526 DDE_Tnp_Tn3: Tn3 tran 21.2 2.3E+02 0.005 23.5 5.0 50 52-105 214-263 (388)
30 PRK05986 cob(I)alamin adenolsy 21.1 18 0.00039 27.2 -1.3 31 72-107 115-148 (191)
31 cd00561 CobA_CobO_BtuR ATP:cor 21.0 25 0.00053 25.6 -0.6 31 72-107 95-128 (159)
32 PF13998 MgrB: MgrB protein 20.8 69 0.0015 17.2 1.3 12 77-88 3-14 (29)
33 PF02268 TFIIA_gamma_N: Transc 20.7 37 0.0008 20.2 0.2 13 79-91 18-30 (49)
34 TIGR00708 cobA cob(I)alamin ad 20.3 25 0.00054 26.0 -0.7 31 72-107 97-130 (173)
No 1
>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=100.00 E-value=7.1e-32 Score=190.53 Aligned_cols=104 Identities=30% Similarity=0.489 Sum_probs=98.4
Q ss_pred CceEEEeeecCCcEEEEc-----------------------------------CeEEEEEEeccEEEEEEEcCCCCHHHH
Q 033894 1 MILAVLFANSEGNILVER-----------------------------------SVYIVYTVLGDVSIFVVGKDEYDELAL 45 (109)
Q Consensus 1 mi~~~l~~~~~g~i~l~~-----------------------------------~~~iVyr~~~dl~~~vvg~~~eNEL~l 45 (109)
||+|+++.|++|++++.+ ++.+|||+++|++|+++|+.+|||+++
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~~ 80 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRNSKQSPIFEHDNYRIVYKRYSDLYFVVVGDENENELLL 80 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSSSSSTSEEEETTEEEEEEEETTEEEEEEESSTSBHHHH
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhcccccceeeecccceeeeEeeccEEEEEEeecccchHHH
Confidence 999999999999999999 899999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHHHHHhhcCC
Q 033894 46 AEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKP 105 (109)
Q Consensus 46 ~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I~~rv~~k~ 105 (109)
++++|+++++|+.+|+ ++||+++++||++++++|||++|+|+++|||+++|++|++++-
T Consensus 81 ~e~l~~~v~~l~~~~~-~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~~ 139 (141)
T PF01217_consen 81 LEFLHRLVEVLDDYFG-NVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQD 139 (141)
T ss_dssp HHHHHHHHHHHHHHHS-S-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHCC
T ss_pred HHHHHHhhhhhhhhhc-cccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHhh
Confidence 9999999999999998 6999999999999999999999999999999999999998863
No 2
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.97 E-value=3.3e-31 Score=189.35 Aligned_cols=101 Identities=22% Similarity=0.290 Sum_probs=96.5
Q ss_pred CceEEEeeecCCcEEEEc-----------------------------------CeEEEEEEeccEEEEEEEcCCCCHHHH
Q 033894 1 MILAVLFANSEGNILVER-----------------------------------SVYIVYTVLGDVSIFVVGKDEYDELAL 45 (109)
Q Consensus 1 mi~~~l~~~~~g~i~l~~-----------------------------------~~~iVyr~~~dl~~~vvg~~~eNEL~l 45 (109)
||||+|++|+||++||.+ +.++||||||+|+|.++.+.++|||++
T Consensus 1 ~i~~vli~nrqgk~RL~K~yt~~~~~e~~kli~~i~~lIs~R~~ke~N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnEl~i 80 (152)
T COG5030 1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIEGKNEKIVYRRYATLYFVFGVDNDDNELII 80 (152)
T ss_pred CeEEEEEEcCCCceeeeEeeccCCcHHHHHHHHHHHHHHHcCCchhcccccccCcEEEeeecCcEEEEEEEcCCCCcchH
Confidence 899999999999999999 679999999999888888889999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHHHHHhh
Q 033894 46 AEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVR 102 (109)
Q Consensus 46 ~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I~~rv~ 102 (109)
+++||.|+|+||++|++ |||+|+++||.+++.+|||++.+|.+.|+|+..+++++.
T Consensus 81 L~lIh~FVE~lDr~Fgn-VCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~v~ 136 (152)
T COG5030 81 LELIHNFVEILDRFFGN-VCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEHVY 136 (152)
T ss_pred HHHHHHHHHHHHHHhcc-ceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHHHH
Confidence 99999999999999875 999999999999999999999999999999999998874
No 3
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=3.1e-30 Score=187.27 Aligned_cols=106 Identities=21% Similarity=0.244 Sum_probs=101.7
Q ss_pred CceEEEeeecCCcEEEEc-----------------------------------------CeEEEEEEeccEEEEEEEcCC
Q 033894 1 MILAVLFANSEGNILVER-----------------------------------------SVYIVYTVLGDVSIFVVGKDE 39 (109)
Q Consensus 1 mi~~~l~~~~~g~i~l~~-----------------------------------------~~~iVyr~~~dl~~~vvg~~~ 39 (109)
|||+++++|.+|+.||.+ +.+++||+||.|||..+.|++
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~~~~~Qq~lir~vf~lvs~R~~n~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvvD~s 80 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPVDEEKQQQLIREVFHLVSKRPDNVCNFLEGNSLIGGSDNRLIYRHYATLYFVFVVDSS 80 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcCChHHHHHHHHHHHHHHHcCCchHhhhhccccccCCccceeehheeeeEEEEEEEcCC
Confidence 999999999999999999 789999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHHHHHhhcCCCC
Q 033894 40 YDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKPPN 107 (109)
Q Consensus 40 eNEL~l~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I~~rv~~k~p~ 107 (109)
|+||+++++||.|+|+||++|. +|||+|+++||++++.+|+|++.||+++||+.+.|+..+..+.|.
