Query 032448
Match_columns 140
No_of_seqs 104 out of 744
Neff 8.8
Searched_HMMs 46136
Date Fri Mar 29 14:13:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032448.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032448hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0859 Synaptobrevin/VAMP-lik 100.0 4.4E-46 9.4E-51 258.1 14.4 139 1-139 1-139 (217)
2 KOG0862 Synaptobrevin/VAMP-lik 100.0 4.6E-29 9.9E-34 176.3 13.1 135 3-138 2-147 (216)
3 PF13774 Longin: Regulated-SNA 99.9 2.3E-24 4.9E-29 134.5 10.0 81 28-109 1-82 (83)
4 KOG0861 SNARE protein YKT6, sy 99.9 2.3E-23 5E-28 142.5 11.0 134 1-139 1-151 (198)
5 COG5143 SNC1 Synaptobrevin/VAM 99.6 4.2E-15 9.1E-20 104.1 9.6 135 1-139 1-143 (190)
6 PF04086 SRP-alpha_N: Signal r 96.6 0.013 2.7E-07 44.1 7.8 67 25-94 4-72 (279)
7 PF01217 Clat_adaptor_s: Clath 94.1 1.1 2.4E-05 30.0 10.1 79 11-92 12-96 (141)
8 KOG0781 Signal recognition par 93.9 0.7 1.5E-05 37.7 9.1 88 3-93 3-96 (587)
9 KOG0938 Adaptor complexes medi 93.9 2.5 5.4E-05 33.0 11.6 110 4-119 5-118 (446)
10 PF04628 Sedlin_N: Sedlin, N-t 91.4 2.1 4.5E-05 28.6 7.6 109 7-116 1-131 (132)
11 PF09426 Nyv1_N: Vacuolar R-SN 91.4 1 2.2E-05 30.2 5.9 60 26-85 44-110 (141)
12 PF04099 Sybindin: Sybindin-li 86.9 7.6 0.00016 26.3 9.9 74 41-116 65-141 (142)
13 PF03164 Mon1: Trafficking pro 81.5 17 0.00038 29.1 8.9 87 6-92 15-104 (415)
14 KOG2740 Clathrin-associated pr 66.2 27 0.00058 27.7 6.1 44 49-92 53-96 (418)
15 PRK11546 zraP zinc resistance 64.4 12 0.00026 25.5 3.6 54 78-139 50-103 (143)
16 PHA01811 hypothetical protein 62.8 11 0.00024 22.0 2.7 19 41-59 4-22 (78)
17 KOG0860 Synaptobrevin/VAMP-lik 62.7 5 0.00011 26.4 1.4 18 122-139 26-43 (116)
18 PF03607 DCX: Doublecortin; I 61.8 12 0.00026 21.3 2.8 48 22-69 8-57 (60)
19 PF07897 DUF1675: Protein of u 53.5 15 0.00032 28.1 2.8 25 48-72 238-262 (284)
20 PF10504 DUF2452: Protein of u 53.4 6.6 0.00014 27.2 0.9 57 25-81 64-126 (159)
21 COG5122 TRS23 Transport protei 49.4 74 0.0016 20.9 8.7 74 39-116 55-132 (134)
22 KOG3369 Transport protein part 43.4 1.2E+02 0.0026 21.6 8.5 72 41-116 121-196 (199)
23 KOG4131 Ngg1-interacting facto 42.7 14 0.0003 27.6 1.2 32 7-38 223-256 (272)
24 cd00223 TOPRIM_TopoIIB_SPO TOP 39.8 8.2 0.00018 26.5 -0.4 26 62-87 25-50 (160)
25 PRK01622 OxaA-like protein pre 39.6 38 0.00082 25.3 3.2 33 105-137 94-126 (256)
26 PF11675 DUF3271: Protein of u 39.6 1.3E+02 0.0028 22.4 5.7 50 2-53 30-79 (249)
27 PF12128 DUF3584: Protein of u 36.9 19 0.00041 32.9 1.3 34 49-82 67-102 (1201)
28 PF13326 PSII_Pbs27: Photosyst 36.8 54 0.0012 22.4 3.3 65 73-138 73-142 (145)
29 PF08923 MAPKK1_Int: Mitogen-a 36.7 1.2E+02 0.0027 19.8 9.6 80 6-86 20-111 (119)
30 cd01617 DCX Ubiquitin-like dom 36.7 96 0.0021 18.6 5.5 51 21-71 24-78 (80)
31 PLN00064 photosystem II protei 36.6 1.5E+02 0.0032 20.7 5.6 68 70-138 87-159 (166)
32 TIGR03044 PS_II_psb27 photosys 35.7 1.4E+02 0.003 20.2 5.6 66 72-138 60-129 (135)
33 COG4051 Uncharacterized protei 32.2 1.8E+02 0.0039 20.8 5.3 58 10-73 3-62 (202)
34 smart00537 DCX Domain in the D 30.0 78 0.0017 19.5 3.0 51 21-71 29-83 (89)
35 PHA02979 hypothetical protein; 29.7 89 0.0019 20.5 3.2 32 41-72 59-90 (140)
36 PF11813 DUF3334: Protein of u 28.0 2.5E+02 0.0053 20.6 6.1 73 52-135 51-124 (229)
37 PRK10050 curli assembly protei 26.9 2.1E+02 0.0045 19.5 6.4 45 27-73 78-122 (138)
38 PTZ00032 60S ribosomal protein 25.1 1.5E+02 0.0033 21.5 4.0 25 30-54 170-194 (211)
39 TIGR00060 L18_bact ribosomal p 24.7 1.9E+02 0.0041 18.9 4.2 51 4-54 36-97 (114)
40 KOG3368 Transport protein part 24.6 2.3E+02 0.005 19.2 5.6 57 27-85 43-102 (140)
41 cd03164 CD53_like_LEL Tetraspa 23.5 1.7E+02 0.0036 17.2 3.6 29 106-134 10-39 (86)
42 cd00633 Secretoglobin Secretog 23.1 1.3E+02 0.0027 17.3 2.9 25 110-134 18-43 (67)
43 smart00335 ANX Annexin repeats 22.9 75 0.0016 16.9 1.8 15 80-94 19-33 (53)
44 PF06694 Plant_NMP1: Plant nuc 22.3 1.6E+02 0.0036 22.8 3.9 54 80-140 220-277 (325)
45 PF13077 DUF3909: Protein of u 22.2 1.6E+02 0.0034 18.3 3.2 24 59-82 83-108 (108)
46 PF05303 DUF727: Protein of un 22.2 2.2E+02 0.0047 18.3 4.0 46 47-92 39-97 (108)
47 PF08506 Cse1: Cse1; InterPro 22.0 1.1E+02 0.0024 24.2 3.2 46 67-124 222-267 (370)
48 COG2957 Peptidylarginine deimi 21.9 2.2E+02 0.0047 22.3 4.6 50 6-59 288-342 (346)
49 PF08053 Tna_leader: Tryptopha 21.3 98 0.0021 13.9 1.6 10 1-10 1-10 (24)
50 COG4678 Muramidase (phage lamb 20.1 3.3E+02 0.0071 19.3 5.0 67 26-92 34-107 (180)
No 1
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.4e-46 Score=258.11 Aligned_cols=139 Identities=50% Similarity=0.830 Sum_probs=135.7
Q ss_pred CceEEEEEEeCCeeEeeecCCCCCHHHHHHHHhccCCCCCCCceEEeeCCeEEEEEEeCCeEEEEEecCCCCcccHHHHH
Q 032448 1 MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFL 80 (140)
Q Consensus 1 M~I~Ya~Var~~~iL~e~~~~~~~~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~citd~~~~~~~af~fL 80 (140)
|+|+|++||||++|||||++.+|||..++..+|+++|+.+++|.+|..|+|+|||+++||++||||+|++.++++||.||
T Consensus 1 m~iiYs~VARGTvvLaeft~~~gNf~sva~qiL~klp~~~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFL 80 (217)
T KOG0859|consen 1 MSIIYSFVARGTVILAEFTEFSGNFSSIAAQILQKLPSSSNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFL 80 (217)
T ss_pred CceeEEEEecceEEEEeeeeccCCHHHHHHHHHHhCCCCCCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHH
Confidence 89999999999999999999999999999999999998667899999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhccccccccCCCccchhhHHHHHHHHHHhcCCchhhHHHHHHhhhhhhcc
Q 032448 81 EDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVEM 139 (140)
Q Consensus 81 ~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dkl~~l~~~l~evk~ 139 (140)
++|+.+|.+.||....++.+|++|++|++.|++.|++|.++|+.|+|++++.|++|||.
