Query 031220
Match_columns 163
No_of_seqs 110 out of 747
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 10:59:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031220.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031220hhsearch_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 5E-52 1.1E-56 301.1 17.3 155 1-158 1-155 (217)
2 KOG0862 Synaptobrevin/VAMP-lik 100.0 1.5E-31 3.3E-36 197.7 14.9 152 3-158 2-164 (216)
3 KOG0861 SNARE protein YKT6, sy 100.0 4.5E-29 9.7E-34 178.2 12.7 152 1-160 1-169 (198)
4 PF13774 Longin: Regulated-SNA 99.9 5.1E-22 1.1E-26 129.5 10.0 81 28-109 1-82 (83)
5 COG5143 SNC1 Synaptobrevin/VAM 99.8 1.6E-20 3.6E-25 137.3 12.3 152 1-159 1-160 (190)
6 KOG0860 Synaptobrevin/VAMP-lik 99.1 1.4E-10 3.1E-15 78.5 3.8 36 122-160 26-61 (116)
7 PF00957 Synaptobrevin: Synapt 98.5 3.3E-08 7.1E-13 65.0 1.6 33 124-159 2-34 (89)
8 PF04086 SRP-alpha_N: Signal r 96.7 0.0082 1.8E-07 47.3 7.3 66 26-94 5-72 (279)
9 PF09426 Nyv1_N: Vacuolar R-SN 95.8 0.033 7.2E-07 38.9 5.7 60 26-85 44-110 (141)
10 KOG0781 Signal recognition par 94.5 0.52 1.1E-05 40.1 9.9 87 4-93 4-96 (587)
11 PF04099 Sybindin: Sybindin-li 94.0 1.2 2.5E-05 31.7 9.7 74 41-116 65-141 (142)
12 KOG0938 Adaptor complexes medi 92.4 4 8.6E-05 33.3 11.3 124 4-133 5-131 (446)
13 PF04628 Sedlin_N: Sedlin, N-t 88.7 4.9 0.00011 28.0 8.0 73 43-116 54-131 (132)
14 PF01217 Clat_adaptor_s: Clath 87.7 7.5 0.00016 27.2 12.5 79 11-92 12-96 (141)
15 PF03164 Mon1: Trafficking pro 80.5 15 0.00034 30.7 8.7 68 25-92 37-104 (415)
16 COG5122 TRS23 Transport protei 78.6 19 0.0004 24.7 9.0 74 39-116 55-132 (134)
17 PRK11546 zraP zinc resistance 73.8 25 0.00053 25.1 6.9 58 78-143 50-107 (143)
18 cd00633 Secretoglobin Secretog 66.3 17 0.00036 22.1 4.3 44 109-152 17-61 (67)
19 KOG0972 Huntingtin interacting 66.3 25 0.00054 28.3 6.1 17 75-91 245-261 (384)
20 TIGR01478 STEVOR variant surfa 61.5 5.4 0.00012 31.7 1.7 35 109-144 58-92 (295)
21 PF01099 Uteroglobin: Uteroglo 61.5 13 0.00029 22.6 3.2 44 109-152 17-61 (67)
22 smart00096 UTG Uteroglobin. 58.9 27 0.00059 21.7 4.2 39 112-150 22-61 (69)
23 KOG3369 Transport protein part 58.7 73 0.0016 23.6 8.7 72 41-116 121-196 (199)
24 PTZ00370 STEVOR; Provisional 55.6 7.5 0.00016 30.9 1.6 20 125-144 102-121 (296)
25 PF02520 DUF148: Domain of unk 53.6 65 0.0014 21.5 6.8 62 82-152 2-63 (113)
26 PF03607 DCX: Doublecortin; I 49.8 23 0.0005 21.0 2.8 48 23-70 9-58 (60)
27 KOG2740 Clathrin-associated pr 49.4 51 0.0011 27.3 5.4 42 51-92 55-96 (418)
28 PF06345 Drf_DAD: DRF Autoregu 48.8 12 0.00026 15.7 1.0 12 145-156 3-14 (15)
29 KOG2635 Medium subunit of clat 45.9 81 0.0018 26.9 6.2 38 43-80 46-83 (512)
30 PF11675 DUF3271: Protein of u 45.7 61 0.0013 25.1 5.1 50 2-53 30-79 (249)
31 PTZ00032 60S ribosomal protein 44.5 44 0.00096 25.3 4.1 51 4-54 117-194 (211)
32 TIGR00060 L18_bact ribosomal p 43.3 60 0.0013 22.2 4.3 51 4-54 36-97 (114)
33 PF00957 Synaptobrevin: Synapt 41.2 26 0.00056 22.3 2.2 35 125-159 10-44 (89)
34 PLN00064 photosystem II protei 39.4 1.1E+02 0.0024 22.3 5.3 67 71-138 88-159 (166)
35 PF05659 RPW8: Arabidopsis bro 38.3 18 0.00038 25.9 1.2 50 106-158 31-81 (147)
36 COG3543 Uncharacterized conser 37.9 23 0.0005 24.8 1.6 18 141-158 25-42 (135)
37 PF10504 DUF2452: Protein of u 37.6 15 0.00032 26.7 0.7 55 26-80 65-125 (159)
38 TIGR02284 conserved hypothetic 37.4 1.4E+02 0.0031 20.8 6.3 52 106-157 44-98 (139)
39 PF13228 DUF4037: Domain of un 35.9 52 0.0011 21.8 3.1 50 106-162 24-73 (100)
40 cd07634 BAR_GAP10-like The Bin 33.4 2.2E+02 0.0047 21.7 6.9 69 76-149 14-94 (207)
41 PF15278 Sec3_C_2: Sec3 exocys 33.2 1.2E+02 0.0026 19.1 4.1 40 106-145 14-55 (86)
42 PF10112 Halogen_Hydrol: 5-bro 31.9 73 0.0016 23.6 3.7 50 107-156 134-187 (199)
43 PF04220 YihI: Der GTPase acti 31.6 39 0.00084 24.8 2.0 16 145-160 110-125 (169)
44 PF13326 PSII_Pbs27: Photosyst 31.2 1.3E+02 0.0029 21.4 4.7 66 73-139 73-143 (145)
45 PF04100 Vps53_N: Vps53-like, 30.6 2.2E+02 0.0048 23.6 6.6 43 106-148 138-180 (383)
46 cd00223 TOPRIM_TopoIIB_SPO TOP 30.5 65 0.0014 23.0 3.1 26 62-87 25-50 (160)
47 PF06238 Borrelia_lipo_2: Borr 30.3 1.7E+02 0.0037 19.6 4.7 7 151-157 104-110 (111)
48 PF07340 Herpes_IE1: Cytomegal 29.4 3.2E+02 0.0068 22.9 7.0 84 66-154 23-129 (392)
49 PHA01811 hypothetical protein 29.3 86 0.0019 19.1 2.9 19 41-59 4-22 (78)
50 CHL00139 rpl18 ribosomal prote 28.2 1.1E+02 0.0023 20.8 3.6 51 4-54 27-92 (109)
51 PF12579 DUF3755: Protein of u 28.0 44 0.00096 17.8 1.4 19 124-142 16-34 (35)
52 PF13314 DUF4083: Domain of un 27.9 45 0.00097 19.9 1.5 14 141-154 44-57 (58)
53 cd09238 V_Alix_like_1 Protein- 27.7 1.1E+02 0.0025 24.8 4.4 42 85-126 110-151 (339)
54 PF09862 DUF2089: Protein of u 27.6 79 0.0017 21.6 2.9 17 76-92 30-46 (113)
55 PRK05593 rplR 50S ribosomal pr 26.9 1.5E+02 0.0032 20.3 4.2 51 4-54 36-100 (117)
56 KOG3230 Vacuolar assembly/sort 26.7 79 0.0017 23.9 2.9 18 132-149 133-150 (224)
57 TIGR03044 PS_II_psb27 photosys 25.9 2.4E+02 0.0053 19.9 7.0 67 72-139 60-130 (135)
58 PF12277 DUF3618: Protein of u 25.2 1.4E+02 0.003 16.9 3.5 24 127-150 5-28 (49)
59 PF14805 THDPS_N_2: Tetrahydro 24.8 76 0.0017 19.7 2.2 17 141-157 26-42 (70)
60 PHA02557 22 prohead core prote 24.3 3.7E+02 0.0079 21.4 6.5 74 76-149 89-165 (271)
61 PF15457 HopW1-1: Type III T3S 24.2 1.4E+02 0.0031 23.5 4.0 47 109-160 235-281 (320)
62 PF10158 LOH1CR12: Tumour supp 24.1 2.3E+02 0.005 19.8 4.8 25 124-148 86-110 (131)
63 PRK05244 Der GTPase activator; 24.1 64 0.0014 23.9 2.0 16 145-160 109-124 (177)
64 PF07897 DUF1675: Protein of u 24.1 83 0.0018 25.1 2.8 25 48-72 238-262 (284)
65 PF03231 Bunya_NS-S_2: Bunyavi 24.0 41 0.00089 28.5 1.1 31 59-90 333-363 (444)
66 PF13068 DUF3932: Protein of u 22.3 79 0.0017 19.4 1.9 20 108-127 32-51 (81)
67 PF05542 DUF760: Protein of un 22.2 75 0.0016 20.4 1.9 28 125-152 13-41 (86)
68 PF08900 DUF1845: Domain of un 22.2 2E+02 0.0043 21.9 4.5 49 106-154 41-91 (217)
69 PF12325 TMF_TATA_bd: TATA ele 21.8 2.8E+02 0.006 19.1 4.9 43 106-148 72-119 (120)
70 PF11867 DUF3387: Domain of un 21.8 2.1E+02 0.0046 23.1 4.9 17 105-121 197-213 (335)
71 cd01617 DCX Ubiquitin-like dom 21.8 2.1E+02 0.0047 17.8 6.0 50 22-71 25-78 (80)