T Consensus 81 EsEL~iLDLIQvfVEtLDkCF~-nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~nkl 147 (182)
T KOG0936|consen 81 ESELGILDLIQVFVETLDKCFE-NVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQNKL 147 (182)
T ss_pred cchhHHHHHHHHHHHHHHHHHH-hhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhchh
Confidence 9999999999999999999885 599999999999999999999999999999999999999877653
No 4
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=4.6e-30 Score=186.92 Aligned_cols=97 Identities=31% Similarity=0.456 Sum_probs=93.4
Q ss_pred ecCCcEEEEcCeEEEEEEeccEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCE
Q 033894 9 NSEGNILVERSVYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGL 88 (109)
Q Consensus 9 ~~~g~i~l~~~~~iVyr~~~dl~~~vvg~~~eNEL~l~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~Gi 88 (109)
+++.+|.+++|..+|||.+.||+|||+|+.+||||+|+++++++++|++.+++++|+|+.+++|||.++|++||+||+|+
T Consensus 51 kt~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENEl~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~Gv 130 (175)
T KOG3343|consen 51 KTESEILLLDGNTVVYKSVIDLHFYVVGSEEENELMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGV 130 (175)
T ss_pred cccceeEEecCcEEEEEecccEEEEEecCcchhHHHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCce
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeCHHHHHHHhhcCC
Q 033894 89 LENTEKDRIRRLVRLKP 105 (109)
Q Consensus 89 I~Etd~~~I~~rv~~k~ 105 (109)
|+||||+.|++|++.+|
T Consensus 131 ILEtdp~~ia~rv~~~~ 147 (175)
T KOG3343|consen 131 ILETDPNQIAQRVALRP 147 (175)
T ss_pred EEecCHHHHHHHhccCC
Confidence 99999999999996554
No 5
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.95 E-value=1.8e-28 Score=174.76 Aligned_cols=101 Identities=22% Similarity=0.319 Sum_probs=94.7
Q ss_pred CceEEEeeecCCcEEEEc-----------------------------------CeEEEEEEeccEEEEEEEcCCCCHHHH
Q 033894 1 MILAVLFANSEGNILVER-----------------------------------SVYIVYTVLGDVSIFVVGKDEYDELAL 45 (109)
Q Consensus 1 mi~~~l~~~~~g~i~l~~-----------------------------------~~~iVyr~~~dl~~~vvg~~~eNEL~l 45 (109)
||||+|+.|+||++||.+ ++++||||||+|+|.+...+++|||+.
T Consensus 1 mi~f~LlvsrQGk~rL~k~y~~~~~~er~~i~re~i~~~Lar~pk~csfie~kd~kvVyrryasl~f~~~v~~~dNEL~~ 80 (145)
T KOG0934|consen 1 MIKFFLLVSRQGKTRLQKWYEALSIKERKKIERELIKSVLARKPKMCSFIEYKDEKVVYRRYASLFFCVGVEDNDNELAI 80 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhhcHHHHHHHHHHHHHHHHhCCcccccchhccCceehhhhhhhEEEEEEEecCCchhhH
Confidence 899999999999999998 999999999999666666679999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHHHHHhh
Q 033894 46 AEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVR 102 (109)
Q Consensus 46 ~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I~~rv~ 102 (109)
+|+||.++|.||++|++ |||+|+++||++++.+|||++.+|.+.|+.++..+..++
T Consensus 81 LE~IH~~vE~lDkYFg~-VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~~~~i~ 136 (145)
T KOG0934|consen 81 LEFIHNYVELLDKYFGS-VCELDIIFNFEKAYFILDEFLLGGEIQETSKNDVLKAIA 136 (145)
T ss_pred HHHHHHHHHHHHHHhcc-ceeeEEEEehHhHHHHHHHHhcCcchHhhhcccHHHHHH
Confidence 99999999999999975 999999999999999999999999999999998888774
No 6
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.95 E-value=1.6e-27 Score=167.52 Aligned_cols=102 Identities=18% Similarity=0.200 Sum_probs=96.0
Q ss_pred CceEEEeeecCCcEEEEc------------------------------------CeEEEEEEeccEEEEEEEcCCCCHHH
Q 033894 1 MILAVLFANSEGNILVER------------------------------------SVYIVYTVLGDVSIFVVGKDEYDELA 44 (109)
Q Consensus 1 mi~~~l~~~~~g~i~l~~------------------------------------~~~iVyr~~~dl~~~vvg~~~eNEL~ 44 (109)
||+|+|+.|++|+.||.+ +.++.+|||++|+|.++.+..+||++
T Consensus 1 mi~FILiqNr~Gk~RLak~yv~~dd~ek~~~~~~vh~lvs~Rd~K~~~~~~~~~~~~~~~rryagLyf~~~vd~tDnela 80 (143)
T KOG0935|consen 1 MIRFILIQNRAGKTRLAKWYVQFDDDEKQKLIEEVHALVTVRDAKHTNFVEFRNFKIIYRRRYAGLYFCICVDVTDNELA 80 (143)
T ss_pred CeEEEEEEccccceeheeeeeccCchHHHHHHHHHHHHHhhccchhhhheeeeeceEEEEEeeCCEEEEEEEecCCchHH
Confidence 899999999999999998 45566669999998888889999999
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHHHHHhhc
Q 033894 45 LAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRL 103 (109)
Q Consensus 45 l~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I~~rv~~ 103 (109)
.++.||.|+|.|+.+|+| |||+|+++||.+|++++|||+.+|.|.||++..+++|+.+
T Consensus 81 yLe~IHlFVEvLd~fF~N-VCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl~~ 138 (143)
T KOG0935|consen 81 YLEHIHLFVEVLDEFFHN-VCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLERLLM 138 (143)
T ss_pred HHHHHHHHHHHHHHHhcc-ccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHHHH
Confidence 999999999999999875 9999999999999999999999999999999999999865
No 7
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=3.5e-22 Score=145.79 Aligned_cols=99 Identities=27% Similarity=0.350 Sum_probs=95.3
Q ss_pred ecCCcEEEEcCeEEEEEEeccEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCE
Q 033894 9 NSEGNILVERSVYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGL 88 (109)
Q Consensus 9 ~~~g~i~l~~~~~iVyr~~~dl~~~vvg~~~eNEL~l~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~Gi 88 (109)
.++.+|.+++++.++|+++-|+.+|++|+-+|||..+.+++..|..||..+++...+|+.+.+|||.+.+++||+||+|+
T Consensus 58 k~~~~Il~f~d~lV~~k~~~dv~~yiv~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gv 137 (187)
T COG5541 58 KDRESILMFYDRLVMCKRLDDVLLYIVSPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGV 137 (187)
T ss_pred cCccceeeEcceeeeeeeehhEEEEEecccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccce
Confidence 46789999999999999999999999999999999999999999999999999889999999999999999999999999
Q ss_pred EEEeCHHHHHHHhhcCCCCC
Q 033894 89 LENTEKDRIRRLVRLKPPNE 108 (109)
Q Consensus 89 I~Etd~~~I~~rv~~k~p~~ 108 (109)
|+||+++.|++|+ .|||+.
T Consensus 138 ilet~s~~ia~rv-~K~p~~ 156 (187)
T COG5541 138 ILETKSDEIADRV-PKPPNF 156 (187)
T ss_pred EeecChHHHHHhC-CCCCCc
Confidence 9999999999999 898874
No 8
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.85 E-value=9.4e-09 Score=83.68 Aligned_cols=104 Identities=23% Similarity=0.412 Sum_probs=86.3
Q ss_pred CceEEEeeecCCcEEEEc----------------------------------CeEEEEEEeccEEEEEEEcC-CCCHHHH
Q 033894 1 MILAVLFANSEGNILVER----------------------------------SVYIVYTVLGDVSIFVVGKD-EYDELAL 45 (109)
Q Consensus 1 mi~~~l~~~~~g~i~l~~----------------------------------~~~iVyr~~~dl~~~vvg~~-~eNEL~l 45 (109)
||+++.+.|++|++.+.. .+--.+.-+.+..+++..+. +---|..
T Consensus 1 mi~siflidtsg~l~lek~~~g~t~~rsic~~f~e~~~~~~~~e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~pPL~~ 80 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGSTVVRSICDYFFEDQSSDDDLEHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPPLMV 80 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCceeeeehHHHHHHhhhhccccccCCceecCCceeeeeeeccCcEEEEEEeccCCChhH
Confidence 899999999999998876 34445555666656666554 4447999
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHHHHHhhcCCCC
Q 033894 46 AEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKPPN 107 (109)
Q Consensus 46 ~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I~~rv~~k~p~ 107 (109)
.|+++.+++++..+|++ .++..+-+|++.++.+||||+|.|.-.-|+++.+-+.+ +||+
T Consensus 81 iefL~rv~dv~~eyFg~-~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i--~pps 139 (418)
T KOG2740|consen 81 IEFLHRVVDVLLEYFGG-LSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELI--PPPS 139 (418)
T ss_pred HHHHHHHHHHHHHHhcc-cCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhc--CChH
Confidence 99999999999999985 99999999999999999999999999999997766665 4553
No 9
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.80 E-value=6.9e-08 Score=78.49 Aligned_cols=103 Identities=20% Similarity=0.315 Sum_probs=97.0
Q ss_pred CceEEEeeecCCcEEEEc--------------------------------CeEEEEEEeccEEEEEEEcCCCCHHHHHHH
Q 033894 1 MILAVLFANSEGNILVER--------------------------------SVYIVYTVLGDVSIFVVGKDEYDELALAEV 48 (109)
Q Consensus 1 mi~~~l~~~~~g~i~l~~--------------------------------~~~iVyr~~~dl~~~vvg~~~eNEL~l~e~ 48 (109)
||-++++.|-.|++.+.+ +...+|-+..+|++..+..++.|=.+..|+