T Consensus 81 e~Ik~~F~k~YG~~a~ta~AysmN~EFs~vL~qqm~y~s~~p~id~lskvkaqv~evk~ 139 (217)
T KOG0859|consen 81 ERIKEDFKKRYGGGAHTAVAYSMNKEFSSVLKQQMQYCSEHPEISKLAKVKAQVTEVKG 139 (217)
T ss_pred HHHHHHHHHHhccchhHHHHhHhHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHH
Confidence 99999999999988999999999999999999999999999999999999999999984
No 2
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=4.6e-29 Score=176.30 Aligned_cols=135 Identities=24% Similarity=0.521 Sum_probs=122.6
Q ss_pred eEEEEEEeC--CeeEeeecC-C--CCC----HHHHHHHHhccCCCCCCCceEEeeCCeEEEEEEeCCeEEEEEecCCCCc
Q 032448 3 ILFSLVARG--SVVLAECSA-T--ATN----ASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGR 73 (140)
Q Consensus 3 I~Ya~Var~--~~iL~e~~~-~--~~~----~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~citd~~~~~ 73 (140)
|++++|+|. ++|||...+ . +|+ .++.++.+++++.+.++.|++++.|.|.|||++++|+||+||||+.||+
T Consensus 2 i~~T~I~RV~DGLPLa~s~d~~e~~~~s~~e~r~q~K~L~kkLs~~s~~r~Sietg~f~fHfli~~~Vcylvicd~~yP~ 81 (216)
T KOG0862|consen 2 ILLTLIARVRDGLPLAASTDDNEQSGDSLLEYRQQAKSLFKKLSQQSPTRCSIETGPFVFHFLIESGVCYLVICDKSYPR 81 (216)
T ss_pred ceeEEEEEecCCcccccccCcccCCCchHHHHHHHHHHHHHhccCCCCcccccccCCeEEEEEecCCEEEEEEecCCCcH
Confidence 789999995 799998775 2 233 4799999999999867999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHhhcccccc--ccCCCccchhhHHHHHHHHHHhcCCchhhHHHHHHhhhhhhc
Q 032448 74 RIPFAFLEDIHQRFVKTYGRAVL--SAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVE 138 (140)
Q Consensus 74 ~~af~fL~~i~~~F~~~~~~~~~--~~~~~~~~~~F~~~l~~~~~~yn~~~~~dkl~~l~~~l~evk 138 (140)
+.||+||++|.++|.+.|+.... ..+||++. +|++.|++..++|||++..+.+.+++.++.+|+
T Consensus 82 kLAF~YLedL~~EF~~~~~~~~~~~~~RPY~Fi-eFD~~IQk~Kk~ynd~r~~~n~~~~n~el~~v~ 147 (216)
T KOG0862|consen 82 KLAFSYLEDLAQEFDKSYGKNIIQPASRPYAFI-EFDTFIQKTKKRYNDTRSQRNLLKLNQELQDVQ 147 (216)
T ss_pred HHHHHHHHHHHHHHHHhcccccCCccCCCeeEE-ehhHHHHHHHHHhcCcHHHHHHHHHHHHHHHHH
Confidence 99999999999999999997643 57999997 999999999999999988899999999998886
No 3
>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=99.92 E-value=2.3e-24 Score=134.49 Aligned_cols=81 Identities=43% Similarity=0.838 Sum_probs=73.8
Q ss_pred HHHHHhccCCCCCCCceEEeeCCeEEEEEEeCCeEEEEEecCCCCcccHHHHHHHHHHHHHhhcc-ccccccCCCccchh
Q 032448 28 IARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG-RAVLSAQAYGMNDE 106 (140)
Q Consensus 28 ~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~citd~~~~~~~af~fL~~i~~~F~~~~~-~~~~~~~~~~~~~~ 106 (140)
+|++||++++++.++|.+++.|+|.||+++++|++||||||+++|+|+||.||++|+++|..+|+ +++.++.+|++ .+
T Consensus 1 ~a~~il~~i~~~~~~k~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~~~~~~~a~~~~~-~~ 79 (83)
T PF13774_consen 1 QARKILKRIPPNGNSKMSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYGGDQIKSASPYSF-KE 79 (83)
T ss_dssp HHHHHHHTS-TTSESEEEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCTTTTTTTSTTTTT-HH
T ss_pred CHHHHHHhcCCCCCCeEEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcCcchhcccCCcch-hh
Confidence 58999999996445899999999999999999999999999999999999999999999999999 78889889999 79
Q ss_pred hHH
Q 032448 107 FSR 109 (140)
Q Consensus 107 F~~ 109 (140)
|++
T Consensus 80 F~~ 82 (83)
T PF13774_consen 80 FDS 82 (83)
T ss_dssp HHH
T ss_pred cCC
Confidence 986
No 4
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.90 E-value=2.3e-23 Score=142.48 Aligned_cols=134 Identities=19% Similarity=0.334 Sum_probs=111.4
Q ss_pred CceEEEEEEeCC----eeEeeecCCC-------CC----HHHHHHHHhccCCCCCCCceEEeeCCeEEE-EEEeCCeEEE
Q 032448 1 MAILFSLVARGS----VVLAECSATA-------TN----ASAIARQILDKIPGNNDSHVSYSQDRYIFH-VKRTDGLTVL 64 (140)
Q Consensus 1 M~I~Ya~Var~~----~iL~e~~~~~-------~~----~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h-~l~~~~~~~~ 64 (140)
|.|++..|.+.+ .+|+.-++.+ ++ +..+++.+.+|.+| +.|+++++++|.+| |.+.+|++++
T Consensus 1 Mki~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F~sktvaeRt~~--g~rqsvk~~~Y~~h~yvrndgL~~V 78 (198)
T KOG0861|consen 1 MKIYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTFISKTVAERTGP--GQRQSVKHEEYLVHVYVRNDGLCGV 78 (198)
T ss_pred CceEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHHHHHHHHHhcCc--ccccccccceeEEEEEEecCCeeEE
Confidence 888998888873 5666544322 22 35788999999998 99999999999999 7777899999
Q ss_pred EEecCCCCcccHHHHHHHHHHHHHhhc-cccccccCCCccchhhHHHHHHHHHHhcCCchhhHHHHHHhhhhhhcc
Q 032448 65 CMADDTAGRRIPFAFLEDIHQRFVKTY-GRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVEM 139 (140)
Q Consensus 65 citd~~~~~~~af~fL~~i~~~F~~~~-~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dkl~~l~~~l~evk~ 139 (140)
+++|.+||.|+||.+|++|.++|..+. +.+|+...+-.. . .|.|..++.+|+||.++|+|.+||+||||+|.
T Consensus 79 ~~~D~eYP~rvA~tLL~kvld~~~~k~~~~~W~~~~~~~~--~-~~~L~~~l~kyqdP~ead~l~kvQ~EldETKi 151 (198)
T KOG0861|consen 79 LIADDEYPVRVAFTLLNKVLDEFTTKVPATQWPVGETADL--S-YPYLDTLLSKYQDPAEADPLLKVQNELDETKI 151 (198)
T ss_pred EEecCcCchhHHHHHHHHHHHHHhhcCcccccCcCCCcCC--C-chhHHHHHHHhcChhhhChHHHHHHHHHHHHH
Confidence 999999999999999999999997665 477874322222 3 58899999999999999999999999999984
No 5
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=99.62 E-value=4.2e-15 Score=104.06 Aligned_cols=135 Identities=15% Similarity=0.348 Sum_probs=104.5
Q ss_pred CceEEEEEEeCC--eeEeeec-CCCCCH--HHHHHHHhccCCCCCCCceEEeeCCeEEEEEEe-CCeEEEEEecCCCCcc
Q 032448 1 MAILFSLVARGS--VVLAECS-ATATNA--SAIARQILDKIPGNNDSHVSYSQDRYIFHVKRT-DGLTVLCMADDTAGRR 74 (140)
Q Consensus 1 M~I~Ya~Var~~--~iL~e~~-~~~~~~--~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~-~~~~~~citd~~~~~~ 74 (140)
|.++|..+..+. .+|++-- ..+..| ...+..+|.++.|...++.+++.++|.|||... .|++|.|+|+.++|.+
T Consensus 1 i~s~~~~~~~~~~~~~~~~~~s~~~~~ff~~~~v~~~l~~~~~~~a~~~~ies~~~~~~~~~~s~gi~y~~~~~~e~p~~ 80 (190)
T COG5143 1 IASISLFRVKGEPLRTLSDAESLSSFSFFHRSKVKEVLRFLSKTSASRASIESGDYFFHYLKMSSGIVYVPISDKEYPNK 80 (190)
T ss_pred CceEEEEeecCCcceeeccccccCcccccccchHHHHHHHhcccccchhccccCceEEEEEecCCCceeEEecccccchh
Confidence 567777777773 3344322 222222 578888888888766778999999999998766 5999999999999999
Q ss_pred cHHHHHHHHHHHHHhhcc-ccccc-cCCCccchhhHHHHHHHHHHhcCCchhhHHHHHHhhhhhhcc
Q 032448 75 IPFAFLEDIHQRFVKTYG-RAVLS-AQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVEM 139 (140)
Q Consensus 75 ~af~fL~~i~~~F~~~~~-~~~~~-~~~~~~~~~F~~~l~~~~~~yn~~~~~dkl~~l~~~l~evk~ 139 (140)
.||+.++++..+|....+ .+|.. ..++.+. +|++.+++ .|+++..+|++.+++.++++||.
T Consensus 81 la~~~~~~~~~~~~~s~~~~~~~d~~~~~~~~-~~d~~~e~---~y~d~s~~D~~d~l~~el~e~K~ 143 (190)
T COG5143 81 LAYGYLNSIATEFLKSSALEQLIDDTVGIMRV-NIDKVIEK---GYRDPSIQDKLDQLQQELEETKR 143 (190)
T ss_pred hhhHHHHhhccHhhhhhhHhhcccCccchhhh-hHHHHHHh---hcCCchhhhHHHHHHHHHHHHHH
Confidence 999999999999998887 34433 3444443 77777777 39999999999999999999973
No 6
>PF04086 SRP-alpha_N: Signal recognition particle, alpha subunit, N-terminal; InterPro: IPR007222 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents the alpha subunit of the SR receptor.; GO: 0003924 GTPase activity, 0005047 signal recognition particle binding, 0005525 GTP binding, 0006184 GTP catabolic process, 0006886 intracellular protein transport, 0005785 signal recognition particle receptor complex; PDB: 2FH5_A 2GO5_1.
Probab=96.65 E-value=0.013 Score=44.11 Aligned_cols=67 Identities=21% Similarity=0.350 Sum_probs=43.1
Q ss_pred HHHHHHHHhccCCCCCCCceEEeeCCeEEEEEEeC--CeEEEEEecCCCCcccHHHHHHHHHHHHHhhcccc
Q 032448 25 ASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTD--GLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRA 94 (140)
Q Consensus 25 ~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~--~~~~~citd~~~~~~~af~fL~~i~~~F~~~~~~~ 94 (140)
...+++.||-.=. ....+|++++|..+|...| +|+|++|=.+-..-...=.||+.|+..|...|+..