72 PF00191 Annexin: Annexin; In 21.7 67 0.0014 18.8 1.6 10 82-91 34-43 (66)
73 PF05384 DegS: Sensor protein 21.4 62 0.0013 23.5 1.5 32 125-157 27-58 (159)
74 smart00335 ANX Annexin repeats 21.3 76 0.0016 17.7 1.7 15 80-94 19-33 (53)
75 PF10168 Nup88: Nuclear pore c 20.6 1.4E+02 0.0031 27.1 3.9 20 72-91 533-552 (717)
76 PF12128 DUF3584: Protein of u 20.5 52 0.0011 31.6 1.2 41 41-81 53-101 (1201)
77 PF09537 DUF2383: Domain of un 20.3 1.7E+02 0.0038 19.1 3.5 53 106-158 45-100 (111)
78 PF08028 Acyl-CoA_dh_2: Acyl-C 20.2 1.9E+02 0.0042 19.4 3.8 36 124-159 41-76 (134)
79 cd07642 BAR_ASAP2 The Bin/Amph 20.0 4.1E+02 0.0089 20.4 6.0 44 105-148 40-89 (215)
No 1
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5e-52 Score=301.08 Aligned_cols=155 Identities=46% Similarity=0.750 Sum_probs=151.2
Q ss_pred CceEEEEEEeCCeeEeeeeCCCCCHHHHHHHHhccCCCCCCCeeEEEeCCEEEEEEEeCCEEEEEEecCCCCcccHHHHH
Q 031220 1 MAILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFL 80 (163)
Q Consensus 1 M~I~Y~~Iar~~~iLae~~~~~~~~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~~itd~~~~~~~af~fL 80 (163)
|+|+|+.||||++|||||++.+|||..++..+|+++|++++.|.+|.+|+|+|||+.+||++|+||+|++.++++||.||
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 89999999999999999999999999999999999998768899999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhcccccccCCCCchhhhHHHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCCCc
Q 031220 81 EDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQETRSASESRLGVSEAQYGGETS 158 (163)
Q Consensus 81 ~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~NI~kvle~l~RGe~~ 158 (163)
++|++.|.+.|+..+.++.+|++|++|++.|++-|++|.++|+.|++.+++.||+|||+||++|||||+| |||+|
T Consensus 81 e~Ik~~F~k~YG~~a~ta~AysmN~EFs~vL~qqm~y~s~~p~id~lskvkaqv~evk~vM~eNIekvld---RGeki 155 (217)
T KOG0859|consen 81 ERIKEDFKKRYGGGAHTAVAYSMNKEFSSVLKQQMQYCSEHPEISKLAKVKAQVTEVKGVMMENIEKVLD---RGEKI 155 (217)
T ss_pred HHHHHHHHHHhccchhHHHHhHhHHHHHHHHHHHHHHHHcCcchhHHHHHHHHHHHHHHHHHHHHHHHHh---ccCeE
Confidence 9999999999998899999999999999999999999999999999999999999999999999999886 99995
No 2
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.98 E-value=1.5e-31 Score=197.72 Aligned_cols=152 Identities=23% Similarity=0.451 Sum_probs=137.0
Q ss_pred eEEEEEEeC--CeeEeeeeCC---CCC----HHHHHHHHhccCCCCCCCeeEEEeCCEEEEEEEeCCEEEEEEecCCCCc
Q 031220 3 ILFSLVARG--SVVLAECSAT---ATN----ASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGR 73 (163)
Q Consensus 3 I~Y~~Iar~--~~iLae~~~~---~~~----~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~~itd~~~~~ 73 (163)
|++++|+|. +.|||.-.+. +++ ....++.+.+++.+...+|.|++.|+|+|||++++|++|+||||..||+
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 6999987762 233 3789999999999866999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHhhhcccc--cccCCCCchhhhHHHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHhcHHHHHhh
Q 031220 74 RIPFAFLEDIHQRFVKTYGRAV--LSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQETRSASESRLGVSEA 151 (163)
Q Consensus 74 ~~af~fL~~i~~~F~~~~~~~~--~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~NI~kvle~ 151 (163)
.+||.||++|.++|.+.|+... ...+||++. +|++.|+..-++||+++..+.+.++.+++.+|+.||.+||+ |+
T Consensus 82 kLAF~YLedL~~EF~~~~~~~~~~~~~RPY~Fi-eFD~~IQk~Kk~ynd~r~~~n~~~~n~el~~v~~im~~nie---dv 157 (216)
T KOG0862|consen 82 KLAFSYLEDLAQEFDKSYGKNIIQPASRPYAFI-EFDTFIQKTKKRYNDTRSQRNLLKLNQELQDVQRIMVENLE---DV 157 (216)
T ss_pred HHHHHHHHHHHHHHHHhcccccCCccCCCeeEE-ehhHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHHhHH---HH
Confidence 9999999999999999998653 357999996 99999999999999988889999999999999999999977 56
Q ss_pred hhcCCCc
Q 031220 152 QYGGETS 158 (163)
Q Consensus 152 l~RGe~~ 158 (163)
++|||.|
T Consensus 158 l~rg~~l 164 (216)
T KOG0862|consen 158 LQRGEVL 164 (216)
T ss_pred HhhchHH
Confidence 7899984
No 3
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=4.5e-29 Score=178.23 Aligned_cols=152 Identities=20% Similarity=0.288 Sum_probs=127.6
Q ss_pred CceEEEEEEeCC----eeEeeeeCCC-------CC---H-HHHHHHHhccCCCCCCCeeEEEeCCEEEEEEEe-CCEEEE
Q 031220 1 MAILFSLVARGS----VVLAECSATA-------TN---A-SAIARQILDKIPGNNDSHVSYSQDRYIFHVKRT-DGLTVL 64 (163)
Q Consensus 1 M~I~Y~~Iar~~----~iLae~~~~~-------~~---~-~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~-~~~~~~ 64 (163)
|.|++..|.+-+ .+|+.-++.+ ++ | ..+++++.+|.+| .+|+++.++.|.+|.... ||++++
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 889999998873 6677666532 22 3 5778999999998 899999999999996654 699999
Q ss_pred EEecCCCCcccHHHHHHHHHHHHHhhh-cccccccCCCCchhhhHHHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHh
Q 031220 65 CMADDTAGRRIPFAFLEDIHQRFVKTY-GRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQETRSASE 143 (163)
Q Consensus 65 ~itd~~~~~~~af~fL~~i~~~F~~~~-~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~ 143 (163)
|++|.+||.|+||.+|+++.++|.... +.+|....+..+ . .|.|..++.+|+||.++|+|.++|++|+|||.||++
T Consensus 79 ~~~D~eYP~rvA~tLL~kvld~~~~k~~~~~W~~~~~~~~--~-~~~L~~~l~kyqdP~ead~l~kvQ~EldETKiiLhk 155 (198)
T KOG0861|consen 79 LIADDEYPVRVAFTLLNKVLDEFTTKVPATQWPVGETADL--S-YPYLDTLLSKYQDPAEADPLLKVQNELDETKIILHK 155 (198)
T ss_pred EEecCcCchhHHHHHHHHHHHHHhhcCcccccCcCCCcCC--C-chhHHHHHHHhcChhhhChHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999997665 466763222221 3 488999999999999999999999999999999999
Q ss_pred cHHHHHhhhhcCCCccc
Q 031220 144 SRLGVSEAQYGGETSSS 160 (163)
Q Consensus 144 NI~kvle~l~RGe~~~~ 160 (163)
.|+.||+ |||||++
T Consensus 156 TiesVL~---RgEKLDd 169 (198)
T KOG0861|consen 156 TIESVLE---RGEKLDD 169 (198)
T ss_pred HHHHHHH---ccchHHH
Confidence 9999875 9999875
No 4
>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=99.88 E-value=5.1e-22 Score=129.49 Aligned_cols=81 Identities=43% Similarity=0.838 Sum_probs=73.0
Q ss_pred HHHHHhccCCCCCCCeeEEEeCCEEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhc-ccccccCCCCchhh
Q 031220 28 IARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG-RAVLSAQAYGMNDE 106 (163)
Q Consensus 28 ~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~~itd~~~~~~~af~fL~~i~~~F~~~~~-~~~~~~~~~~~~~~ 106 (163)
+++++|++++++.++|.+++.+++.|||++++|++|+||||++||+++||.||++|+++|.++|+ .++.++.|+++ .+