T Consensus 1 misglfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eF 80 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNLDVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEF 80 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhccccCCCeeEecceeEEEEeeccEEEEEEecCCCchhhHHHH
Confidence 899999999999999988 678899999999999999999999999999
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHHHHHhhcC
Q 033894 49 IFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLK 104 (109)
Q Consensus 49 i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I~~rv~~k 104 (109)
+-.+.+.+..+|++ .+|..+-+||-.+|=+||||+|-|+...|++++....++.|
T Consensus 81 l~kl~avm~aYfgk-~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~ 135 (446)
T KOG0938|consen 81 LYKLDAVMNAYFGK-DREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQK 135 (446)
T ss_pred HHHHHHHHHHHhcc-cchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhh
Confidence 99999999999985 89999999999999999999999999999999998888655
No 10
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.85 E-value=0.00024 Score=59.05 Aligned_cols=90 Identities=13% Similarity=0.190 Sum_probs=78.3
Q ss_pred EEEEcCeEEEEEEeccEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeC
Q 033894 14 ILVERSVYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTE 93 (109)
Q Consensus 14 i~l~~~~~iVyr~~~dl~~~vvg~~~eNEL~l~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd 93 (109)
+...++...+|-+..++++.+.+..+-|=..++++++.+++.+..+|+ .+.|..+.+|+..++=.|||+.|=|+.+-|+
T Consensus 47 ~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~v~~~l~~~~~v~~~y~~-~l~e~si~~n~vlvyElLde~mDFGypQ~t~ 125 (424)
T KOG0937|consen 47 FLVHDGSRFIHIKHSNLYLVAGTRPNVSAALVLSFLYAVADVFGDYLS-ELEEESIRDNFVLVYELLDEVMDFGYPQTTD 125 (424)
T ss_pred eEEeCCceEEEEeecceEEEEEeccCCCHHHHHHHHHHHHHHHHHHhc-cCCccceecchHHHHHHHHHHhccCCcccch
Confidence 334447889999999998888887899999999999999999999997 6999999999999999999999999997777
Q ss_pred HHHHHHHhhcC
Q 033894 94 KDRIRRLVRLK 104 (109)
Q Consensus 94 ~~~I~~rv~~k 104 (109)
++.+-+.+.++
T Consensus 126 s~iL~~yi~~~ 136 (424)
T KOG0937|consen 126 SEILKNYITQK 136 (424)
T ss_pred HHHHHHHhccc
Confidence 76666666544
No 11
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=96.71 E-value=0.022 Score=42.97 Aligned_cols=79 Identities=13% Similarity=0.108 Sum_probs=69.9
Q ss_pred CeEEEEEEeccEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHH
Q 033894 19 SVYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRI 97 (109)
Q Consensus 19 ~~~iVyr~~~dl~~~vvg~~~eNEL~l~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I 97 (109)
...++|+..+++.|..|++.+||=++.-.+++.++..|...++.-..-..++.+-|.+..+|+.+.-.|-.+=.|.+.+
T Consensus 103 ~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~ 181 (189)
T PF15001_consen 103 PKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFV 181 (189)
T ss_pred CcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHH
Confidence 5689999999999999999999999999999999999987775423347888899999999999999999998887764
No 12
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.20 E-value=0.048 Score=46.09 Aligned_cols=86 Identities=22% Similarity=0.319 Sum_probs=72.5
Q ss_pred EEEEcCeEEEEEEeccEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeC
Q 033894 14 ILVERSVYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTE 93 (109)
Q Consensus 14 i~l~~~~~iVyr~~~dl~~~vvg~~~eNEL~l~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd 93 (109)
..-.++++-||+..-.+|+.++...+.|=|-=++.|+-|-.....+|. .++|+.+++|-=-...+.||+|-=|+=..++
T Consensus 48 ~vEt~~VRYVYqP~d~lY~vLITtk~SNIleDl~TL~Lfskvipey~~-slde~eI~~~~FelifAFDEivsLGyre~v~ 126 (512)
T KOG2635|consen 48 FVETDSVRYVYQPLDNLYIVLITTKQSNILEDLETLRLFSKVIPEYCS-SLDEKEILENAFELIFAFDEIVSLGYRENVN 126 (512)
T ss_pred EEecccEEEEEEecccEEEEEEeccccchhhHHHHHHHHHHhchhhhh-hhhHHHHHHhhhhhhhccchhhhhccccccc
Confidence 333338899999999999999999999999999999999999999997 5999999999888889999999999655555
Q ss_pred HHHHHHH
Q 033894 94 KDRIRRL 100 (109)
Q Consensus 94 ~~~I~~r 100 (109)
-..|-..