T Consensus 4 in~LI~~vlleeR---~~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~~ 72 (279)
T PF04086_consen 4 INALIRDVLLEER---SGNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKNQ 72 (279)
T ss_dssp HHHHHHHTGGG----------------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHHH
T ss_pred HHHHHHHhheeec---cCCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhHH
Confidence 3567777774411 3456689999999988775 89999998888876666699999999999999865
No 7
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=94.13 E-value=1.1 Score=30.02 Aligned_cols=79 Identities=14% Similarity=0.282 Sum_probs=56.3
Q ss_pred CCeeEeeecCCCCC------HHHHHHHHhccCCCCCCCceEEeeCCeEEEEEEeCCeEEEEEecCCCCcccHHHHHHHHH
Q 032448 11 GSVVLAECSATATN------ASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIH 84 (140)
Q Consensus 11 ~~~iL~e~~~~~~~------~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~citd~~~~~~~af~fL~~i~ 84 (140)
|..+++-|-..... ++.+.+.+..+-+ ..--.+..+++.+-|..-+++.++++++.+...-....||+.+.
T Consensus 12 G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~~---~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~~~e~l~~~v 88 (141)
T PF01217_consen 12 GKRILSKYYRDVSEEERQKLFEKFIKKKSSRNS---KQSPIFEHDNYRIVYKRYSDLYFVVVGDENENELLLLEFLHRLV 88 (141)
T ss_dssp SEEEEEEESSTSTSHHHHHHHHHHHHHHHTSSS---SSTSEEEETTEEEEEEEETTEEEEEEESSTSBHHHHHHHHHHHH
T ss_pred CCEEEehhcCCccHHHHHHHHHHHHHHHHhccc---ccceeeecccceeeeEeeccEEEEEEeecccchHHHHHHHHHhh
Confidence 34677766432211 3444455554422 22344678999988988999999999999999889999999999
Q ss_pred HHHHhhcc
Q 032448 85 QRFVKTYG 92 (140)
Q Consensus 85 ~~F~~~~~ 92 (140)
+-+..-++
T Consensus 89 ~~l~~~~~ 96 (141)
T PF01217_consen 89 EVLDDYFG 96 (141)
T ss_dssp HHHHHHHS
T ss_pred hhhhhhhc
Confidence 88877666
No 8
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.90 E-value=0.7 Score=37.69 Aligned_cols=88 Identities=17% Similarity=0.231 Sum_probs=66.3
Q ss_pred eEEEEEEeCCeeEeeecCCCCCH----HHHHHHHhccCCCCCCCceEEeeCCeEEEEEEe--CCeEEEEEecCCCCcccH
Q 032448 3 ILFSLVARGSVVLAECSATATNA----SAIARQILDKIPGNNDSHVSYSQDRYIFHVKRT--DGLTVLCMADDTAGRRIP 76 (140)
Q Consensus 3 I~Ya~Var~~~iL~e~~~~~~~~----~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~--~~~~~~citd~~~~~~~a 76 (140)
=.++...+|+.||+-|....-+| ..+++.+|-.=. .+--+++.+.|+.-|-.+ -+++|+|+-.+-.--..+
T Consensus 3 d~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~er---~~~~~~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~yv 79 (587)
T KOG0781|consen 3 DQFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLSER---GGVNSFTFEAYTLKYQLDNQYSLVFVVVFQKILTLTYV 79 (587)
T ss_pred ceeeeecCCcEEEEEecccchhccchHHHHHHHHHHHhh---cCcccCchhheeEeeeecCCccEEEEEEEeccchhhhH
Confidence 36789999999999998765444 456666653312 222337888898877665 489999998888877778
Q ss_pred HHHHHHHHHHHHhhccc
Q 032448 77 FAFLEDIHQRFVKTYGR 93 (140)
Q Consensus 77 f~fL~~i~~~F~~~~~~ 93 (140)
-.+|+++.+.|...|..
T Consensus 80 ~~ll~~v~~~f~e~~~~ 96 (587)
T KOG0781|consen 80 DKLLNDVLNLFREKYDT 96 (587)
T ss_pred HHHHHHHHHHHHHHhcc
Confidence 89999999999998863
No 9
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.86 E-value=2.5 Score=33.01 Aligned_cols=110 Identities=17% Similarity=0.257 Sum_probs=73.6
Q ss_pred EEEEEEeCCeeEeeec--CCCCCHHHHHHHH-hccCCCCCCCc-eEEeeCCeEEEEEEeCCeEEEEEecCCCCcccHHHH
Q 032448 4 LFSLVARGSVVLAECS--ATATNASAIARQI-LDKIPGNNDSH-VSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAF 79 (140)
Q Consensus 4 ~Ya~Var~~~iL~e~~--~~~~~~~~~~~~v-l~~i~~~~~~k-~~~~~~~~~~h~l~~~~~~~~citd~~~~~~~af~f 79 (140)
+|..=.||.++++-.= +-.++..++-|-- +... +.| -..+.|+-+||+...+++-.++||.......+.|.|
T Consensus 5 lfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~----d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eF 80 (446)
T KOG0938|consen 5 LFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNL----DVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEF 80 (446)
T ss_pred EEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhcc----ccCCCeeEecceeEEEEeeccEEEEEEecCCCchhhHHHH
Confidence 5566678888887542 2345655554433 2221 223 234689999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccccccCCCccchhhHHHHHHHHHHhc
Q 032448 80 LEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYS 119 (140)
Q Consensus 80 L~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn 119 (140)
|..+-+.+..-+|...+.+....+.-. -..|.++|. |-
T Consensus 81 l~kl~avm~aYfgk~~Eeaiknnf~lI-~ElLDemld-~G 118 (446)
T KOG0938|consen 81 LYKLDAVMNAYFGKDREEAIKNNFVLI-YELLDEMLD-FG 118 (446)
T ss_pred HHHHHHHHHHHhcccchhhhhhceEeH-HHHHHHHHh-cC
Confidence 999999998877744444433333212 234556555 53
No 10
>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=91.42 E-value=2.1 Score=28.57 Aligned_cols=109 Identities=10% Similarity=0.136 Sum_probs=58.1
Q ss_pred EEEeCCeeEeeecCCC---CC-------HHHH---HHHHhccCCCC-C---CCceEEeeCCeEEE-EEEeCCeEEEEEec
Q 032448 7 LVARGSVVLAECSATA---TN-------ASAI---ARQILDKIPGN-N---DSHVSYSQDRYIFH-VKRTDGLTVLCMAD 68 (140)
Q Consensus 7 ~Var~~~iL~e~~~~~---~~-------~~~~---~~~vl~~i~~~-~---~~k~~~~~~~~~~h-~l~~~~~~~~citd 68 (140)
.|++.+.+|.+.+..+ .. +..+ +..+++..-+. . .=+.....+++..+ |+...++-|+.+++
T Consensus 1 IIg~~n~PLy~~~~~~~~~~~~~~~~~l~~~~~h~sLD~iee~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~ 80 (132)
T PF04628_consen 1 IIGPNNNPLYIRSFPSEKESSSSDARHLYQFIAHSSLDVIEEKLWKSSSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHD 80 (132)
T ss_dssp EE-TTS-EEEEEEE--ST-CGHHHHHHHHHHHHHHHHHHHHHCCHCSSSCSEEEEEEEETTEEEEEEETTT--EEEEEEC
T ss_pred CCCCCCcceEEEecCCCcccccchHHHHHHHHHHHHHHHHHHHHhhcccccccCceehhhhHHHHhhhccCceeEEEEEe
Confidence 4788888888776322 11 3333 33444332221 1 11344566887766 88888999999998
Q ss_pred ---CCCCcccHHHHHHHHHHHHHhhcccccccc-CCCccchhhHHHHHHHHH
Q 032448 69 ---DTAGRRIPFAFLEDIHQRFVKTYGRAVLSA-QAYGMNDEFSRVLSQQME 116 (140)
Q Consensus 69 ---~~~~~~~af~fL~~i~~~F~~~~~~~~~~~-~~~~~~~~F~~~l~~~~~ 116 (140)
........-.|+.+|+..|....-+-.... .+.. ...|+..++++.+
T Consensus 81 ~~~~~~~d~~ik~fF~~vh~~Y~~~~~NPF~~~~~~I~-S~~Fd~~v~~l~~ 131 (132)
T PF04628_consen 81 MSDNSIRDEDIKQFFKEVHELYVKALCNPFYQPGTPIK-SPKFDSRVRALAK 131 (132)
T ss_dssp GGG-S--HHHHHHHHHHHHHHHHHHHTSTTCGCT-HHH-HHHHHHHHHHHHH
T ss_pred cccCCcchHHHHHHHHHHHHHHHHHccCCCCCCCCCcC-CHHHHHHHHHHhc
Confidence 445556678888888888876443221110 1111 2467777777665
No 11
>PF09426 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro: IPR019005 This entry represents the N-terminal domain of vacuolar R-SNARE Nyv1, which adopts a longin fold []. Vacuolar v-SNARE is required for docking and is only involved in homotypic vacuole fusion. Nyv1 is required for Ca(2+) efflux from the vacuolar lumen, a required signal for subsequent membrane fusion events, by inhibiting vacuolar Ca(2+)-ATPase PMC1 and promoting Ca(2+) release when forming trans-SNARE assemblies during the docking step. In yeast, the N-terminal domain of Nyv1 is sufficient to direct the transport of Nyv1 to limiting membrane of the vacuole []. ; PDB: 2FZ0_A.
Probab=91.41 E-value=1 Score=30.20 Aligned_cols=60 Identities=17% Similarity=0.287 Sum_probs=40.8
Q ss_pred HHHHHHHhccCCCCCCCceEEe----eCCeEEEEEE---eCCeEEEEEecCCCCcccHHHHHHHHHH
Q 032448 26 SAIARQILDKIPGNNDSHVSYS----QDRYIFHVKR---TDGLTVLCMADDTAGRRIPFAFLEDIHQ 85 (140)
Q Consensus 26 ~~~~~~vl~~i~~~~~~k~~~~----~~~~~~h~l~---~~~~~~~citd~~~~~~~af~fL~~i~~ 85 (140)
+.+-.-|++++-|-.++|.+=. .+||-++|.. +++-+++|.|..+.|+-.+-..|.+++.