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 58999999997445899999999999999999999999999999999999999999999999998 67888889999 68
Q ss_pred hHH
Q 031220 107 FSR 109 (163)
Q Consensus 107 F~~ 109 (163)
|++
T Consensus 80 F~~ 82 (83)
T PF13774_consen 80 FDS 82 (83)
T ss_dssp HHH
T ss_pred cCC
Confidence 875
No 5
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=99.85 E-value=1.6e-20 Score=137.26 Aligned_cols=152 Identities=16% Similarity=0.329 Sum_probs=117.6
Q ss_pred CceEEEEEEeCC--eeEeeeeC-CCCCH--HHHHHHHhccCCCCCCCeeEEEeCCEEEEEEEeC-CEEEEEEecCCCCcc
Q 031220 1 MAILFSLVARGS--VVLAECSA-TATNA--SAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTD-GLTVLCMADDTAGRR 74 (163)
Q Consensus 1 M~I~Y~~Iar~~--~iLae~~~-~~~~~--~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~-~~~~~~itd~~~~~~ 74 (163)
|+++|..+..+. .+|++-.+ .+..| ...+..+|.++.|...++.+++.++|.|||+-.+ |++|+|+|+++||.+
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 567777776664 44444332 22333 5778888888877556688899999999988665 999999999999999
Q ss_pred cHHHHHHHHHHHHHhhhccc-ccc-cCCCCchhhhHHHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHhcHHHHHhhh
Q 031220 75 IPFAFLEDIHQRFVKTYGRA-VLS-AQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQETRSASESRLGVSEAQ 152 (163)
Q Consensus 75 ~af~fL~~i~~~F~~~~~~~-~~~-~~~~~~~~~F~~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~NI~kvle~l 152 (163)
+|++.++++..+|...++.+ +.. ..++.+ .+|.+.++. .|+++...|++.+++.++++||.+|.+||++|+
T Consensus 81 la~~~~~~~~~~~~~s~~~~~~~d~~~~~~~-~~~d~~~e~---~y~d~s~~D~~d~l~~el~e~K~~l~k~ie~~l--- 153 (190)
T COG5143 81 LAYGYLNSIATEFLKSSALEQLIDDTVGIMR-VNIDKVIEK---GYRDPSIQDKLDQLQQELEETKRVLNKNIEKVL--- 153 (190)
T ss_pred hhhHHHHhhccHhhhhhhHhhcccCccchhh-hhHHHHHHh---hcCCchhhhHHHHHHHHHHHHHHHHHHHHHHHH---
Confidence 99999999999999887633 333 223333 256665555 299998899999999999999999999999876
Q ss_pred hcCCCcc
Q 031220 153 YGGETSS 159 (163)
Q Consensus 153 ~RGe~~~ 159 (163)
+|||+|+
T Consensus 154 ~R~ekl~ 160 (190)
T COG5143 154 YRDEKLD 160 (190)
T ss_pred HccchHH
Confidence 5999953
No 6
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.06 E-value=1.4e-10 Score=78.50 Aligned_cols=36 Identities=17% Similarity=0.236 Sum_probs=32.8
Q ss_pred chhhHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCCCccc
Q 031220 122 PNADRINRIKGEMSQETRSASESRLGVSEAQYGGETSSS 160 (163)
Q Consensus 122 ~~~dki~~i~~~v~evk~im~~NI~kvle~l~RGe~~~~ 160 (163)
+..+++.++|.||+||++||++||+||+| |||+||+
T Consensus 26 ~~~~k~~~tq~QvdeVv~IMr~NV~KVlE---R~ekL~~ 61 (116)
T KOG0860|consen 26 TANDKLQQTQAQVDEVVDIMRENVEKVLE---RGEKLDE 61 (116)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHhHHHHHH---hcchHHH
Confidence 34789999999999999999999999875 9999985
No 7
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=98.53 E-value=3.3e-08 Score=64.99 Aligned_cols=33 Identities=15% Similarity=0.198 Sum_probs=30.0
Q ss_pred hhHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCCCcc
Q 031220 124 ADRINRIKGEMSQETRSASESRLGVSEAQYGGETSS 159 (163)
Q Consensus 124 ~dki~~i~~~v~evk~im~~NI~kvle~l~RGe~~~ 159 (163)
.|++.+++++|++|+++|.+||++++ +|||+|+
T Consensus 2 ~dkl~~i~~~v~~v~~im~~Ni~~ll---~Rge~L~ 34 (89)
T PF00957_consen 2 NDKLEQIQEQVEEVKNIMRENIDKLL---ERGEKLE 34 (89)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHH---HcCchHH
Confidence 58999999999999999999999876 5999975
No 8
>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=96.68 E-value=0.0082 Score=47.26 Aligned_cols=66 Identities=21% Similarity=0.359 Sum_probs=42.3
Q ss_pred HHHHHHHhccCCCCCCCeeEEEeCCEEEEEEEeC--CEEEEEEecCCCCcccHHHHHHHHHHHHHhhhccc
Q 031220 26 SAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTD--GLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYGRA 94 (163)
Q Consensus 26 ~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~--~~~~~~itd~~~~~~~af~fL~~i~~~F~~~~~~~ 94 (163)
+.+++.||-.=. ..-.+|.+++|..+|...+ +|+||||=..-..-.-.=.||+.|+..|...|+..
T Consensus 5 n~LI~~vlleeR---~~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~~ 72 (279)
T PF04086_consen 5 NALIRDVLLEER---SGNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKNQ 72 (279)
T ss_dssp HHHHHHTGGG----------------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHHH
T ss_pred HHHHHHhheeec---cCCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhHH
Confidence 566777764321 2445689999999998876 89999998887776666689999999999999754
No 9
>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=95.84 E-value=0.033 Score=38.88 Aligned_cols=60 Identities=17% Similarity=0.298 Sum_probs=39.4
Q ss_pred HHHHHHHhccCCCCCCC---eeEEE-eCCEEEEEEE---eCCEEEEEEecCCCCcccHHHHHHHHHH
Q 031220 26 SAIARQILDKIPGNNDS---HVSYS-QDRYIFHVKR---TDGLTVLCMADDTAGRRIPFAFLEDIHQ 85 (163)
Q Consensus 26 ~~~~~~vl~~i~~~~~~---k~~~~-~~~~~~h~l~---~~~~~~~~itd~~~~~~~af~fL~~i~~ 85 (163)
..+-..|++++-|-.+. |++.. .+||-++|.. +++-+++|+|..+.|+-+|...|.|++.
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 34446677888653344 44444 4999999987 3689999999999999999999999864
No 10
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.53 E-value=0.52 Score=40.13 Aligned_cols=87 Identities=17% Similarity=0.267 Sum_probs=66.3
Q ss_pred EEEEEEeCCeeEeeeeCCCCCH----HHHHHHHhccCCCCCCCeeEEEeCCEEEEEEEeC--CEEEEEEecCCCCcccHH
Q 031220 4 LFSLVARGSVVLAECSATATNA----SAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTD--GLTVLCMADDTAGRRIPF 77 (163)
Q Consensus 4 ~Y~~Iar~~~iLae~~~~~~~~----~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~--~~~~~~itd~~~~~~~af 77 (163)
.++...+|++||+.|.....+| ..+++.+|-.=. .+-.+++.+.|+.-|-.++ +++|+|+-.+-.--.-+-
T Consensus 4 ~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~er---~~~~~~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~yv~ 80 (587)
T KOG0781|consen 4 QFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLSER---GGVNSFTFEAYTLKYQLDNQYSLVFVVVFQKILTLTYVD 80 (587)
T ss_pred eeeeecCCcEEEEEecccchhccchHHHHHHHHHHHhh---cCcccCchhheeEeeeecCCccEEEEEEEeccchhhhHH
Confidence 5788899999999999866555 456666654322 2222378888988887664 899999988877777777
Q ss_pred HHHHHHHHHHHhhhcc
Q 031220 78 AFLEDIHQRFVKTYGR 93 (163)
Q Consensus 78 ~fL~~i~~~F~~~~~~ 93 (163)
.+|+++.+.|+..|..