T Consensus 127 laQikty 133 (512)
T KOG2635|consen 127 LAQIKTY 133 (512)
T ss_pred HHHhhhh
Confidence 4444433
No 13
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=65.40 E-value=5.7 Score=25.12 Aligned_cols=24 Identities=33% Similarity=0.570 Sum_probs=17.9
Q ss_pred CCEEE--EeCHHHHHHHhhcCCCCCC
Q 033894 86 KGLLE--NTEKDRIRRLVRLKPPNEF 109 (109)
Q Consensus 86 ~GiI~--Etd~~~I~~rv~~k~p~~~ 109 (109)
.|+++ +++++.|++|+..+-|..|
T Consensus 34 ~G~~iIidpe~SeIAkrlgi~~Pg~y 59 (64)
T COG2093 34 FGLLIIIDPEKSEIAKRLGIKIPGKY 59 (64)
T ss_pred ccEEEEEcCcHHHHHHHhCCCCCceE
Confidence 36554 4555569999999999876
No 14
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=61.41 E-value=17 Score=19.48 Aligned_cols=32 Identities=13% Similarity=0.179 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHH
Q 033894 46 AEVIFAITSAVKDACGKIPTERLFLDKYGKIC 77 (109)
Q Consensus 46 ~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~ 77 (109)
-++.+.++..++..++++-++..+..-++.++
T Consensus 4 C~~C~~~v~~i~~~l~~~~t~~~I~~~l~~~C 35 (39)
T PF05184_consen 4 CDICKFVVKEIEKLLKNNKTEEEIKKALEKAC 35 (39)
T ss_dssp HHHHHHHHHHHHHHHHSTCHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHcCccHHHHHHHHHHHH
Confidence 35778889999999988889999998888776
No 15
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=53.26 E-value=31 Score=24.83 Aligned_cols=65 Identities=22% Similarity=0.299 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHHhCCCC---CHHHHHhcH-----HHHHHHHHHHHh----CCEEEEeCHHHHHHHhhcCCCCCC
Q 033894 45 LAEVIFAITSAVKDACGKIP---TERLFLDKY-----GKICLCLDEIVW----KGLLENTEKDRIRRLVRLKPPNEF 109 (109)
Q Consensus 45 l~e~i~~~~e~L~~~~~~~v---~e~~ll~n~-----d~v~l~lDEii~----~GiI~Etd~~~I~~rv~~k~p~~~ 109 (109)
=...++.+.++++...+.+. =|++|+.++ |.-+.++||+=. +|-....|+..+++.|+.+.|+=|
T Consensus 57 p~~~l~~Li~~~k~~~~E~f~lkLEk~I~q~~PIDF~Dvw~VAm~ei~~~~~~~~~~~~id~~~lvk~IKk~HPNLF 133 (137)
T PF10788_consen 57 PQKSLQNLIESLKNAQKENFELKLEKDILQQMPIDFEDVWAVAMDEIKKMRQKDGNLPNIDLDKLVKNIKKEHPNLF 133 (137)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHhCCCee
Confidence 35667777777777665432 356777764 677889999976 577899999999999999999855
No 16
>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents Mitogen-activated protein kinase kinase 1 interacting protein, which is a small subcellular adaptor protein required for MAPK signalling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer []. ; PDB: 1VEU_A 1VET_A 1SKO_A 2ZL1_A 3CPT_A.
Probab=52.37 E-value=76 Score=21.96 Aligned_cols=46 Identities=9% Similarity=-0.022 Sum_probs=39.0
Q ss_pred EEEEcCeEEEEEEeccEEEEEEEcCCCCHHHHHHHHHHHHHHHHHH
Q 033894 14 ILVERSVYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDA 59 (109)
Q Consensus 14 i~l~~~~~iVyr~~~dl~~~vvg~~~eNEL~l~e~i~~~~e~L~~~ 59 (109)
|-.++++.++--....+++.++++.+.|==.++..-+-+...+..+
T Consensus 70 i~~Y~~~qvv~~~~~pl~it~ias~~aN~G~il~l~~~L~~~l~~l 115 (119)
T PF08923_consen 70 IAYYDSYQVVQFNKLPLYITFIASSNANTGLILSLEEELAPILNEL 115 (119)
T ss_dssp EEEESSEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHH
T ss_pred EEEeCCEEEEEEeCCCeEEEEEecCCCCHHHHHHhHHHHHHHHHHH
Confidence 5677899999999999999999999999988888888887777764
No 17
>smart00836 DALR_1 DALR anticodon binding domain. This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids PUBMED:10447505.