T Consensus 44 ~Li~dmVlPkVV~v~GNKVTK~S~~lIDGyDCYYTT~~~d~~~vlVCFt~~~vPKILPiRlLSeLK~ 110 (141)
T PF09426_consen 44 KLIHDMVLPKVVPVEGNKVTKMSMHLIDGYDCYYTTEDNDDNKVLVCFTRVDVPKILPIRLLSELKG 110 (141)
T ss_dssp HHHHHTTGGG----SS-SSEE--S--SSSEEEEE---SS-TTEEEEEEEETTS-SSHHHHHHHHHTT
T ss_pred HHHhhccccceEEccCCeEEEEEeecccccceeeecccCCCCeEEEEEEecCCcceecHHHHHhhcc
Confidence 3455667788887666665532 4899999887 4789999999999999999999999875
No 12
>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=86.86 E-value=7.6 Score=26.29 Aligned_cols=74 Identities=16% Similarity=0.205 Sum_probs=41.4
Q ss_pred CCceEEeeCCeEEEEEE-eCCeEEEEEecCCCCcccHHHHHHHHHHHHHhhc-ccc-ccccCCCccchhhHHHHHHHHH
Q 032448 41 DSHVSYSQDRYIFHVKR-TDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTY-GRA-VLSAQAYGMNDEFSRVLSQQME 116 (140)
Q Consensus 41 ~~k~~~~~~~~~~h~l~-~~~~~~~citd~~~~~~~af~fL~~i~~~F~~~~-~~~-~~~~~~~~~~~~F~~~l~~~~~ 116 (140)
.+-.+++.+.|..|+.- --|+-|+++||...+. ..=.+++.+..-|...- .+- .....|-. +..|+..|.++++
T Consensus 65 ~g~~~~~T~~yklh~~eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~dyV~KNPfy~~~~pI~-~~lF~~~l~~~~~ 141 (142)
T PF04099_consen 65 SGFESFETDTYKLHCFETPTGLKFVLITDPNVPS-LRDELLRIYYELYVDYVVKNPFYSLEMPIR-CELFDTKLDQYVK 141 (142)
T ss_dssp -SEEEEEESS-EEEEEE-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHHHHHS-TTS-TTS-----HHHHHHHHHHHH
T ss_pred eeEEEEEeCCEEEEEEEcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHHHHhhCCCCCCCCcEe-hHHHHHHHHHHHh
Confidence 56778899999999765 4899999999999863 33344555555444321 111 11122322 3577777777664
No 13
>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=81.51 E-value=17 Score=29.08 Aligned_cols=87 Identities=7% Similarity=0.043 Sum_probs=60.5
Q ss_pred EEEEeCCeeEeeecCCC---CCHHHHHHHHhccCCCCCCCceEEeeCCeEEEEEEeCCeEEEEEecCCCCcccHHHHHHH
Q 032448 6 SLVARGSVVLAECSATA---TNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLED 82 (140)
Q Consensus 6 a~Var~~~iL~e~~~~~---~~~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~citd~~~~~~~af~fL~~ 82 (140)
.+....++++...-..+ ..+..+...++.-.....+.-..+..|+..|.|+..+.+.++||+..+.+...--.-|+-
T Consensus 15 fIlS~AGKPIysr~G~e~~l~~~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ 94 (415)
T PF03164_consen 15 FILSSAGKPIYSRYGDEDKLSSLMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDY 94 (415)
T ss_pred EEECCCCceeEEecCChHHHHHHHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHH
Confidence 34445566665443222 125566666666554333555678889999999999999999999999998777788888
Q ss_pred HHHHHHhhcc
Q 032448 83 IHQRFVKTYG 92 (140)
Q Consensus 83 i~~~F~~~~~ 92 (140)
|.........
T Consensus 95 ly~qils~lt 104 (415)
T PF03164_consen 95 LYSQILSILT 104 (415)
T ss_pred HHHHHHHhcc
Confidence 8777666443
No 14
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.16 E-value=27 Score=27.69 Aligned_cols=44 Identities=9% Similarity=0.134 Sum_probs=35.2
Q ss_pred CCeEEEEEEeCCeEEEEEecCCCCcccHHHHHHHHHHHHHhhcc
Q 032448 49 DRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG 92 (140)
Q Consensus 49 ~~~~~h~l~~~~~~~~citd~~~~~~~af~fL~~i~~~F~~~~~ 92 (140)
..|.++-...+++.+|+++..+.|--.++.||.+|-+-|..-||
T Consensus 53 p~hylfsv~~~~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg 96 (418)
T KOG2740|consen 53 PHHYLFSVYRDLIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFG 96 (418)
T ss_pred CceeeeeeeccCcEEEEEEeccCCChhHHHHHHHHHHHHHHHhc
Confidence 33444444567888888899999988999999999999988777
No 15
>PRK11546 zraP zinc resistance protein; Provisional
Probab=64.41 E-value=12 Score=25.51 Aligned_cols=54 Identities=17% Similarity=0.230 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhhccccccccCCCccchhhHHHHHHHHHHhcCCchhhHHHHHHhhhhhhcc
Q 032448 78 AFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVEM 139 (140)
Q Consensus 78 ~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dkl~~l~~~l~evk~ 139 (140)
.-++.|.++|......-+... ..-...|+.++. +++|+..+|.+|.+||.+++.
T Consensus 50 a~~q~I~~~f~~~t~~LRqqL------~aKr~ELnALl~--~~~pD~~kI~aL~kEI~~Lr~ 103 (143)
T PRK11546 50 AAWQKIHNDFYAQTSALRQQL------VSKRYEYNALLT--ANPPDSSKINAVAKEMENLRQ 103 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHc--CCCCCHHHHHHHHHHHHHHHH
Confidence 457788888876553211111 011234555543 356788899999999988764
No 16
>PHA01811 hypothetical protein
Probab=62.85 E-value=11 Score=21.99 Aligned_cols=19 Identities=32% Similarity=0.469 Sum_probs=15.8
Q ss_pred CCceEEeeCCeEEEEEEeC
Q 032448 41 DSHVSYSQDRYIFHVKRTD 59 (140)
Q Consensus 41 ~~k~~~~~~~~~~h~l~~~ 59 (140)
+.-.++...||.+||+-++
T Consensus 4 ddivtlrvkgyi~hyldd~ 22 (78)
T PHA01811 4 DDIVTLRVKGYILHYLDDD 22 (78)
T ss_pred ccEEEEEEeeEEEEEEcCc
Confidence 5667888999999999874
No 17
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.71 E-value=5 Score=26.36 Aligned_cols=18 Identities=11% Similarity=0.322 Sum_probs=15.3
Q ss_pred chhhHHHHHHhhhhhhcc
Q 032448 122 PNADRINRIKGEMSQVEM 139 (140)
Q Consensus 122 ~~~dkl~~l~~~l~evk~ 139 (140)
+..+++.++|.|+++|++
T Consensus 26 ~~~~k~~~tq~QvdeVv~ 43 (116)
T KOG0860|consen 26 TANDKLQQTQAQVDEVVD 43 (116)
T ss_pred hhhHHHHHHHHHHHHHHH
Confidence 457999999999999874
No 18
>PF03607 DCX: Doublecortin; InterPro: IPR003533 X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder []. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling []. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation []. Some proteins known to contain a DC domain are listed below: Doublecortin. It is required for neuronal migration []. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains []. Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controling neuronal migration in the developing brain []. Retinitis pigmentosa 1 protein. It could play a role in the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 []. ; GO: 0035556 intracellular signal transduction; PDB: 1UF0_A 1MG4_A 1MFW_A 2DNF_A 2XRP_I 2BQQ_A 1MJD_A.
Probab=61.77 E-value=12 Score=21.32 Aligned_cols=48 Identities=13% Similarity=0.122 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHhccCCCCCCCceEEeeCCeEEEEEE--eCCeEEEEEecC
Q 032448 22 ATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKR--TDGLTVLCMADD 69 (140)
Q Consensus 22 ~~~~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~--~~~~~~~citd~ 69 (140)
-.+|+++...+-+++....+-|..|+.++...+=+. ++|-.|+|...+
T Consensus 8 ~~s~e~lL~~it~~v~l~~gVr~lyt~~G~~V~~l~~l~dg~~yVa~g~e 57 (60)
T PF03607_consen 8 FRSFEQLLDEITEKVQLPSGVRKLYTLDGKRVKSLDELEDGGSYVASGRE 57 (60)
T ss_dssp HSSHHHHHHHHHHSSSSTTS-SEEEETTSSEESSGGGS-TTEEEEEESSS
T ss_pred hcCHHHHHHHHHhhcCCCcccceEECCCCCEeCCHHHHCCCCEEEEEcCC
Confidence 367899999999999986678888998886555433 378889988554
No 19
>PF07897 DUF1675: Protein of unknown function (DUF1675); InterPro: IPR012463 The members of this family are sequences derived from hypothetical plant proteins of unknown function. One member of this family (Q9SFV5 from SWISSPROT) is annotated as a putative RNA-binding protein, but no evidence was found to support this.
Probab=53.46 E-value=15 Score=28.07 Aligned_cols=25 Identities=4% Similarity=0.402 Sum_probs=21.1
Q ss_pred eCCeEEEEEEeCCeEEEEEecCCCC
Q 032448 48 QDRYIFHVKRTDGLTVLCMADDTAG 72 (140)
Q Consensus 48 ~~~~~~h~l~~~~~~~~citd~~~~ 72 (140)
.++++|-|-..+++.++|||+..+-
T Consensus 238 i~g~ly~y~~~~~v~i~c~chg~~~ 262 (284)
T PF07897_consen 238 IEGFLYKYGKGEEVRIVCVCHGSFL 262 (284)
T ss_pred eeEEEEEecCCCeEEEEEEecCCCC
Confidence 4678888866789999999999884
No 20
>PF10504 DUF2452: Protein of unknown function (DUF2452); InterPro: IPR019534 This entry contains proteins that have no known function.