T Consensus 81 ~ll~~v~~~f~e~~~~ 96 (587)
T KOG0781|consen 81 KLLNDVLNLFREKYDT 96 (587)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 9999999999998854
No 11
>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=94.04 E-value=1.2 Score=31.71 Aligned_cols=74 Identities=16% Similarity=0.201 Sum_probs=41.7
Q ss_pred CCeeEEEeCCEEEEEEE-eCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhc-ccc-cccCCCCchhhhHHHHHHHHH
Q 031220 41 DSHVSYSQDRYIFHVKR-TDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG-RAV-LSAQAYGMNDEFSRVLSQQME 116 (163)
Q Consensus 41 ~~k~~~~~~~~~~h~l~-~~~~~~~~itd~~~~~~~af~fL~~i~~~F~~~~~-~~~-~~~~~~~~~~~F~~~l~~~~~ 116 (163)
.+-.+++.+.|..|++- -.|+-|+++||+..+. ..-.+++.+.+-|..-.- +.. ....|-. +..|...|+++++
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 56788899999999874 5799999999999863 444455555555543221 111 1112222 2467777776654
No 12
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.43 E-value=4 Score=33.33 Aligned_cols=124 Identities=18% Similarity=0.224 Sum_probs=78.3
Q ss_pred EEEEEEeCCeeEeeee--CCCCCHHHHHHHHhccCCCCCCCee-EEEeCCEEEEEEEeCCEEEEEEecCCCCcccHHHHH
Q 031220 4 LFSLVARGSVVLAECS--ATATNASAIARQILDKIPGNNDSHV-SYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFL 80 (163)
Q Consensus 4 ~Y~~Iar~~~iLae~~--~~~~~~~~~~~~vl~~i~~~~~~k~-~~~~~~~~~h~l~~~~~~~~~itd~~~~~~~af~fL 80 (163)
+|..=.||.++++-.- +.+++..++-+--+-.- .+.|. ..+.++-+|||...+++-.++||..+....+.|.||
T Consensus 5 lfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n---~d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl 81 (446)
T KOG0938|consen 5 LFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINN---LDVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFL 81 (446)
T ss_pred EEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhc---cccCCCeeEecceeEEEEeeccEEEEEEecCCCchhhHHHHH
Confidence 4555678888888654 23456555444322211 12332 345799999999999999999999999999999999
Q ss_pred HHHHHHHHhhhcccccccCCCCchhhhHHHHHHHHHHhcCCchhhHHHHHHHh
Q 031220 81 EDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGE 133 (163)
Q Consensus 81 ~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dki~~i~~~ 133 (163)
.++-+-+..-|+.....+....+--. -..|.+++. |.- |+......++.+
T Consensus 82 ~kl~avm~aYfgk~~Eeaiknnf~lI-~ElLDemld-~G~-pqnte~~al~~~ 131 (446)
T KOG0938|consen 82 YKLDAVMNAYFGKDREEAIKNNFVLI-YELLDEMLD-FGI-PQNTEPNALKAQ 131 (446)
T ss_pred HHHHHHHHHHhcccchhhhhhceEeH-HHHHHHHHh-cCC-CccCChhHHHhh
Confidence 99999999888744333433333111 244666665 533 443333333333
No 13
>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=88.68 E-value=4.9 Score=27.99 Aligned_cols=73 Identities=11% Similarity=0.193 Sum_probs=43.8
Q ss_pred eeEEEeCCEEEE-EEEeCCEEEEEEec---CCCCcccHHHHHHHHHHHHHhhhcccccccC-CCCchhhhHHHHHHHHH
Q 031220 43 HVSYSQDRYIFH-VKRTDGLTVLCMAD---DTAGRRIPFAFLEDIHQRFVKTYGRAVLSAQ-AYGMNDEFSRVLSQQME 116 (163)
Q Consensus 43 k~~~~~~~~~~h-~l~~~~~~~~~itd---~~~~~~~af~fL~~i~~~F~~~~~~~~~~~~-~~~~~~~F~~~l~~~~~ 116 (163)
+..+..+++..+ |+...++=|+.+++ ........-.|+.+++..|.+..-+...... +-. ...|...++++++
T Consensus 54 g~l~~~~~~~vygyvT~t~~Kfvl~~~~~~~~~~d~~ik~fF~~vh~~Y~~~~~NPF~~~~~~I~-S~~Fd~~v~~l~~ 131 (132)
T PF04628_consen 54 GLLDPFEDYKVYGYVTNTGIKFVLVHDMSDNSIRDEDIKQFFKEVHELYVKALCNPFYQPGTPIK-SPKFDSRVRALAK 131 (132)
T ss_dssp EEEEEETTEEEEEEETTT--EEEEEECGGG-S--HHHHHHHHHHHHHHHHHHHTSTTCGCT-HHH-HHHHHHHHHHHHH
T ss_pred CceehhhhHHHHhhhccCceeEEEEEecccCCcchHHHHHHHHHHHHHHHHHccCCCCCCCCCcC-CHHHHHHHHHHhc
Confidence 455667887776 77778888988888 5667778889999999999876533321111 111 1356666665554
No 14
>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=87.72 E-value=7.5 Score=27.15 Aligned_cols=79 Identities=14% Similarity=0.282 Sum_probs=57.3
Q ss_pred CCeeEeeeeCCCCC------HHHHHHHHhccCCCCCCCeeEEEeCCEEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHH
Q 031220 11 GSVVLAECSATATN------ASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIH 84 (163)
Q Consensus 11 ~~~iLae~~~~~~~------~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~~itd~~~~~~~af~fL~~i~ 84 (163)
|.++++-|-..-.. ++.+.+.+..+-+ +.--.+.++++.+-|..-+++.++++++.+...-....||+.+.
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 34777777643221 3444444444422 22445678999998888899999999999999999999999999
Q ss_pred HHHHhhhc
Q 031220 85 QRFVKTYG 92 (163)
Q Consensus 85 ~~F~~~~~ 92 (163)
+-+..-++
T Consensus 89 ~~l~~~~~ 96 (141)
T PF01217_consen 89 EVLDDYFG 96 (141)
T ss_dssp HHHHHHHS
T ss_pred hhhhhhhc
Confidence 88887775
No 15
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=80.55 E-value=15 Score=30.72 Aligned_cols=68 Identities=9% Similarity=0.056 Sum_probs=54.4
Q ss_pred HHHHHHHHhccCCCCCCCeeEEEeCCEEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhc
Q 031220 25 ASAIARQILDKIPGNNDSHVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG 92 (163)
Q Consensus 25 ~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~~~~~~~~~itd~~~~~~~af~fL~~i~~~F~~~~~ 92 (163)
+..+.+.++.-+....++=.++..|+..|.|+..+.+.++||+....+...-..-|+-+.....+...
T Consensus 37 ~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly~qils~lt 104 (415)
T PF03164_consen 37 LMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLYSQILSILT 104 (415)
T ss_pred HHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHHHHHHHhcc
Confidence 55666777766644335556788899999999999999999999999988888888888888877654
No 16
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=78.60 E-value=19 Score=24.73 Aligned_cols=74 Identities=15% Similarity=0.237 Sum_probs=42.4
Q ss_pred CCCCeeEEEeCCEEEEEE-EeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhc--ccccc-cCCCCchhhhHHHHHHH
Q 031220 39 NNDSHVSYSQDRYIFHVK-RTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG--RAVLS-AQAYGMNDEFSRVLSQQ 114 (163)
Q Consensus 39 ~~~~k~~~~~~~~~~h~l-~~~~~~~~~itd~~~~~~~af~fL~~i~~~F~~~~~--~~~~~-~~~~~~~~~F~~~l~~~ 114 (163)
++.++..+..++++.|.. ...|.-|+.++.+ -+...+|+ |+.+...|- +|. +...+ ..|-.. .-|++.++++
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 GSSGRLVLYFRNFVMTIFQTTTGTKFVFVAEK-RTVNALFQ-LQKIYSLYS-DYVTKNPFYSPEMPIQC-SLFDEHLKRM 130 (134)
T ss_pred CCCceEEEEeccEEEEEEEecCCcEEEEEecC-CchhHHHH-HHHHHHHHH-HHhhcCCCCCcccceeh-hhhhHHHHHH
Confidence 357888888999999966 4579999999933 23344555 333333332 222 11111 123222 3678888776
Q ss_pred HH
Q 031220 115 ME 116 (163)
Q Consensus 115 ~~ 116 (163)
.+
T Consensus 131 ~e 132 (134)
T COG5122 131 FE 132 (134)
T ss_pred hc
Confidence 53
No 17
>PRK11546 zraP zinc resistance protein; Provisional
Probab=73.78 E-value=25 Score=25.13 Aligned_cols=58 Identities=19% Similarity=0.241 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhhhcccccccCCCCchhhhHHHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHh
Q 031220 78 AFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQETRSASE 143 (163)
Q Consensus 78 ~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~ 143 (163)
+-++.|.++|......-... + ..-...|..++ .+++|+..+|.++.+||.+++.-|.+
T Consensus 50 a~~q~I~~~f~~~t~~LRqq-----L-~aKr~ELnALl--~~~~pD~~kI~aL~kEI~~Lr~kL~e 107 (143)
T PRK11546 50 AAWQKIHNDFYAQTSALRQQ-----L-VSKRYEYNALL--TANPPDSSKINAVAKEMENLRQSLDE 107 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHH-----H-HHHHHHHHHHH--cCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45788888888765311100 0 01123455553 23456778999999999999987764
No 18
>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=66.32 E-value=17 Score=22.10 Aligned_cols=44 Identities=11% Similarity=0.235 Sum_probs=31.7
Q ss_pred HHHHHHHHHhcCCch-hhHHHHHHHhHHHHHHHHHhcHHHHHhhh
Q 031220 109 RVLSQQMEYYSDDPN-ADRINRIKGEMSQETRSASESRLGVSEAQ 152 (163)
Q Consensus 109 ~~l~~~~~~yn~~~~-~dki~~i~~~v~evk~im~~NI~kvle~l 152 (163)
..+...++.||.++. .....++|+-+++...-=..|+-++++.+
T Consensus 17 ~~y~~~L~~f~~~~~~~~A~~~lK~C~d~~~~e~k~~~~~~m~~I 61 (67)
T cd00633 17 EEYKAELEKFNATPEAVEAKEKLKQCVDEQSLETKENIAKLLEKI 61 (67)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCHhHHHHHHHHHHHH
Confidence 446667788988875 48888999888887666666666666543
No 19
>KOG0972 consensus Huntingtin interacting protein 1 (Hip1) interactor Hippi [Signal transduction mechanisms]
Probab=66.29 E-value=25 Score=28.27 Aligned_cols=17 Identities=18% Similarity=0.360 Sum_probs=13.3
Q ss_pred cHHHHHHHHHHHHHhhh
Q 031220 75 IPFAFLEDIHQRFVKTY 91 (163)
Q Consensus 75 ~af~fL~~i~~~F~~~~ 91 (163)
-+-.||+.++++|....