Probab=50.58 E-value=70 Score=21.00 Aligned_cols=62 Identities=13% Similarity=0.087 Sum_probs=49.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeC-HHHHHHHh
Q 033894 39 EYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTE-KDRIRRLV 101 (109)
Q Consensus 39 ~eNEL~l~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd-~~~I~~rv 101 (109)
++.|..|+..+..+-+.+...+.+ -+-..+..-.-.+.-.++++-++-.|+..| ++.-.+|+
T Consensus 35 ~~~E~~L~~~i~~~~~~i~~~~~~-~~~~~l~~~l~~L~~~~~~fy~~v~V~~~~~~~~~~~RL 97 (122)
T smart00836 35 EPEELALLRLLARFPEVLEAAAET-LEPHRLANYLYDLASAFHSFYNKCRVLGEENPELRAARL 97 (122)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHH-CCcHHHHHHHHHHHHHHHHHHccCcccCCCCHHHHHHHH
Confidence 678999999999999998887754 455677788888899999999998888776 55444444
No 18
>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=41.92 E-value=2e+02 Score=23.81 Aligned_cols=37 Identities=22% Similarity=0.180 Sum_probs=30.7
Q ss_pred CeEEEEEEeccEEEEEEEcCCCCHHHHHHHHHHHHHH
Q 033894 19 SVYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSA 55 (109)
Q Consensus 19 ~~~iVyr~~~dl~~~vvg~~~eNEL~l~e~i~~~~e~ 55 (109)
+.++||-.=+-|+++.+....|.+-.|..-++.++.-
T Consensus 62 ~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly~q 98 (415)
T PF03164_consen 62 DHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLYSQ 98 (415)
T ss_pred CEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHHHH
Confidence 8999999999998888888889888777777665543
No 19
>cd07956 Anticodon_Ia_Arg Anticodon-binding domain of arginyl tRNA synthetases. This domain is found in arginyl tRNA synthetases (ArgRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. ArgRS catalyzes the transfer of arginine to the 3'-end of its tRNA.
Probab=40.37 E-value=1.2e+02 Score=21.14 Aligned_cols=63 Identities=13% Similarity=0.051 Sum_probs=49.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHHHHHhh
Q 033894 39 EYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVR 102 (109)
Q Consensus 39 ~eNEL~l~e~i~~~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I~~rv~ 102 (109)
++.|..|+..+..+.+.+....++ -+-..++.....+.-.+++.-++-.|+..|.+.=.+|+.
T Consensus 70 ~~~E~~L~~~l~~~~~~i~~~~~~-~~~~~l~~~l~~L~~~~~~ffd~v~V~~~~~~i~~nRL~ 132 (156)
T cd07956 70 EPDERDLILLLAKFPEVVKNAAET-LEPHTIATYLFDLAHAFSKFYNACPVLGAEEELRNARLA 132 (156)
T ss_pred CHHHHHHHHHHHHhHHHHHHHHHH-cCcHHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHH
Confidence 567999999999999988887764 455677888888899999999988888777665455553
No 20
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=31.02 E-value=44 Score=16.43 Aligned_cols=17 Identities=18% Similarity=0.167 Sum_probs=14.0
Q ss_pred cHHHHHHHHHHHHhCCE
Q 033894 72 KYGKICLCLDEIVWKGL 88 (109)
Q Consensus 72 n~d~v~l~lDEii~~Gi 88 (109)
+++.+..++++|...|+
T Consensus 16 ~~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 16 DPDAALQLFDEMKEQGV 32 (34)
T ss_pred CHHHHHHHHHHHHHhCC
Confidence 46778999999998884
No 21
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=29.17 E-value=71 Score=19.06 Aligned_cols=21 Identities=0% Similarity=0.147 Sum_probs=16.3
Q ss_pred hCCEEEEeCHHHHHHHhhcCC
Q 033894 85 WKGLLENTEKDRIRRLVRLKP 105 (109)
Q Consensus 85 ~~GiI~Etd~~~I~~rv~~k~ 105 (109)
.+.+++|||...+++.++.+.
T Consensus 21 ~~~i~v~sDs~~vv~~i~~~~ 41 (87)
T PF13456_consen 21 IRKIIVESDSQLVVDAINGRS 41 (87)
T ss_dssp -SCEEEEES-HHHHHHHTTSS
T ss_pred CCEEEEEecCccccccccccc
Confidence 346899999999999997763
No 22
>PF08866 DUF1831: Putative amino acid metabolism; InterPro: IPR014965 These short proteins are functionally uncharacterised. ; PDB: 2IAY_A.
Probab=26.27 E-value=62 Score=22.55 Aligned_cols=18 Identities=33% Similarity=0.590 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHhCCEEE
Q 033894 73 YGKICLCLDEIVWKGLLE 90 (109)
Q Consensus 73 ~d~v~l~lDEii~~GiI~ 90 (109)
-++.+.++|++|+.|++.
T Consensus 94 ve~~~Fi~d~lveR~Vl~ 111 (112)
T PF08866_consen 94 VEKYYFIMDDLVERGVLE 111 (112)
T ss_dssp HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHhccccc
Confidence 456688999999999875
No 23
>COG2047 Uncharacterized protein (ATP-grasp superfamily) [General function prediction only]
Probab=26.26 E-value=2.8e+02 Score=21.95 Aligned_cols=52 Identities=19% Similarity=0.325 Sum_probs=42.2
Q ss_pred EeeecCCcEEEEcCeEEEEEEec---cEEEEEEEcC-CCCHHHHHHHHHHHHHHHHH
Q 033894 6 LFANSEGNILVERSVYIVYTVLG---DVSIFVVGKD-EYDELALAEVIFAITSAVKD 58 (109)
Q Consensus 6 l~~~~~g~i~l~~~~~iVyr~~~---dl~~~vvg~~-~eNEL~l~e~i~~~~e~L~~ 58 (109)
.+.|.++.+++.+|..-.+|.-+ |+ ++++|+. .-....=+++...+.+.-..