Probab=53.44 E-value=6.6 Score=27.23 Aligned_cols=57 Identities=26% Similarity=0.458 Sum_probs=38.3
Q ss_pred HHHHHHHHhccCCCC---CCCceEEee-CCeEEE-EEEeCCeEEEEEecCC-CCcccHHHHHH
Q 032448 25 ASAIARQILDKIPGN---NDSHVSYSQ-DRYIFH-VKRTDGLTVLCMADDT-AGRRIPFAFLE 81 (140)
Q Consensus 25 ~~~~~~~vl~~i~~~---~~~k~~~~~-~~~~~h-~l~~~~~~~~citd~~-~~~~~af~fL~ 81 (140)
.+..+++|+++...+ .+.++.|+- =|.+|| |..++|-.|+.|...+ .+.+.++.||.
T Consensus 64 Lq~QA~~ile~~~~~~~l~~A~cnF~pipG~iYhLY~r~~G~~ylSmisP~EWg~~~p~~flG 126 (159)
T PF10504_consen 64 LQEQARKILEEAERNEELHHAKCNFEPIPGQIYHLYRRENGQDYLSMISPEEWGGSCPHEFLG 126 (159)
T ss_pred HHHHHHHHHHHHHHhHHHhhcccCceecCCCEEEEEECCCCCEEEEeeCHHHhCCCCCcCEEE
Confidence 367788888877642 367788754 466778 7778888877776654 35556655443
No 21
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=49.38 E-value=74 Score=20.94 Aligned_cols=74 Identities=15% Similarity=0.243 Sum_probs=42.5
Q ss_pred CCCCceEEeeCCeEEEEEEe-CCeEEEEEecCCCCcccHHHHHHHHHHHHHhhcc--ccccc-cCCCccchhhHHHHHHH
Q 032448 39 NNDSHVSYSQDRYIFHVKRT-DGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG--RAVLS-AQAYGMNDEFSRVLSQQ 114 (140)
Q Consensus 39 ~~~~k~~~~~~~~~~h~l~~-~~~~~~citd~~~~~~~af~fL~~i~~~F~~~~~--~~~~~-~~~~~~~~~F~~~l~~~ 114 (140)
.+.++..+..++++.|+... -|.-|+.++.+. +...+|+ |+.+...|. .|- +-..+ ..|.. ...|++.++++
T Consensus 55 gssg~~~l~~~~f~m~I~qT~TG~kFV~~~~k~-t~na~~q-l~kiY~lYs-dYV~knPfys~EMPI~-c~lFde~lkrm 130 (134)
T COG5122 55 GSSGRLVLYFRNFVMTIFQTTTGTKFVFVAEKR-TVNALFQ-LQKIYSLYS-DYVTKNPFYSPEMPIQ-CSLFDEHLKRM 130 (134)
T ss_pred CCCceEEEEeccEEEEEEEecCCcEEEEEecCC-chhHHHH-HHHHHHHHH-HHhhcCCCCCccccee-hhhhhHHHHHH
Confidence 45788888899999996654 799999999433 2234455 333333332 221 11111 12222 24788877776
Q ss_pred HH
Q 032448 115 ME 116 (140)
Q Consensus 115 ~~ 116 (140)
.+
T Consensus 131 ~e 132 (134)
T COG5122 131 FE 132 (134)
T ss_pred hc
Confidence 53
No 22
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.35 E-value=1.2e+02 Score=21.61 Aligned_cols=72 Identities=17% Similarity=0.244 Sum_probs=46.5
Q ss_pred CCceEEeeCCeEEEEEEe-CCeEEEEEecCCCCcccHHHHHHHHHHHHHhhcc--ccccc-cCCCccchhhHHHHHHHHH
Q 032448 41 DSHVSYSQDRYIFHVKRT-DGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG--RAVLS-AQAYGMNDEFSRVLSQQME 116 (140)
Q Consensus 41 ~~k~~~~~~~~~~h~l~~-~~~~~~citd~~~~~~~af~fL~~i~~~F~~~~~--~~~~~-~~~~~~~~~F~~~l~~~~~ 116 (140)
.+...++.+.+..|+... -|+-|++||+... ..|=.+|+.|...|. .|. +-..+ ..|.- ...|++.|+.+.+
T Consensus 121 SGie~LetdtF~l~~~QTlTG~KFVvis~~~~--~~aD~lLrKiYelYs-DyvlKNPfYSlEMPIR-c~lFDe~lk~~le 196 (199)
T KOG3369|consen 121 SGIEVLETDTFTLHIFQTLTGTKFVVIAEPGT--QGADSLLRKIYELYS-DYVLKNPFYSLEMPIR-CELFDEKLKFLLE 196 (199)
T ss_pred CceEEEEeccEEEEEEEccCCcEEEEEecCCc--hhHHHHHHHHHHHHH-HHhhcCCccCccccee-HHHhhHHHHHHHh
Confidence 466777889999886654 8999999999887 366677777766553 232 11111 12222 2477777777654
No 23
>KOG4131 consensus Ngg1-interacting factor 3 protein NIF3L1 [General function prediction only]
Probab=42.75 E-value=14 Score=27.60 Aligned_cols=32 Identities=28% Similarity=0.377 Sum_probs=23.9
Q ss_pred EEEeC-CeeEeeecCCCCCH-HHHHHHHhccCCC
Q 032448 7 LVARG-SVVLAECSATATNA-SAIARQILDKIPG 38 (140)
Q Consensus 7 ~Var~-~~iL~e~~~~~~~~-~~~~~~vl~~i~~ 38 (140)
+.+.| ++||||+++.+..| ..+..++.+.++.
T Consensus 223 ~~~~g~sVilc~HSNtERgfL~d~~~kl~~~l~~ 256 (272)
T KOG4131|consen 223 AAANGISVILCEHSNTERGFLSDLCDKLASSLEE 256 (272)
T ss_pred HHHcCCeEEEecCCCccchhHHHHHHHHHhhCCc
Confidence 45666 48999999988766 6677777777663
No 24
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=39.77 E-value=8.2 Score=26.47 Aligned_cols=26 Identities=15% Similarity=0.315 Sum_probs=23.4
Q ss_pred EEEEEecCCCCcccHHHHHHHHHHHH
Q 032448 62 TVLCMADDTAGRRIPFAFLEDIHQRF 87 (140)
Q Consensus 62 ~~~citd~~~~~~~af~fL~~i~~~F 87 (140)
.++.||.++||.+....||..+.++.
T Consensus 25 ~~ilit~kG~P~~~tr~~l~~L~~~~ 50 (160)
T cd00223 25 NCILITGKGYPDRATRRFLRRLHEEL 50 (160)
T ss_pred CEEEEEcCCcCCHHHHHHHHHHHHhh
Confidence 57899999999999999999998874
No 25
>PRK01622 OxaA-like protein precursor; Validated
Probab=39.64 E-value=38 Score=25.29 Aligned_cols=33 Identities=9% Similarity=0.100 Sum_probs=22.8
Q ss_pred hhhHHHHHHHHHHhcCCchhhHHHHHHhhhhhh
Q 032448 105 DEFSRVLSQQMEYYSDDPNADRINRIKGEMSQV 137 (140)
Q Consensus 105 ~~F~~~l~~~~~~yn~~~~~dkl~~l~~~l~ev 137 (140)
....|.++++.++|.+.++.++-.++++|+.++
T Consensus 94 ~~iqP~l~~iq~kyk~~~d~~~~~~~~~e~~~L 126 (256)
T PRK01622 94 AVMKPELDKIQAKLKVTKDLEKQKEYQKEMMEL 126 (256)
T ss_pred HHhCHHHHHHHHHHhccCCHHHHHHHHHHHHHH
Confidence 357899999999997655545545566666543
No 26
>PF11675 DUF3271: Protein of unknown function (DUF3271); InterPro: IPR021689 This family of proteins with unknown function appears to be restricted to Plasmodium.
Probab=39.60 E-value=1.3e+02 Score=22.43 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=31.8
Q ss_pred ceEEEEEEeCCeeEeeecCCCCCHHHHHHHHhccCCCCCCCceEEeeCCeEE
Q 032448 2 AILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIF 53 (140)
Q Consensus 2 ~I~Ya~Var~~~iL~e~~~~~~~~~~~~~~vl~~i~~~~~~k~~~~~~~~~~ 53 (140)
+|-|+.||.-+..+...-..-..+=.++-.++..=.. +-+..++.|+|.|
T Consensus 30 ~i~y~sv~qpt~~f~~~~k~h~~YLdiIN~il~~eSe--N~Kyayeg~nYHw 79 (249)
T PF11675_consen 30 PIAYISVAQPTATFEHDEKKHTKYLDIINDILRDESE--NIKYAYEGGNYHW 79 (249)
T ss_pred ceeEEeccCceEEEeecCccchhHHHHHHHHHhcccc--ccceeeeCCceEE
Confidence 4788888887666654432223456788888877443 5667776666543
No 27
>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins.
Probab=36.91 E-value=19 Score=32.91 Aligned_cols=34 Identities=26% Similarity=0.681 Sum_probs=26.0
Q ss_pred CCeEEE-EEEeCC-eEEEEEecCCCCcccHHHHHHH
Q 032448 49 DRYIFH-VKRTDG-LTVLCMADDTAGRRIPFAFLED 82 (140)
Q Consensus 49 ~~~~~h-~l~~~~-~~~~citd~~~~~~~af~fL~~ 82 (140)
+.|+++ |-.++| +|+++++-++-+..|.|.|++.
T Consensus 67 nSyIIYEY~R~~G~~~~vvl~~~s~g~~V~YRFId~ 102 (1201)
T PF12128_consen 67 NSYIIYEYQREDGQLCCVVLSRKSDGRGVQYRFIDA 102 (1201)
T ss_pred CceEEEeeeccCCceeEEEEeecCCCCceeeeeccC
Confidence 678877 888888 6666666576677889999875
No 28
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=36.77 E-value=54 Score=22.37 Aligned_cols=65 Identities=18% Similarity=0.171 Sum_probs=43.2
Q ss_pred cccHHHHHHHHHHHHHhhccccccccCCCccchhhHHHHHHHHHHhcCCc-----hhhHHHHHHhhhhhhc
Q 032448 73 RRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDP-----NADRINRIKGEMSQVE 138 (140)
Q Consensus 73 ~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~-----~~dkl~~l~~~l~evk 138 (140)
++-+-.=+.+.-.+|...|.........-++ ..+...|..+-.+|+..+ ..+...+|.+|++++.