T Consensus 245 ~~~~~Ldklh~eit~~L 261 (384)
T KOG0972|consen 245 NVGPYLDKLHKEITKAL 261 (384)
T ss_pred chhHHHHHHHHHHHHHH
Confidence 45578999999998654
No 20
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=61.55 E-value=5.4 Score=31.65 Aligned_cols=35 Identities=6% Similarity=0.098 Sum_probs=14.6
Q ss_pred HHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHhc
Q 031220 109 RVLSQQMEYYSDDPNADRINRIKGEMSQETRSASES 144 (163)
Q Consensus 109 ~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~N 144 (163)
|.++++|+.+|+ ....|..+..+--+|-++.|.+|
T Consensus 58 pEmK~iid~~n~-eaikkyqqT~~~f~e~~e~~~k~ 92 (295)
T TIGR01478 58 PELKEIIDKLNE-EAIKKYQETHDPYEQLQELVEKN 92 (295)
T ss_pred HHHHHHHHHHhH-HHhhhhhhhcchHHHHHHHHHhc
Confidence 444444444433 12233333344444444444444
No 21
>PF01099 Uteroglobin: Uteroglobin family; InterPro: IPR006038 Uteroglobin (or blastokinin) is a mammalian steroid-inducible secreted protein originally isolated from the uterus of rabbits during early pregnancy. The mucosal epithelia of several organs that communicate with the external environment express uteroglobin. Its tissue-specific expression is regulated by steroid hormones, and is augmented in the uterus by non-steroidal prolactin. Uteroglobin may be a multi-functional protein with anti-inflammatory/immunomodulatory properties, acting to inhibit phospholipase A2 activity, and binding to (and possibly sequestering) several hydrophobic ligands such as progesterone, retinols, polychlorinated biphenyls, phospholipids and prostaglandins. In addition, uteroglobin has anti-chemotactic, anti-allergic, anti-tumourigenic and embryo growth-stimulatory properties. Uteroglobin may have a homeostatic role against oxidative damage, inflammation, autoimmunity and cancer [, , , ]. Uteroglobin consists of a disulphide-linked dimer of two identical polypeptides, each polypeptide being composed of four helices. It is a member of the secretoglobin superfamily. This entry represents uteroglobin proteins from several mammalian species, as well as other members of the secretoglobin superfamily, such as lipophilin B [], prostatic steroid-binding protein [], mammaglobin [], and the related allergen Fel d 1 (Felis domesticus allergen 1) [].; GO: 0005488 binding, 0005576 extracellular region; PDB: 1UTR_B 1CCD_A 1UTG_A 2UTG_A 1ZKR_B 1PUO_B 2EJN_B.
Probab=61.46 E-value=13 Score=22.60 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=29.5
Q ss_pred HHHHHHHHHhcCCch-hhHHHHHHHhHHHHHHHHHhcHHHHHhhh
Q 031220 109 RVLSQQMEYYSDDPN-ADRINRIKGEMSQETRSASESRLGVSEAQ 152 (163)
Q Consensus 109 ~~l~~~~~~yn~~~~-~dki~~i~~~v~evk~im~~NI~kvle~l 152 (163)
+..+..++.|+.++. .....++++-+++...-=..||.++++.+
T Consensus 17 ~~Y~~~l~~y~~~~~~~~A~~~lK~C~d~ls~e~~~~i~~~l~~I 61 (67)
T PF01099_consen 17 EEYKESLQKYNPPPEAVEAKLELKQCVDKLSNETRENILKLLEKI 61 (67)
T ss_dssp HHHHHHHHCC---HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 445667788988765 47888889888887777777877776544
No 22
>smart00096 UTG Uteroglobin.
Probab=58.95 E-value=27 Score=21.68 Aligned_cols=39 Identities=15% Similarity=0.302 Sum_probs=28.6
Q ss_pred HHHHHHhcCCch-hhHHHHHHHhHHHHHHHHHhcHHHHHh
Q 031220 112 SQQMEYYSDDPN-ADRINRIKGEMSQETRSASESRLGVSE 150 (163)
Q Consensus 112 ~~~~~~yn~~~~-~dki~~i~~~v~evk~im~~NI~kvle 150 (163)
..-++.||.++. .+...++++-+|....-=..||-++++
T Consensus 22 ~~~l~~y~~~~~~~ea~~~lK~cvD~L~~~~k~~i~~ll~ 61 (69)
T smart00096 22 EASLKQFKPDPDMLEAGRQLKKLVDTLPQETRENILKLTE 61 (69)
T ss_pred HHHHHhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence 455677988876 478888998888766666677666664
No 23
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=58.71 E-value=73 Score=23.64 Aligned_cols=72 Identities=15% Similarity=0.218 Sum_probs=47.9
Q ss_pred CCeeEEEeCCEEEEEE-EeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhc--ccccc-cCCCCchhhhHHHHHHHHH
Q 031220 41 DSHVSYSQDRYIFHVK-RTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG--RAVLS-AQAYGMNDEFSRVLSQQME 116 (163)
Q Consensus 41 ~~k~~~~~~~~~~h~l-~~~~~~~~~itd~~~~~~~af~fL~~i~~~F~~~~~--~~~~~-~~~~~~~~~F~~~l~~~~~ 116 (163)
.+....+.+.|..|+. .-.|+-|++|+++.. ..|-.+|+.+..-|. .|. +...+ ..|-. ..-|++.|+.+++
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 4567778899999966 458999999999987 477788887776665 332 12111 12222 1367777777654
No 24
>PTZ00370 STEVOR; Provisional
Probab=55.61 E-value=7.5 Score=30.94 Aligned_cols=20 Identities=5% Similarity=0.147 Sum_probs=9.9
Q ss_pred hHHHHHHHhHHHHHHHHHhc
Q 031220 125 DRINRIKGEMSQETRSASES 144 (163)
Q Consensus 125 dki~~i~~~v~evk~im~~N 144 (163)
+...++++|+-|.=+-|.-+
T Consensus 102 e~k~klEKel~e~~ee~fg~ 121 (296)
T PTZ00370 102 EPMSTLEKELLETYEEMFGD 121 (296)
T ss_pred chhHHHHHHHHHHHHHHhcC
Confidence 34455555555555444443
No 25
>PF02520 DUF148: Domain of unknown function DUF148; InterPro: IPR003677 This entry represents the domain DUF148, which has no known function.
Probab=53.56 E-value=65 Score=21.51 Aligned_cols=62 Identities=16% Similarity=0.291 Sum_probs=38.2
Q ss_pred HHHHHHHhhhcccccccCCCCchhhhHHHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHhcHHHHHhhh
Q 031220 82 DIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADRINRIKGEMSQETRSASESRLGVSEAQ 152 (163)
Q Consensus 82 ~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~NI~kvle~l 152 (163)
+.+.+|...+.+...+ ..+....+.+...+|+ -.+.+.+...++..-+.-+.+|+..++..|
T Consensus 2 ea~~ef~~I~~n~~lt------~~e~~~~l~~Wa~~~~---v~~~~~~f~~~~~~~~~~~~~~~~~vi~~L 63 (113)
T PF02520_consen 2 EARKEFFQIFQNPNLT------KAEIEEQLDEWAEKYG---VQDQYNEFKAQVQAQKEEVRKNVTAVISNL 63 (113)
T ss_pred hHHHHHHHHHcCCCCC------HHHHHHHHHHHHHHCC---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777766432111 1355566677777665 356777777777777777777776665433
No 26
>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=49.80 E-value=23 Score=21.03 Aligned_cols=48 Identities=13% Similarity=0.139 Sum_probs=35.2
Q ss_pred CCHHHHHHHHhccCCCCCCCeeEEEeCCEEEEEEE--eCCEEEEEEecCC
Q 031220 23 TNASAIARQILDKIPGNNDSHVSYSQDRYIFHVKR--TDGLTVLCMADDT 70 (163)
Q Consensus 23 ~~~~~~~~~vl~~i~~~~~~k~~~~~~~~~~h~l~--~~~~~~~~itd~~ 70 (163)
.+|+.+-..+=+++..+..-|.-|+.+|...+-+- .+|-.|+|...+.
T Consensus 9 ~s~e~lL~~it~~v~l~~gVr~lyt~~G~~V~~l~~l~dg~~yVa~g~e~ 58 (60)
T PF03607_consen 9 RSFEQLLDEITEKVQLPSGVRKLYTLDGKRVKSLDELEDGGSYVASGREP 58 (60)
T ss_dssp SSHHHHHHHHHHSSSSTTS-SEEEETTSSEESSGGGS-TTEEEEEESSSS
T ss_pred cCHHHHHHHHHhhcCCCcccceEECCCCCEeCCHHHHCCCCEEEEEcCCc
Confidence 67888888888898875568888998886665432 4788899986553
No 27
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.39 E-value=51 Score=27.30 Aligned_cols=42 Identities=10% Similarity=0.141 Sum_probs=35.1
Q ss_pred EEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhc
Q 031220 51 YIFHVKRTDGLTVLCMADDTAGRRIPFAFLEDIHQRFVKTYG 92 (163)
Q Consensus 51 ~~~h~l~~~~~~~~~itd~~~~~~~af~fL~~i~~~F~~~~~ 92 (163)
|.++-...+++.+|+++.-+.|--.++.||..|.+-|..-|+
T Consensus 55 hylfsv~~~~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg 96 (418)
T KOG2740|consen 55 HYLFSVYRDLIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFG 96 (418)
T ss_pred eeeeeeeccCcEEEEEEeccCCChhHHHHHHHHHHHHHHHhc
Confidence 333334568899999999999999999999999999998776
No 28
>PF06345 Drf_DAD: DRF Autoregulatory Domain; InterPro: IPR010465 This domain is found in Diaphanous-related formins (Drfs). It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of diaphanous activating domains (DAD) to mammalian cells induces actin filament formation, stabilises microtubules, and activates serum-response mediated transcription [].; PDB: 3O4X_H 3OBV_E 2BAP_C 2F31_B.
Probab=48.81 E-value=12 Score=15.72 Aligned_cols=12 Identities=25% Similarity=0.080 Sum_probs=8.1
Q ss_pred HHHHHhhhhcCC
Q 031220 145 RLGVSEAQYGGE 156 (163)
Q Consensus 145 I~kvle~l~RGe 156 (163)
+|.++|.|+-|.