T Consensus 59 V~V~dD~~vel~~ne~Y~~k~~~~~~Dl-iil~Gd~Q~~~~~gqyel~~~~Ld~a~e 114 (258)
T COG2047 59 VLVNDDSTVELMRNEFYYWKSPGGERDL-IILVGDTQATSSEGQYELTGKILDIAKE 114 (258)
T ss_pred eEecCCceEEeeeceeEEEecCCCCCcE-EEEeccccccCcchhHHHHHHHHHHHHH
Confidence 46789999999999999998655 88 8888885 66777778888777777665
No 24
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=25.85 E-value=71 Score=20.69 Aligned_cols=46 Identities=11% Similarity=0.034 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHhC--CCCCHHHHHhcH----HHHHHHHHHHHhCCEEEEe
Q 033894 47 EVIFAITSAVKDACG--KIPTERLFLDKY----GKICLCLDEIVWKGLLENT 92 (109)
Q Consensus 47 e~i~~~~e~L~~~~~--~~v~e~~ll~n~----d~v~l~lDEii~~GiI~Et 92 (109)
.+-+.+++.++.-.. ..+....|..++ +.|--++|+++++|.|..|
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEES
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecc
Confidence 333444444444111 246666666664 7899999999999999887
No 25
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=25.15 E-value=2.8e+02 Score=20.35 Aligned_cols=41 Identities=12% Similarity=0.121 Sum_probs=28.2
Q ss_pred HHHHHHHhCCCCCHHHHHhcH------HHHHHHHHHHHhCCEEEEeC
Q 033894 53 TSAVKDACGKIPTERLFLDKY------GKICLCLDEIVWKGLLENTE 93 (109)
Q Consensus 53 ~e~L~~~~~~~v~e~~ll~n~------d~v~l~lDEii~~GiI~Etd 93 (109)
+..|-..+.+.-+..+|.+.. +.+.-+|+++.+.|+|.|..
T Consensus 32 ~~~L~~lLdG~rt~~eI~~~l~~~~p~~~v~~~L~~L~~~G~l~~~~ 78 (193)
T TIGR03882 32 YCQLAPLLDGRRTLDEIIAALAGRFPAEEVLYALDRLERRGYLVEDA 78 (193)
T ss_pred HHHHHHHHcCCCCHHHHHHHhhccCCHHHHHHHHHHHHHCCCEeccC
Confidence 333444444445666665554 77999999999999999843
No 26
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=22.76 E-value=77 Score=15.04 Aligned_cols=18 Identities=17% Similarity=0.383 Sum_probs=13.7
Q ss_pred hcHHHHHHHHHHHHhCCE
Q 033894 71 DKYGKICLCLDEIVWKGL 88 (109)
Q Consensus 71 ~n~d~v~l~lDEii~~Gi 88 (109)
.+++.+.-+++|+...|+
T Consensus 14 ~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 14 GQFEEALEVFDEMRERGI 31 (31)
T ss_pred chHHHHHHHHHHHhHCcC
Confidence 357778888888888774
No 27
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=21.83 E-value=2.5e+02 Score=18.55 Aligned_cols=15 Identities=20% Similarity=0.381 Sum_probs=10.6
Q ss_pred CCCCHHHHHHHHHHH
Q 033894 38 DEYDELALAEVIFAI 52 (109)
Q Consensus 38 ~~eNEL~l~e~i~~~ 52 (109)
++|+|+.+++.+-.+
T Consensus 8 S~eDEi~iL~gl~~~ 22 (98)
T PF04504_consen 8 SEEDEIVILQGLIDF 22 (98)
T ss_pred CchHHHHHHHHHHHH
Confidence 467888888776543
No 28
>KOG1511 consensus Mevalonate kinase MVK/ERG12 [Lipid transport and metabolism]
Probab=21.57 E-value=82 Score=26.42 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=22.1
Q ss_pred CceEEEeeecCCcEEEEcCeEEEEEEec
Q 033894 1 MILAVLFANSEGNILVERSVYIVYTVLG 28 (109)
Q Consensus 1 mi~~~l~~~~~g~i~l~~~~~iVyr~~~ 28 (109)
|-++ |.++.=|+++|+..|-+||.+-+
T Consensus 1 ms~~-l~vsaPGKvILfGEHAVVyg~~A 27 (397)
T KOG1511|consen 1 MSKV-LLVSAPGKVILFGEHAVVYGRTA 27 (397)
T ss_pred CCce-eeecCCccEEEeccceeEECCce
Confidence 3444 77888999999999999998754
No 29
>PF01526 DDE_Tnp_Tn3: Tn3 transposase DDE domain; InterPro: IPR002513 Proteins containing this domain include transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926 transposons from Escherichia coli. The specific binding of the Tn3 transposase to DNA has been demonstrated. Sequence analysis has suggested that the invariant triad of Asp689, Asp765, Glu895 (numbering as in Tn3) may correspond to the D-D-35-E motif previously implicated in the catalytic performance of numerous transposases [].; GO: 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=21.16 E-value=2.3e+02 Score=23.47 Aligned_cols=50 Identities=14% Similarity=0.037 Sum_probs=43.4