T Consensus 73 ~~~~~~~ar~~in~~vs~YRr~~~v~g~~Sf-~~m~tAln~LaghY~s~g~raPlP~k~k~rll~el~~Ae 142 (145)
T PF13326_consen 73 RAEAAAEARELINDYVSRYRRGPSVSGLPSF-TTMYTALNALAGHYSSYGNRAPLPEKLKERLLKELDQAE 142 (145)
T ss_dssp HHHHHHHHHHHHHHHHCCCCCCHHCCTSHHH-HHHHHHHHHHHHHCHHHTTS-S--HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCcCCcchH-HHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHH
Confidence 3445566677778888888644322222333 377788999999998743 2466688888888764
No 29
>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=36.70 E-value=1.2e+02 Score=19.85 Aligned_cols=80 Identities=14% Similarity=0.140 Sum_probs=49.5
Q ss_pred EEEEe-CCeeEeeecCCC-C----------CHHHHHHHHhccCCCCCCCceEEeeCCeEEEEEEeCCeEEEEEecCCCCc
Q 032448 6 SLVAR-GSVVLAECSATA-T----------NASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGR 73 (140)
Q Consensus 6 a~Var-~~~iL~e~~~~~-~----------~~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~citd~~~~~ 73 (140)
..|+. ++.+|+.....+ + .|. .+.+.+.|+.-..++.....+++|.........+....||+.+...
T Consensus 20 I~itDrDGvpi~~v~~~~~~~~~~~~~~~~tf~-~a~~Q~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~ias~~aN~ 98 (119)
T PF08923_consen 20 IVITDRDGVPIAKVSSDSAPESAMRPSLLSTFA-MAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSNANT 98 (119)
T ss_dssp EEEEETTS-EEEEEE-TTS-GGGGSHHHHCCHH-HHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETTS-H
T ss_pred EEEECCCCcEEEEecCCCCcchhhhhHHHHHHH-HHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCCCCH
Confidence 34443 368888765332 2 233 4555688888654555556789988776677899999999998875
Q ss_pred ccHHHHHHHHHHH
Q 032448 74 RIPFAFLEDIHQR 86 (140)
Q Consensus 74 ~~af~fL~~i~~~ 86 (140)
-.-..+-+++..-
T Consensus 99 G~il~l~~~L~~~ 111 (119)
T PF08923_consen 99 GLILSLEEELAPI 111 (119)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHhHHHHHHH
Confidence 5555555555443
No 30
>cd01617 DCX Ubiquitin-like domain of DCX. DCX The ubiquitin-like DCX domain is present in tandem within the N-terminal half of the doublecortin protein. Doublecortin is expressed in migrating neurons. Mutations in the gene encoding doublecortin cause lissencephaly in males and 'double-cortex syndrome' in females.
Probab=36.69 E-value=96 Score=18.58 Aligned_cols=51 Identities=12% Similarity=0.104 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHhccCCC-CCCCceEEeeCC-eEEEEEE--eCCeEEEEEecCCC
Q 032448 21 TATNASAIARQILDKIPG-NNDSHVSYSQDR-YIFHVKR--TDGLTVLCMADDTA 71 (140)
Q Consensus 21 ~~~~~~~~~~~vl~~i~~-~~~~k~~~~~~~-~~~h~l~--~~~~~~~citd~~~ 71 (140)
.-.+|+.+...+-+++.+ ..+-+..++.++ ....-+. ++|-.|+|...+.+
T Consensus 24 ~~~sfd~lL~~lt~~l~l~~~~Vr~lyt~~g~~~v~~~~~l~~g~~yVa~g~e~f 78 (80)
T cd01617 24 RFKSFDALLDDLTEKVQLDPGAVRKLYTLDGGHRVSLLDELEDGGVYVASGREPF 78 (80)
T ss_pred hhCCHHHHHHHHHHHhCCCCCcEEEEEcCCCCeEeccHHHhcCCCEEEEECCCCC
Confidence 347899999998888885 346678888877 5544332 48889998866544
No 31
>PLN00064 photosystem II protein Psb27; Provisional
Probab=36.62 E-value=1.5e+02 Score=20.74 Aligned_cols=68 Identities=21% Similarity=0.169 Sum_probs=46.4
Q ss_pred CCCcccHHHHHHHHHHHHHhhccccccccCCCccchhhHHHHHHHHHHhcCCc-h----hhHHHHHHhhhhhhc
Q 032448 70 TAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDP-N----ADRINRIKGEMSQVE 138 (140)
Q Consensus 70 ~~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~-~----~dkl~~l~~~l~evk 138 (140)
+-.+.-+-.=+.+....|...|.........-+| ..+...|..+--||++-. . +..-.+|.+|++++.
T Consensus 87 dp~~a~a~aeaR~~iNdyvSrYRr~~~v~Gl~SF-ttMyTALNaLAGHY~SfgpnrPlPeKlK~RL~qE~~~AE 159 (166)
T PLN00064 87 DPNVADAVAELRETSNSWVAKYRREKALLGRPSF-RDMYSALNAVSGHYISFGPTAPIPAKRKARILEEMDTAE 159 (166)
T ss_pred CccHHHHHHHHHHHHHHHHHHhcCCCcccCcccH-HHHHHHHHHHHHHhhccCCCCCCcHHHHHHHHHHHHHHH
Confidence 3345567788888899999999754333333344 477888999999996542 2 344478888888764
No 32
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=35.71 E-value=1.4e+02 Score=20.20 Aligned_cols=66 Identities=14% Similarity=0.187 Sum_probs=44.2
Q ss_pred CcccHHHHHHHHHHHHHhhccccccccCCCccchhhHHHHHHHHHHhcCCch----hhHHHHHHhhhhhhc
Q 032448 72 GRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPN----ADRINRIKGEMSQVE 138 (140)
Q Consensus 72 ~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~----~dkl~~l~~~l~evk 138 (140)
.++-+-.=..+.-.+|...|..+......-+| ......|..+--+|++-++ ...-.+|.+|++++.
T Consensus 60 ~~~~a~~~ar~~indyvsrYRr~~~v~g~~SF-ttm~TALNsLAGHY~sy~~rPlPeklk~Rl~~El~~AE 129 (135)
T TIGR03044 60 NKSEAQAEARQLINDYISRYRRRPRVNGLSSF-TTMQTALNSLAGHYKSYANRPLPEKLKERLEKELKKAE 129 (135)
T ss_pred cHHHHHHHHHHHHHHHHHHhcCCCCcCCcccH-HHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHH
Confidence 34556677778888999888654333333344 3778889999999987542 344477888887753
No 33
>COG4051 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.22 E-value=1.8e+02 Score=20.77 Aligned_cols=58 Identities=19% Similarity=0.355 Sum_probs=35.5
Q ss_pred eCCeeEeeecCCCCC--HHHHHHHHhccCCCCCCCceEEeeCCeEEEEEEeCCeEEEEEecCCCCc
Q 032448 10 RGSVVLAECSATATN--ASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGR 73 (140)
Q Consensus 10 r~~~iL~e~~~~~~~--~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~citd~~~~~ 73 (140)
+|.+|++++.+.+|. +..+++..|.-+... -..+...||.-.++.+..++|-.+...+
T Consensus 3 ~g~~ivV~~~dk~gae~Y~kIir~al~dL~La------raI~r~~f~ld~eeplfi~aV~tr~t~r 62 (202)
T COG4051 3 SGETIVVECADKSGAEFYRKIIRDALADLKLA------RAIGRIKFVLDPEEPLFIMAVITRDTGR 62 (202)
T ss_pred CCceEEEEecChhhhHHHHHHHHHHHHHhccc------cccceEEEEEcCCCceeEEEEeeccCCC
Confidence 467899999877664 678888888776641 1233444444445555555555555443
No 34
>smart00537 DCX Domain in the Doublecortin (DCX) gene product. Tandemly-repeated domain in doublin, the Doublecortin gene product. Proposed to bind tubulin. Doublecortin (DCX) is mutated in human X-linked neuronal migration defects.