T Consensus 3 mdsllealqtg~ 14 (15)
T PF06345_consen 3 MDSLLEALQTGS 14 (15)
T ss_dssp HHHHHHHHHHST
T ss_pred HHHHHHHHHccC
Confidence 456777787763
No 29
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.89 E-value=81 Score=26.89 Aligned_cols=38 Identities=13% Similarity=0.143 Sum_probs=28.4
Q ss_pred eeEEEeCCEEEEEEEeCCEEEEEEecCCCCcccHHHHH
Q 031220 43 HVSYSQDRYIFHVKRTDGLTVLCMADDTAGRRIPFAFL 80 (163)
Q Consensus 43 k~~~~~~~~~~h~l~~~~~~~~~itd~~~~~~~af~fL 80 (163)
...++.+.+-|-|-.-|.+-++.||.+++.--....-|
T Consensus 46 hT~vEt~~VRYVYqP~d~lY~vLITtk~SNIleDl~TL 83 (512)
T KOG2635|consen 46 HTFVETDSVRYVYQPLDNLYIVLITTKQSNILEDLETL 83 (512)
T ss_pred ccEEecccEEEEEEecccEEEEEEeccccchhhHHHHH
Confidence 34456678888788889999999999999755544433
No 30
>PF11675 DUF3271: Protein of unknown function (DUF3271); InterPro: IPR021689 This family of proteins with unknown function appears to be restricted to Plasmodium.
Probab=45.70 E-value=61 Score=25.14 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=33.2
Q ss_pred ceEEEEEEeCCeeEeeeeCCCCCHHHHHHHHhccCCCCCCCeeEEEeCCEEE
Q 031220 2 AILFSLVARGSVVLAECSATATNASAIARQILDKIPGNNDSHVSYSQDRYIF 53 (163)
Q Consensus 2 ~I~Y~~Iar~~~iLae~~~~~~~~~~~~~~vl~~i~~~~~~k~~~~~~~~~~ 53 (163)
+|-|+.||.-++.+......-..+=.++..++..-+. +.+..|+.++|.|
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 5788888877766665543334455777778776553 5677777777665
No 31
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=44.53 E-value=44 Score=25.31 Aligned_cols=51 Identities=14% Similarity=0.215 Sum_probs=30.6
Q ss_pred EEEEEEeCC--eeEeeeeCCCC----------------------CH---HHHHHHHhccCCCCCCCeeEEEeCCEEEE
Q 031220 4 LFSLVARGS--VVLAECSATAT----------------------NA---SAIARQILDKIPGNNDSHVSYSQDRYIFH 54 (163)
Q Consensus 4 ~Y~~Iar~~--~iLae~~~~~~----------------------~~---~~~~~~vl~~i~~~~~~k~~~~~~~~~~h 54 (163)
+||.|.-+. .+||..+..+. |. ..+.+.+.++.....=.++.|+.+||.||
T Consensus 117 IYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI~kVvFDRgGy~YH 194 (211)
T PTZ00032 117 MYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGISKVRFDRAHYKYA 194 (211)
T ss_pred EEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCeeh
Confidence 688888773 67776664221 21 22333333443322346799999999999
No 32
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=43.28 E-value=60 Score=22.21 Aligned_cols=51 Identities=20% Similarity=0.403 Sum_probs=30.4
Q ss_pred EEEEEEeC--CeeEeeeeCC------CCCH---HHHHHHHhccCCCCCCCeeEEEeCCEEEE
Q 031220 4 LFSLVARG--SVVLAECSAT------ATNA---SAIARQILDKIPGNNDSHVSYSQDRYIFH 54 (163)
Q Consensus 4 ~Y~~Iar~--~~iLae~~~~------~~~~---~~~~~~vl~~i~~~~~~k~~~~~~~~~~h 54 (163)
+|+.|..+ +.+||.-+.. .+|. ..+...+.++.....-++..|+.++|.||
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 68888866 3677766643 2443 22333333443322356788999999998
No 33
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=41.21 E-value=26 Score=22.35 Aligned_cols=35 Identities=17% Similarity=0.177 Sum_probs=26.9
Q ss_pred hHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCCCcc
Q 031220 125 DRINRIKGEMSQETRSASESRLGVSEAQYGGETSS 159 (163)
Q Consensus 125 dki~~i~~~v~evk~im~~NI~kvle~l~RGe~~~ 159 (163)
+.+..++..+.+.-+-+.++-+++.++.+|.|.|+
T Consensus 10 ~~v~~v~~im~~Ni~~ll~Rge~L~~L~~kt~~L~ 44 (89)
T PF00957_consen 10 EQVEEVKNIMRENIDKLLERGEKLEELEDKTEELS 44 (89)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHHHH
Confidence 56777777888888888888888887777777664
No 34
>PLN00064 photosystem II protein Psb27; Provisional
Probab=39.40 E-value=1.1e+02 Score=22.28 Aligned_cols=67 Identities=16% Similarity=0.127 Sum_probs=41.2
Q ss_pred CCcccHHHHHHHHHHHHHhhhcccccccCCCCchhhhHHHHHHHHHHhcCCc-h---hhHH-HHHHHhHHHHH
Q 031220 71 AGRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDP-N---ADRI-NRIKGEMSQET 138 (163)
Q Consensus 71 ~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~-~---~dki-~~i~~~v~evk 138 (163)
-.+..+-.=+.+....|...|.........-+| ..+...|..+-.||++-. + .+|+ +.|.+|++++.
T Consensus 88 p~~a~a~aeaR~~iNdyvSrYRr~~~v~Gl~SF-ttMyTALNaLAGHY~SfgpnrPlPeKlK~RL~qE~~~AE 159 (166)
T PLN00064 88 PNVADAVAELRETSNSWVAKYRREKALLGRPSF-RDMYSALNAVSGHYISFGPTAPIPAKRKARILEEMDTAE 159 (166)
T ss_pred ccHHHHHHHHHHHHHHHHHHhcCCCcccCcccH-HHHHHHHHHHHHHhhccCCCCCCcHHHHHHHHHHHHHHH
Confidence 345556677888888888888643222222233 477788999999996642 2 2444 45555555443
No 35
>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].
Probab=38.32 E-value=18 Score=25.87 Aligned_cols=50 Identities=16% Similarity=0.212 Sum_probs=27.0
Q ss_pred hhHHHHHHHHHHhcCC-chhhHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCCCc
Q 031220 106 EFSRVLSQQMEYYSDD-PNADRINRIKGEMSQETRSASESRLGVSEAQYGGETS 158 (163)
Q Consensus 106 ~F~~~l~~~~~~yn~~-~~~dki~~i~~~v~evk~im~~NI~kvle~l~RGe~~ 158 (163)
.|.+.++++...-+.- |-.+.|.+...+++.-. .+=++++.+.|++|++|
T Consensus 31 ~fk~~l~~L~sTl~~i~P~i~eI~~~~~eld~~~---~ee~e~L~~~L~~g~~L 81 (147)
T PF05659_consen 31 SFKSILKRLESTLESIIPIIKEIDKLNVELDRPR---QEEIERLKELLEKGKEL 81 (147)
T ss_pred hhhhHHHHHHHHHHHhhhHHHHHHHHhhhcCCch---hHHHHHHHHHHHHHHHH
Confidence 5556666655444432 44566666666666553 22234455566677664
No 36
>COG3543 Uncharacterized conserved protein [Function unknown]
Probab=37.85 E-value=23 Score=24.80 Aligned_cols=18 Identities=22% Similarity=0.156 Sum_probs=14.6
Q ss_pred HHhcHHHHHhhhhcCCCc
Q 031220 141 ASESRLGVSEAQYGGETS 158 (163)
Q Consensus 141 m~~NI~kvle~l~RGe~~ 158 (163)
-.+|+++|.+.|++||.+
T Consensus 25 FveN~d~I~~rL~~ge~i 42 (135)
T COG3543 25 FVENYDAIAERLKAGEDI 42 (135)
T ss_pred HHHHHHHHHHHhhcCCCe
Confidence 467888888889999873
No 37
>PF10504 DUF2452: Protein of unknown function (DUF2452); InterPro: IPR019534 This entry contains proteins that have no known function.
Probab=37.59 E-value=15 Score=26.66 Aligned_cols=55 Identities=27% Similarity=0.486 Sum_probs=35.6
Q ss_pred HHHHHHHhccCCCC---CCCeeEEEe-CCEEEE-EEEeCCEEEEEEecCC-CCcccHHHHH
Q 031220 26 SAIARQILDKIPGN---NDSHVSYSQ-DRYIFH-VKRTDGLTVLCMADDT-AGRRIPFAFL 80 (163)
Q Consensus 26 ~~~~~~vl~~i~~~---~~~k~~~~~-~~~~~h-~l~~~~~~~~~itd~~-~~~~~af~fL 80 (163)
.+.+++++++...+ .+.+++|.- =|.+|| |..++|-.|+.+..|+ .+.+.++.||
T Consensus 65 q~QA~~ile~~~~~~~l~~A~cnF~pipG~iYhLY~r~~G~~ylSmisP~EWg~~~p~~fl 125 (159)
T PF10504_consen 65 QEQARKILEEAERNEELHHAKCNFEPIPGQIYHLYRRENGQDYLSMISPEEWGGSCPHEFL 125 (159)
T ss_pred HHHHHHHHHHHHHhHHHhhcccCceecCCCEEEEEECCCCCEEEEeeCHHHhCCCCCcCEE
Confidence 56667777776542 366777764 577787 5556787777766665 4656666554
No 38
>TIGR02284 conserved hypothetical protein. Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.