Q ss_pred HHHHHHHHhCCCCCHHHHHhcHHHHHHHHHHHHhCCEEEEeCHHHHHHHhhcCC
Q 033894 52 ITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKP 105 (109)
Q Consensus 52 ~~e~L~~~~~~~v~e~~ll~n~d~v~l~lDEii~~GiI~Etd~~~I~~rv~~k~ 105 (109)
-+..++..+++.++...|.+|+|-+.=+.=.+-.| .+++..|++|++.-+
T Consensus 214 ~y~~l~~~~~~~I~~~lI~~~wddilRia~Si~~g----~~~as~ilrkl~s~~ 263 (388)
T PF01526_consen 214 DYPHLDPLLGKRINWDLIEEHWDDILRIAASIKLG----KVSASTILRKLSSYS 263 (388)
T ss_pred hhhhhhhhccCccchhhHHHHHHHHHHHHHhcccc----cCCHHHHHHHHhccC
Confidence 46677777888899999999999999999988888 899999999997554
No 30
>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated
Probab=21.12 E-value=18 Score=27.20 Aligned_cols=31 Identities=23% Similarity=0.506 Sum_probs=21.5
Q ss_pred cHHHHHHHHHHHHh---CCEEEEeCHHHHHHHhhcCCCC
Q 033894 72 KYGKICLCLDEIVW---KGLLENTEKDRIRRLVRLKPPN 107 (109)
Q Consensus 72 n~d~v~l~lDEii~---~GiI~Etd~~~I~~rv~~k~p~ 107 (109)
+||. ++|||+.. -|+| +.+.+++.++.|||+
T Consensus 115 ~ydl--vVLDEi~~Al~~gli---~~eevi~~L~~rp~~ 148 (191)
T PRK05986 115 SYDL--VVLDELTYALKYGYL---DVEEVLEALNARPGM 148 (191)
T ss_pred CCCE--EEEehhhHHHHCCCc---cHHHHHHHHHcCCCC
Confidence 3443 57899864 4766 456688888888885
No 31
>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.
Probab=20.98 E-value=25 Score=25.56 Aligned_cols=31 Identities=35% Similarity=0.697 Sum_probs=23.9
Q ss_pred cHHHHHHHHHHHHhC---CEEEEeCHHHHHHHhhcCCCC
Q 033894 72 KYGKICLCLDEIVWK---GLLENTEKDRIRRLVRLKPPN 107 (109)
Q Consensus 72 n~d~v~l~lDEii~~---GiI~Etd~~~I~~rv~~k~p~ 107 (109)
+||. ++|||+... |.+ +.+.+.+-++.|||+
T Consensus 95 ~~dL--lVLDEi~~a~~~gli---~~~~v~~ll~~rp~~ 128 (159)
T cd00561 95 EYDL--VILDEINYALGYGLL---DVEEVVDLLKAKPED 128 (159)
T ss_pred CCCE--EEEechHhHhhCCCC---CHHHHHHHHHcCCCC
Confidence 4554 578998765 766 788899999999885
No 32
>PF13998 MgrB: MgrB protein
Probab=20.78 E-value=69 Score=17.18 Aligned_cols=12 Identities=33% Similarity=0.315 Sum_probs=10.1
Q ss_pred HHHHHHHHhCCE
Q 033894 77 CLCLDEIVWKGL 88 (109)
Q Consensus 77 ~l~lDEii~~Gi 88 (109)
.++||.++|+|.
T Consensus 3 llald~~CDQg~ 14 (29)
T PF13998_consen 3 LLALDSYCDQGE 14 (29)
T ss_pred HHHHHHHhcCCC
Confidence 478999999994
No 33
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=20.73 E-value=37 Score=20.25 Aligned_cols=13 Identities=31% Similarity=0.578 Sum_probs=8.1
Q ss_pred HHHHHHhCCEEEE
Q 033894 79 CLDEIVWKGLLEN 91 (109)
Q Consensus 79 ~lDEii~~GiI~E 91 (109)
.|||+|..|.|-.
T Consensus 18 tLDeli~~~~I~p 30 (49)
T PF02268_consen 18 TLDELIQEGKITP 30 (49)
T ss_dssp HHHHHHHTTSS-H
T ss_pred HHHHHHHcCCCCH
Confidence 5677777776643
No 34
>TIGR00708 cobA cob(I)alamin adenosyltransferase. Alternate name: corrinoid adenosyltransferase.
Probab=20.35 E-value=25 Score=25.95 Aligned_cols=31 Identities=19% Similarity=0.371 Sum_probs=21.6
Q ss_pred cHHHHHHHHHHHH---hCCEEEEeCHHHHHHHhhcCCCC
Q 033894 72 KYGKICLCLDEIV---WKGLLENTEKDRIRRLVRLKPPN 107 (109)
Q Consensus 72 n~d~v~l~lDEii---~~GiI~Etd~~~I~~rv~~k~p~ 107 (109)
+||. ++|||+. .-|+| +.+.+++.++.|||.
T Consensus 97 ~~Dl--vVLDEi~~A~~~gli---~~~~v~~lL~~rp~~ 130 (173)
T TIGR00708 97 ELDL--VLLDELTYALKYGYL---DVEEVVEALQERPGH 130 (173)
T ss_pred CCCE--EEehhhHHHHHCCCc---CHHHHHHHHHhCCCC
Confidence 4554 5789987 44766 445688888888885
Done!