Probab=30.04 E-value=78 Score=19.47 Aligned_cols=51 Identities=12% Similarity=0.115 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHhc--cCCCCCCCceEEeeCCeEEEEEE--eCCeEEEEEecCCC
Q 032448 21 TATNASAIARQILD--KIPGNNDSHVSYSQDRYIFHVKR--TDGLTVLCMADDTA 71 (140)
Q Consensus 21 ~~~~~~~~~~~vl~--~i~~~~~~k~~~~~~~~~~h~l~--~~~~~~~citd~~~ 71 (140)
.-.+|+++...+-+ .++.+.+-+..++.++....-+. ++|=.|+|.+.+.+
T Consensus 29 ~~~s~d~lL~~lt~~v~l~~~~~Vr~lyt~~G~~v~~l~~l~~g~~yVa~g~e~f 83 (89)
T smart00537 29 RFKSFEALLQDLTEVVKLDLPHGVRKLYTLDGKKVTSLDELEDGGSYVASGTEAF 83 (89)
T ss_pred hcCCHHHHHHHHhhhcccCCCCCeeEEEcCCCCEECCHHHhCcCCEEEEEcCCcc
Confidence 34788888887777 55543357888888885544333 37888888877744
No 35
>PHA02979 hypothetical protein; Provisional
Probab=29.68 E-value=89 Score=20.50 Aligned_cols=32 Identities=16% Similarity=0.525 Sum_probs=23.4
Q ss_pred CCceEEeeCCeEEEEEEeCCeEEEEEecCCCC
Q 032448 41 DSHVSYSQDRYIFHVKRTDGLTVLCMADDTAG 72 (140)
Q Consensus 41 ~~k~~~~~~~~~~h~l~~~~~~~~citd~~~~ 72 (140)
+-+.....++|.|-.-...++..+|+|..+++
T Consensus 59 hi~LimD~ndYs~e~gN~SnfiiiCI~Sdd~G 90 (140)
T PHA02979 59 HIKLIMDANDYSFETGNSSNFIIICICSDDCG 90 (140)
T ss_pred heeeEEecccceEEeCCcccEEEEEEeccccc
Confidence 44555566777776655678999999998876
No 36
>PF11813 DUF3334: Protein of unknown function (DUF3334); InterPro: IPR024513 This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Probab=27.97 E-value=2.5e+02 Score=20.63 Aligned_cols=73 Identities=18% Similarity=0.211 Sum_probs=44.9
Q ss_pred EEEEEEeCCeEEEEEecCCCCcccHHHHHHHHHHHHHhhcc-ccccccCCCccchhhHHHHHHHHHHhcCCchhhHHHHH
Q 032448 52 IFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG-RAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRI 130 (140)
Q Consensus 52 ~~h~l~~~~~~~~citd~~~~~~~af~fL~~i~~~F~~~~~-~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dkl~~l 130 (140)
=++.+.++|+.-++|..=+- ..| -+|.+.|...-| ....-+..|.- .+...++.++|.+.- .|-..+|
T Consensus 51 GCFvlFDGGFsGLVviNFsa--~AA----mEiY~~YMl~MGMpE~ELA~~hTS-dEV~nvmGELMNQiv----GdFt~kV 119 (229)
T PF11813_consen 51 GCFVLFDGGFSGLVVINFSA--QAA----MEIYRSYMLNMGMPESELAISHTS-DEVGNVMGELMNQIV----GDFTGKV 119 (229)
T ss_pred ceEEEecCCcceEEEEecCh--HHH----HHHHHHHHHhcCCCHHHHhhhccc-HHHHHHHHHHHHHHH----HHHHHHH
Confidence 34556677777777764332 233 267777777666 33333444443 488889999987652 3666666
Q ss_pred Hhhhh
Q 032448 131 KGEMS 135 (140)
Q Consensus 131 ~~~l~ 135 (140)
+++++
T Consensus 120 ~~eLq 124 (229)
T PF11813_consen 120 RKELQ 124 (229)
T ss_pred HHHHh
Confidence 66664
No 37
>PRK10050 curli assembly protein CsgF; Provisional
Probab=26.88 E-value=2.1e+02 Score=19.45 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=34.0
Q ss_pred HHHHHHhccCCCCCCCceEEeeCCeEEEEEEeCCeEEEEEecCCCCc
Q 032448 27 AIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGR 73 (140)
Q Consensus 27 ~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~citd~~~~~ 73 (140)
++...++..|.+ ++--++..|+|..-+...+|-..+-|+|...+.
T Consensus 78 ~Lls~L~~~i~~--G~~G~~~tgd~~i~i~~~~~~l~i~ItD~~TGe 122 (138)
T PRK10050 78 QILGGLLSNINT--GKPGRMVTNDYIVDIANRDGQLQLNVTDRKTGQ 122 (138)
T ss_pred HHHHHHHhhccC--CCCceEEECCEEEEEEecCCcEEEEEEeCCCcc
Confidence 445556666664 567788899999998767888889999988754
No 38
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=25.06 E-value=1.5e+02 Score=21.54 Aligned_cols=25 Identities=20% Similarity=0.291 Sum_probs=16.2
Q ss_pred HHHhccCCCCCCCceEEeeCCeEEE
Q 032448 30 RQILDKIPGNNDSHVSYSQDRYIFH 54 (140)
Q Consensus 30 ~~vl~~i~~~~~~k~~~~~~~~~~h 54 (140)
..+.++.....=.++.|..++|.||
T Consensus 170 k~IAerAl~kGI~kVvFDRgGy~YH 194 (211)
T PTZ00032 170 KLIGRKALSKGISKVRFDRAHYKYA 194 (211)
T ss_pred HHHHHHHHHCCCCEEEEeCCCCeeh
Confidence 3333443322356788999999999
No 39
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=24.66 E-value=1.9e+02 Score=18.90 Aligned_cols=51 Identities=20% Similarity=0.405 Sum_probs=28.8
Q ss_pred EEEEEEeC--CeeEeeecCC------CCCHH---HHHHHHhccCCCCCCCceEEeeCCeEEE
Q 032448 4 LFSLVARG--SVVLAECSAT------ATNAS---AIARQILDKIPGNNDSHVSYSQDRYIFH 54 (140)
Q Consensus 4 ~Ya~Var~--~~iL~e~~~~------~~~~~---~~~~~vl~~i~~~~~~k~~~~~~~~~~h 54 (140)
+|+-|..+ +.+||.-+.. .+|.+ .+...+.++.....-.+..|..++|.||
T Consensus 36 iyaQiIdd~~~~tlasaST~ek~~~~~~n~~aA~~vG~~la~ra~~~gi~~vvfDrgg~~Yh 97 (114)
T TIGR00060 36 IYAQVIDDSKSEVLASASTLEKKLKYTGNKDAAKKVGKLVAERLKEKGIKDVVFDRGGYKYH 97 (114)
T ss_pred EEEEEEECCCCEEEEEEecchhhhcCCCCHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCcch
Confidence 56766655 3666655532 24432 3333333443332356788888999998
No 40
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.56 E-value=2.3e+02 Score=19.17 Aligned_cols=57 Identities=23% Similarity=0.355 Sum_probs=40.3
Q ss_pred HHHHHHhccCCCC--CCCceEEeeCCeEEEEEE-eCCeEEEEEecCCCCcccHHHHHHHHHH
Q 032448 27 AIARQILDKIPGN--NDSHVSYSQDRYIFHVKR-TDGLTVLCMADDTAGRRIPFAFLEDIHQ 85 (140)
Q Consensus 27 ~~~~~vl~~i~~~--~~~k~~~~~~~~~~h~l~-~~~~~~~citd~~~~~~~af~fL~~i~~ 85 (140)
.-.+.+..|+.|. .++-.+++.+.|-.||.. -.|+-++-+||..... .-.-|+.|.+
T Consensus 43 FSlkS~v~Kls~~d~k~~f~sy~Ts~YklhfyeTptglk~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 43 FSLKSFVSKLSPGDVKDGFLSYKTSKYKLHFYETPTGLKFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred hhHHHHHHhcCCCCcccCeeEEeeceeEEEEEEcCCCcEEEEecCCCccc--HHHHHHHHHH
Confidence 3456677788774 356677888999999765 4899999999987752 2344555555
No 41
>cd03164 CD53_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), CD53_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". CD53 is a tetraspanin of the lymphoid-myeloid lineage and has been implicated in apoptosis protection. It associates with integrin alpha4beta1. Some of the cellular responses modulated by CD53 may be mediated by JNK activation and/or via the AKT pathway.
Probab=23.51 E-value=1.7e+02 Score=17.23 Aligned_cols=29 Identities=17% Similarity=0.344 Sum_probs=15.2
Q ss_pred hhHHHHHHHHHHhcCCc-hhhHHHHHHhhh
Q 032448 106 EFSRVLSQQMEYYSDDP-NADRINRIKGEM 134 (140)
Q Consensus 106 ~F~~~l~~~~~~yn~~~-~~dkl~~l~~~l 134 (140)
.+...+.+.|+.|.+++ ....+..+|+++
T Consensus 10 ~i~~~~~~~~~~y~~~~~~~~~~d~iQ~~l 39 (86)
T cd03164 10 YVKEGLTDSLEQYHKDNNTSEAWDMIQSNL 39 (86)
T ss_pred HHHHHHHHHHHHhcCCccHHHHHHHHHHHh
Confidence 44555666666665432 234555555544
No 42
>cd00633 Secretoglobin Secretoglobins are relatively small, secreted, disulphide-bridged dimeric proteins with encoding genes sharing substantial sequence similarity. Their family subunits may be grouped into five subfamilies, A-E. Uteroglobin (subfamily A), which is identical to Clara cell protein (CC10), forms a globular shaped homodimer with a large hydrophobic pocket located between the two dimers. The uteroglobin monomer structure is composed of four alpha helices that do not form a canonical four helix-bundle motif but rather a boomerang-shaped structure in which helices H1, H3, and H4 are able to bind a homodimeric partner. The hydrophobic pocket binds steroids, particularly progesterone, with high specificity. However, the true biological function of uteroglobin is poorly understood. In mammals, uteroglobin has immunosuppressive and anti-inflammatory properties through the inhibition of phospholipase A2. The other four main subfamilies of secretoglobins are found in heterodimeri
Probab=23.07 E-value=1.3e+02 Score=17.33 Aligned_cols=25 Identities=12% Similarity=0.341 Sum_probs=13.1
Q ss_pred HHHHHHHHhcCCch-hhHHHHHHhhh
Q 032448 110 VLSQQMEYYSDDPN-ADRINRIKGEM 134 (140)
Q Consensus 110 ~l~~~~~~yn~~~~-~dkl~~l~~~l 134 (140)
.+...++.||.++. .+...+||+=+
T Consensus 18 ~y~~~L~~f~~~~~~~~A~~~lK~C~ 43 (67)
T cd00633 18 EYKAELEKFNATPEAVEAKEKLKQCV 43 (67)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 34555566666553 35555555433
No 43
>smart00335 ANX Annexin repeats.
Probab=22.88 E-value=75 Score=16.93 Aligned_cols=15 Identities=40% Similarity=0.784 Sum_probs=10.4
Q ss_pred HHHHHHHHHhhcccc
Q 032448 80 LEDIHQRFVKTYGRA 94 (140)
Q Consensus 80 L~~i~~~F~~~~~~~ 94 (140)
+..|+..|...|+..
T Consensus 19 ~~~i~~~Y~~~~~~~ 33 (53)
T smart00335 19 LQAIKQAYKKRYGKD 33 (53)
T ss_pred HHHHHHHHHHHhCcc
Confidence 466777777777644
No 44
>PF06694 Plant_NMP1: Plant nuclear matrix protein 1 (NMP1); InterPro: IPR010604 This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm [].