Probab=37.43 E-value=1.4e+02 Score=20.81 Aligned_cols=52 Identities=13% Similarity=0.142 Sum_probs=36.2
Q ss_pred hhHHHHHHHHHHhcCCch--hhHHHHHHHhHHHHHHHHH-hcHHHHHhhhhcCCC
Q 031220 106 EFSRVLSQQMEYYSDDPN--ADRINRIKGEMSQETRSAS-ESRLGVSEAQYGGET 157 (163)
Q Consensus 106 ~F~~~l~~~~~~yn~~~~--~dki~~i~~~v~evk~im~-~NI~kvle~l~RGe~ 157 (163)
.|...|+..+..++..|. ..-.-.+..-.-.++..+. ++=+.+|+.++|||+
T Consensus 44 ~~~~eL~~~v~~lGg~p~~~gs~~g~lhr~w~~lks~~~~~~d~aiL~~~e~gEd 98 (139)
T TIGR02284 44 AIVSELQQVVASLGGKPEDHGSMVGSLHQFWGKIRATLTPNDDYVVLEEAERGED 98 (139)
T ss_pred HHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHcCCChHHHHHHHHHhHH
Confidence 556667777777775442 3455667777778888887 444558888899987
No 39
>PF13228 DUF4037: Domain of unknown function (DUF4037)
Probab=35.88 E-value=52 Score=21.78 Aligned_cols=50 Identities=18% Similarity=0.282 Sum_probs=34.0
Q ss_pred hhHHHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCCCcccCC
Q 031220 106 EFSRVLSQQMEYYSDDPNADRINRIKGEMSQETRSASESRLGVSEAQYGGETSSSRL 162 (163)
Q Consensus 106 ~F~~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~NI~kvle~l~RGe~~~~~~ 162 (163)
.|++.=+++ ..| |+.=....+..+...+.+...-|+.+.+ +||+.+++++
T Consensus 24 ~~~~~R~~l-~~Y---P~dl~~~~ia~~~~~~~qa~~~n~~ra~---~R~D~~~~~~ 73 (100)
T PF13228_consen 24 EFTALRERL-AYY---PEDLRLNKIARNLMLLAQAGQYNLGRAL---KRGDILAANH 73 (100)
T ss_pred hHHHHHHHH-HHC---hHHHHHHHHHHHHHHhhhhhHHHHHHHH---HCCCHHHHHH
Confidence 554433333 656 6655666777788778777788988855 6999877654
No 40
>cd07634 BAR_GAP10-like The Bin/Amphiphysin/Rvs (BAR) domain of Rho GTPase activating protein 10-like. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This group is composed of uncharacterized proteins called Rho GTPase activating protein (GAP) 10-like. GAP10-like may be a GAP with activity towards RhoA and Cdc42. Similar to GRAF and GRAF2, it contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domains of the related proteins GRAF and OPHN1, directly interact with their Rho GAP domains and inhibit theiractivity. The autoinhibited proteins are capable of binding membranes and tubulating liposomes, showing that the membrane-tubulation and GAP-inhibitory functions of the BAR domain
Probab=33.44 E-value=2.2e+02 Score=21.68 Aligned_cols=69 Identities=16% Similarity=0.126 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHhhhccc--ccccCCCCchhhhHHHHHHHHHHhcCCc----------hhhHHHHHHHhHHHHHHHHHh
Q 031220 76 PFAFLEDIHQRFVKTYGRA--VLSAQAYGMNDEFSRVLSQQMEYYSDDP----------NADRINRIKGEMSQETRSASE 143 (163)
Q Consensus 76 af~fL~~i~~~F~~~~~~~--~~~~~~~~~~~~F~~~l~~~~~~yn~~~----------~~dki~~i~~~v~evk~im~~ 143 (163)
+..||++|-.......... ...+ +..|...|.++-.++...+ .-.+..+.-++|++-+.+|.+
T Consensus 14 t~~~ik~liK~c~~li~A~k~~~~a-----~~~Fa~sL~~f~~~~igd~~tDde~~i~~~l~~Fs~~l~el~~~~~~L~~ 88 (207)
T cd07634 14 TNKFIKELIKDGSLLIGALRNLSMA-----VQKFSQSLQDFQFECIGDAETDDEISIAQSLKEFARLLIAVEEERRRLIQ 88 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHhhccCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5678888877776554311 1111 3467777777765554433 124667777888889999999
Q ss_pred cHHHHH
Q 031220 144 SRLGVS 149 (163)
Q Consensus 144 NI~kvl 149 (163)
|++.++
T Consensus 89 ~~~~~l 94 (207)
T cd07634 89 NANDVL 94 (207)
T ss_pred HHHHHH
Confidence 987543
No 41
>PF15278 Sec3_C_2: Sec3 exocyst complex subunit
Probab=33.16 E-value=1.2e+02 Score=19.11 Aligned_cols=40 Identities=13% Similarity=0.130 Sum_probs=28.3
Q ss_pred hhHHHHHHHHHHhcCC--chhhHHHHHHHhHHHHHHHHHhcH
Q 031220 106 EFSRVLSQQMEYYSDD--PNADRINRIKGEMSQETRSASESR 145 (163)
Q Consensus 106 ~F~~~l~~~~~~yn~~--~~~dki~~i~~~v~evk~im~~NI 145 (163)
.|.+.++++...+|.. .++..+.+-+-++.+||+++.+-+
T Consensus 14 ~~~~~~~~~~~S~~~s~~~~VE~L~~~~~~~~~i~~~L~D~~ 55 (86)
T PF15278_consen 14 TFKDNQQQTEFSFNESMISNVENLFRQKMQAQNIQSQLQDCI 55 (86)
T ss_pred hHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6777788887777543 235666666777888888888764
No 42
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=31.87 E-value=73 Score=23.59 Aligned_cols=50 Identities=8% Similarity=0.118 Sum_probs=35.4
Q ss_pred hHHHHHHHHHHhcCC----chhhHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCC
Q 031220 107 FSRVLSQQMEYYSDD----PNADRINRIKGEMSQETRSASESRLGVSEAQYGGE 156 (163)
Q Consensus 107 F~~~l~~~~~~yn~~----~~~dki~~i~~~v~evk~im~~NI~kvle~l~RGe 156 (163)
.-|.+.+++++|.+- ...+.+.+..++++++-+-+.+++++-++.+-.++
T Consensus 134 yLp~~~~l~~kY~~l~~~~~~~~~~~~~l~e~~~~L~~l~~~f~~~~~~l~~~d 187 (199)
T PF10112_consen 134 YLPTAVKLLEKYAELESQPVKSEEIKQSLEEIEETLDTLNQAFEKDLDKLLEDD 187 (199)
T ss_pred HhhHHHHHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 347788888888752 23567777788888888888888887766554443
No 43
>PF04220 YihI: Der GTPase activator (YihI); InterPro: IPR007336 This entry contains Escherichia coli (strain K12) YihI. YihI activates the GTPase activity of Der, a 50S ribosomal subunit stability factor and can therefore be considered a GAP (GTPase activating)-like protein. The stimulation is specific to Der as YihI does not stimulate the GTPase activity of Era or ObgE. The interaction of YihI with Der requires only the C-terminal 78 amino acids of YihI []. A yihI deletion mutant is viable and shows a shorter lag period, but the same post-lag growth rate as a wild-type strain. yihI is expressed during the lag period. Overexpression of yihI inhibits cell growth and biogenesis of the 50S ribosomal subunit []. YihI is an unusual, highly hydrophilic protein with an uneven distribution of charged residues, resulting in an N-terminal region with high pI and a C-terminal region with low pI [].
Probab=31.60 E-value=39 Score=24.84 Aligned_cols=16 Identities=25% Similarity=0.094 Sum_probs=13.0
Q ss_pred HHHHHhhhhcCCCccc
Q 031220 145 RLGVSEAQYGGETSSS 160 (163)
Q Consensus 145 I~kvle~l~RGe~~~~ 160 (163)
++.+||.|+.||.||.
T Consensus 110 L~~LLdrle~Ge~Ls~ 125 (169)
T PF04220_consen 110 LNQLLDRLEEGETLSA 125 (169)
T ss_pred HHHHHHHHHCCCcCCH
Confidence 5667888888999985
No 44
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=31.19 E-value=1.3e+02 Score=21.40 Aligned_cols=66 Identities=18% Similarity=0.186 Sum_probs=40.6
Q ss_pred cccHHHHHHHHHHHHHhhhcccccccCCCCchhhhHHHHHHHHHHhcCCch-----hhHHHHHHHhHHHHHH
Q 031220 73 RRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPN-----ADRINRIKGEMSQETR 139 (163)
Q Consensus 73 ~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~-----~dki~~i~~~v~evk~ 139 (163)
.+-+-.=+.+....|...|.........-++ ..+...|..+-.||+..+. .....+|.++++++..