Probab=22.26 E-value=1.6e+02 Score=22.80 Aligned_cols=54 Identities=11% Similarity=0.233 Sum_probs=35.3
Q ss_pred HHHHHHHHHhhcccc---cccc-CCCccchhhHHHHHHHHHHhcCCchhhHHHHHHhhhhhhccC
Q 032448 80 LEDIHQRFVKTYGRA---VLSA-QAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQVEMS 140 (140)
Q Consensus 80 L~~i~~~F~~~~~~~---~~~~-~~~~~~~~F~~~l~~~~~~yn~~~~~dkl~~l~~~l~evk~~ 140 (140)
|.++...|...|... |-.. ....+ ..|+|.-+++...| +.+.++-.+|..+|+|
T Consensus 220 flq~~~~F~~~Y~~EIrpWch~~~~P~L-~gLGPAa~Rlle~y------~~l~klL~nL~~lr~S 277 (325)
T PF06694_consen 220 FLQTAAGFNHCYEKEIRPWCHMMEVPQL-HGLGPAANRLLELY------KMLLKLLGNLATLRDS 277 (325)
T ss_pred HHHHHHHHHHHHHhcchhhhccCccchh-hcccHHHHHHHHHH------HHHHHHHHHHHHHHHH
Confidence 344556677777543 5554 33444 48899999998888 4566777777776654
No 45
>PF13077 DUF3909: Protein of unknown function (DUF3909)
Probab=22.22 E-value=1.6e+02 Score=18.26 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=16.3
Q ss_pred CCeEEEEEecCCC--CcccHHHHHHH
Q 032448 59 DGLTVLCMADDTA--GRRIPFAFLED 82 (140)
Q Consensus 59 ~~~~~~citd~~~--~~~~af~fL~~ 82 (140)
+|++++.|+=.+- .-.-.|+||++
T Consensus 83 dg~~~vsvsy~edalhlqelfqflee 108 (108)
T PF13077_consen 83 DGVCYVSVSYSEDALHLQELFQFLEE 108 (108)
T ss_pred ccEEEEEEeechhhHHHHHHHHHhhC
Confidence 7999998875544 23456777764
No 46
>PF05303 DUF727: Protein of unknown function (DUF727); InterPro: IPR007967 This family consists of several uncharacterised eukaryotic proteins of unknown function.; PDB: 1SGO_A.
Probab=22.21 E-value=2.2e+02 Score=18.34 Aligned_cols=46 Identities=22% Similarity=0.379 Sum_probs=23.7
Q ss_pred eeCCeEEEEEEe-CCeEEEEEecCCCC------------cccHHHHHHHHHHHHHhhcc
Q 032448 47 SQDRYIFHVKRT-DGLTVLCMADDTAG------------RRIPFAFLEDIHQRFVKTYG 92 (140)
Q Consensus 47 ~~~~~~~h~l~~-~~~~~~citd~~~~------------~~~af~fL~~i~~~F~~~~~ 92 (140)
+.++..||+-.. .|+-.+.-+..... -...+++|+.|...|.+.|+
T Consensus 39 TlEg~~~cIelt~~Gf~V~s~~~D~~~~~~~~~~~~~~~~eTl~~LL~~iSP~fr~~F~ 97 (108)
T PF05303_consen 39 TLEGRTYCIELTTKGFRVVSSTFDCMDPDPSQSSLHTKYFETLYALLDSISPLFRKRFG 97 (108)
T ss_dssp -TT--EEEEEEETTEEEEEESSTT---TT---------EESSSHHHHHHH-HHHHHHHH
T ss_pred EecCCEEEEEEECCeEEEeeecCCCcCcccccccccchHHhhHHHHHHHHCHHHHHHHH
Confidence 346666664433 45544433333221 13577889999988887776
No 47
>PF08506 Cse1: Cse1; InterPro: IPR013713 The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments. This domain is found in exportin Cse1 (also known as importin-alpha re-exporter). Exportin Cse1 mediates nuclear transport of importin-alpha back into the cytosol, where importin-alpha functions as a transporter of proteins carrying nuclear localisation signals (NLS) from the cytoplasm into the nucleus [, , ]. This domain contains HEAT repeats. More information about these proteins can be found at Protein of the Month: Importins [].; GO: 0006886 intracellular protein transport; PDB: 1Z3H_B 1WA5_C.
Probab=22.01 E-value=1.1e+02 Score=24.17 Aligned_cols=46 Identities=22% Similarity=0.457 Sum_probs=31.6
Q ss_pred ecCCCCcccHHHHHHHHHHHHHhhccccccccCCCccchhhHHHHHHHHHHhcCCchh
Q 032448 67 ADDTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNA 124 (140)
Q Consensus 67 td~~~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~ 124 (140)
.|-+.+++.|-.||..+.+.|.+... ..+...++.++.+|+.++..
T Consensus 222 sd~~TrR~AA~dfl~~L~~~~~~~v~------------~i~~~~i~~~l~~y~~~~~~ 267 (370)
T PF08506_consen 222 SDSDTRRRAACDFLRSLCKKFEKQVT------------SILMQYIQQLLQQYASNPSN 267 (370)
T ss_dssp S---SHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHH-TTT
T ss_pred cccCCcHHHHHHHHHHHHHHHhHHHH------------HHHHHHHHHHHHHHhhCCcc
Confidence 46667888999999999988765432 35667788888888776654
No 48
>COG2957 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]
Probab=21.91 E-value=2.2e+02 Score=22.31 Aligned_cols=50 Identities=14% Similarity=0.170 Sum_probs=31.5
Q ss_pred EEEEeCCeeEeeecCCCCCHHHHHHHHhccCCCC-----CCCceEEeeCCeEEEEEEeC
Q 032448 6 SLVARGSVVLAECSATATNASAIARQILDKIPGN-----NDSHVSYSQDRYIFHVKRTD 59 (140)
Q Consensus 6 a~Var~~~iL~e~~~~~~~~~~~~~~vl~~i~~~-----~~~k~~~~~~~~~~h~l~~~ 59 (140)
.+|+.+.+|+-.|.+.+ ..+|.++|++.=|. -+.|..+ .++-++|++..+
T Consensus 288 FlI~N~avIvP~y~D~~---D~~a~~~L~~~fP~reVVGVp~r~il-~ggGs~HCiTqQ 342 (346)
T COG2957 288 FLIINGAVIVPQYDDPN---DALALDVLQQAFPGREVVGVPAREIL-LGGGSLHCITQQ 342 (346)
T ss_pred EEEecCeEEeeccCCcc---hHHHHHHHHHhCCCCeEeccccHHhe-ecCCceEEEeec
Confidence 46788888888885443 46777777776651 1334443 455578877653
No 49
>PF08053 Tna_leader: Tryptophanese operon leader peptide; InterPro: IPR012620 This entry defines the apparent leader peptides of tryptophanase operons in Escherichia coli, Vibrio cholerae, Photobacterium profundum, Haemophilus influenzae, and related species. It has been suggested that these peptides act in cis to alter the behaviour of the translating ribosome []. The tryptophanese (tna) operon leader peptide catalyses the degradation of L-tryptophan to indole, pyruvate and ammonia, enabling the bacteria to utilise tryptophan as a source of carbon, nitrogen and energy. The tna operon of Escherichia coli contains two major structural genes, tnaA and tnaB. Preceding tnaA in the tna operon is a 319 -nucleotide transcribed regulatory region that contains the coding region for a 24-residue leader peptide, TnaC. The RNA sequence in the vicinity of the tnaC stop codon is rich in Cytidylate residues which is required for efficient Rho -dependent termination in the leader region of the tna operon [].; GO: 0031554 regulation of transcription termination, DNA-dependent, 0031556 transcriptional attenuation by ribosome
Probab=21.26 E-value=98 Score=13.87 Aligned_cols=10 Identities=40% Similarity=0.414 Sum_probs=6.6
Q ss_pred CceEEEEEEe
Q 032448 1 MAILFSLVAR 10 (140)
Q Consensus 1 M~I~Ya~Var 10 (140)
|.|+..||.-
T Consensus 1 mnilhicvts 10 (24)
T PF08053_consen 1 MNILHICVTS 10 (24)
T ss_pred CceEEEEEee
Confidence 6677777653
No 50
>COG4678 Muramidase (phage lambda lysozyme) [Carbohydrate transport and metabolism]
Probab=20.13 E-value=3.3e+02 Score=19.25 Aligned_cols=67 Identities=6% Similarity=0.126 Sum_probs=41.3
Q ss_pred HHHHHHHhccCCCC---CCCceEEeeCCeEEEEEEeCCeEEEEEecCC---CCc-ccHHHHHHHHHHHHHhhcc
Q 032448 26 SAIARQILDKIPGN---NDSHVSYSQDRYIFHVKRTDGLTVLCMADDT---AGR-RIPFAFLEDIHQRFVKTYG 92 (140)
Q Consensus 26 ~~~~~~vl~~i~~~---~~~k~~~~~~~~~~h~l~~~~~~~~citd~~---~~~-~~af~fL~~i~~~F~~~~~ 92 (140)
....+-.+.-+... -+.-..+-+|+-.|+=+++....++|+-... .+. .-.|+||..-.+++..++.
T Consensus 34 ~p~l~a~m~Ti~~se~~~~~pY~vLvgg~~f~D~S~HP~~~v~i~~~~ng~cSTAAGrYQ~L~~tW~~~~~~l~ 107 (180)
T COG4678 34 DPMLRALMRTISASEPNRNRPYDVLVGGQLFTDLSDHPRKCVTIPTGPNGLCSTAAGRYQLLNRTWDDYAPQLH 107 (180)
T ss_pred CHHHHHHHhhcccccCCCCCCceEEEcCceechhhhCChhhEEeecCCCCccccchhhHHHHHhHHHHhhhhcC
Confidence 34444444444432 2333556678888887777666666665542 332 3479999998888877664
Done!