T Consensus 73 ~~~~~~~ar~~in~~vs~YRr~~~v~g~~Sf-~~m~tAln~LaghY~s~g~raPlP~k~k~rll~el~~Ae~ 143 (145)
T PF13326_consen 73 RAEAAAEARELINDYVSRYRRGPSVSGLPSF-TTMYTALNALAGHYSSYGNRAPLPEKLKERLLKELDQAEK 143 (145)
T ss_dssp HHHHHHHHHHHHHHHHCCCCCCHHCCTSHHH-HHHHHHHHHHHHHCHHHTTS-S--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCcCCcchH-HHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHh
Confidence 3344456667777788777543222222223 3667889999999987422 3555777777777654
No 45
>PF04100 Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007234 Vps53 complexes with Vps52 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=30.59 E-value=2.2e+02 Score=23.62 Aligned_cols=43 Identities=9% Similarity=0.143 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHhcHHHH
Q 031220 106 EFSRVLSQQMEYYSDDPNADRINRIKGEMSQETRSASESRLGV 148 (163)
Q Consensus 106 ~F~~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~NI~kv 148 (163)
..-..+.+++.+|+...+.++|.++..+++.++.-+.+-|-.-
T Consensus 138 ~~L~av~~L~~~F~~yksi~~I~~L~~~i~~l~~~L~~qI~~d 180 (383)
T PF04100_consen 138 SLLQAVKELLEHFKPYKSIPQIAELSKRIDQLQNELKEQIFED 180 (383)
T ss_pred HHHHHHHHHHHHHHcccCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4446788899999888889999999999999888888776543
No 46
>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=30.53 E-value=65 Score=22.97 Aligned_cols=26 Identities=15% Similarity=0.315 Sum_probs=23.7
Q ss_pred EEEEEecCCCCcccHHHHHHHHHHHH
Q 031220 62 TVLCMADDTAGRRIPFAFLEDIHQRF 87 (163)
Q Consensus 62 ~~~~itd~~~~~~~af~fL~~i~~~F 87 (163)
..+.||.++||.+....||..+.++.
T Consensus 25 ~~ilit~kG~P~~~tr~~l~~L~~~~ 50 (160)
T cd00223 25 NCILITGKGYPDRATRRFLRRLHEEL 50 (160)
T ss_pred CEEEEEcCCcCCHHHHHHHHHHHHhh
Confidence 46889999999999999999999886
No 47
>PF06238 Borrelia_lipo_2: Borrelia burgdorferi BBR25 lipoprotein; InterPro: IPR009358 This entry consists of a number of lipoproteins conserved in Borrelia species [].
Probab=30.34 E-value=1.7e+02 Score=19.61 Aligned_cols=7 Identities=29% Similarity=0.249 Sum_probs=3.6
Q ss_pred hhhcCCC
Q 031220 151 AQYGGET 157 (163)
Q Consensus 151 ~l~RGe~ 157 (163)
+|+|||.
T Consensus 104 ~Lk~gen 110 (111)
T PF06238_consen 104 ILKRGEN 110 (111)
T ss_pred HHhcccC
Confidence 4456653
No 48
>PF07340 Herpes_IE1: Cytomegalovirus IE1 protein; InterPro: IPR010855 Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present []. The IE1 protein from cytomegalovirus is also known as UL123.; GO: 0050792 regulation of viral reproduction, 0042025 host cell nucleus
Probab=29.35 E-value=3.2e+02 Score=22.87 Aligned_cols=84 Identities=14% Similarity=0.170 Sum_probs=44.7
Q ss_pred EecCCCCcccHHHHHHHHHHHHHh-hh--ccc-ccccCCCCchhhhHHHHHHHHHHhcCCchhhH----HHHH-------
Q 031220 66 MADDTAGRRIPFAFLEDIHQRFVK-TY--GRA-VLSAQAYGMNDEFSRVLSQQMEYYSDDPNADR----INRI------- 130 (163)
Q Consensus 66 itd~~~~~~~af~fL~~i~~~F~~-~~--~~~-~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dk----i~~i------- 130 (163)
+..++.|-..|-+||+.+-.+=.. .. |+. +..... ..| +++.+++..-+++|..+- +.++
T Consensus 23 ~pr~e~pv~~A~~fLek~l~~E~~~~lsLGDPLf~~~~~----~~~-kt~e~i~~e~~~~p~~~~~q~lv~QiKlrv~~~ 97 (392)
T PF07340_consen 23 MPRPEDPVTRAVQFLEKMLADETNTQLSLGDPLFPDVSE----DPF-KTFEDIINECDDNPGKDVLQELVKQIKLRVARN 97 (392)
T ss_pred CCCCCChHHHHHHHHHHHHHHHHhcccccCCCCCCCCCC----Cch-hhHHHHHhcCCCChHHHHHHHHHHHHHHHHHHH
Confidence 445677778999999987655543 33 222 111111 122 445666666666664332 2332
Q ss_pred --------HHhHHHHHHHHHhcHHHHHhhhhc
Q 031220 131 --------KGEMSQETRSASESRLGVSEAQYG 154 (163)
Q Consensus 131 --------~~~v~evk~im~~NI~kvle~l~R 154 (163)
.++..+++..|..+-+.+-+.++.
T Consensus 98 r~~~k~~~l~qy~~~r~~~~~~F~~i~~~l~n 129 (392)
T PF07340_consen 98 RTEIKEQMLKQYNQIRMVFIGKFNDIQGGLQN 129 (392)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 245566666666665555444443
No 49
>PHA01811 hypothetical protein
Probab=29.30 E-value=86 Score=19.11 Aligned_cols=19 Identities=32% Similarity=0.469 Sum_probs=15.1
Q ss_pred CCeeEEEeCCEEEEEEEeC
Q 031220 41 DSHVSYSQDRYIFHVKRTD 59 (163)
Q Consensus 41 ~~k~~~~~~~~~~h~l~~~ 59 (163)
+.-.+....||.+||+-++
T Consensus 4 ddivtlrvkgyi~hyldd~ 22 (78)
T PHA01811 4 DDIVTLRVKGYILHYLDDD 22 (78)
T ss_pred ccEEEEEEeeEEEEEEcCc
Confidence 5567788899999999653
No 50
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=28.18 E-value=1.1e+02 Score=20.77 Aligned_cols=51 Identities=12% Similarity=0.357 Sum_probs=28.3
Q ss_pred EEEEEEeCC--eeEeeeeCCC----------CCH---HHHHHHHhccCCCCCCCeeEEEeCCEEEE
Q 031220 4 LFSLVARGS--VVLAECSATA----------TNA---SAIARQILDKIPGNNDSHVSYSQDRYIFH 54 (163)
Q Consensus 4 ~Y~~Iar~~--~iLae~~~~~----------~~~---~~~~~~vl~~i~~~~~~k~~~~~~~~~~h 54 (163)
+|+.|..+. .+||.-+..+ +|. ..+...+.++.....-.+..|+.++|.||
T Consensus 27 iyaQvidd~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~gi~~vvfDrgg~~yh 92 (109)
T CHL00139 27 IYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKKGITKVVFDRGGKLYH 92 (109)
T ss_pred EEEEEEECCCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCCCccc
Confidence 688787662 5666555321 232 12223333333322346788888999988
No 51
>PF12579 DUF3755: Protein of unknown function (DUF3755); InterPro: IPR022228 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue N that may be functionally important.
Probab=28.05 E-value=44 Score=17.77 Aligned_cols=19 Identities=26% Similarity=0.225 Sum_probs=13.6
Q ss_pred hhHHHHHHHhHHHHHHHHH
Q 031220 124 ADRINRIKGEMSQETRSAS 142 (163)
Q Consensus 124 ~dki~~i~~~v~evk~im~ 142 (163)
-|.|..|.+++.++-+||.
T Consensus 16 R~NI~~il~~m~~mpgim~ 34 (35)
T PF12579_consen 16 RDNILAILNDMNDMPGIMS 34 (35)
T ss_pred HHHHHHHHHHHHcchhhhc
Confidence 3667777777777777774
No 52
>PF13314 DUF4083: Domain of unknown function (DUF4083)
Probab=27.92 E-value=45 Score=19.92 Aligned_cols=14 Identities=7% Similarity=-0.178 Sum_probs=8.5
Q ss_pred HHhcHHHHHhhhhc
Q 031220 141 ASESRLGVSEAQYG 154 (163)
Q Consensus 141 m~~NI~kvle~l~R 154 (163)
|.+..|+++|+||.
T Consensus 44 ~eqKLDrIIeLLEK 57 (58)
T PF13314_consen 44 MEQKLDRIIELLEK 57 (58)
T ss_pred HHHHHHHHHHHHcc
Confidence 45556666666654
No 53
>cd09238 V_Alix_like_1 Protein-interacting V-domain of an uncharacterized family of the V_Alix_like superfamily. This domain family is comprised of uncharacterized plant proteins. It belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), (His-Domain) type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Alix, HD-PTP, Bro1, a
Probab=27.70 E-value=1.1e+02 Score=24.76 Aligned_cols=42 Identities=12% Similarity=0.113 Sum_probs=22.9
Q ss_pred HHHHhhhcccccccCCCCchhhhHHHHHHHHHHhcCCchhhH
Q 031220 85 QRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPNADR 126 (163)
Q Consensus 85 ~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~~dk 126 (163)
..++..|+..|...++..++..|...+.++-.........|.
T Consensus 110 ~~~R~kyg~rWtr~pS~~~~~~l~~~i~~~r~~L~~A~~sD~ 151 (339)
T cd09238 110 SAARTQYGTAWTRPPSATLTKNLWERLNRFRVNLEQAGDSDE 151 (339)
T ss_pred HHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence 455667777666555555555555555555444444333343
No 54
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=27.64 E-value=79 Score=21.62 Aligned_cols=17 Identities=29% Similarity=0.288 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHhhhc
Q 031220 76 PFAFLEDIHQRFVKTYG 92 (163)
Q Consensus 76 af~fL~~i~~~F~~~~~ 92 (163)
.|..|..=..+|...|-
T Consensus 30 ~~~~L~~E~~~Fi~~Fi 46 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFI 46 (113)
T ss_pred hhhcCCHHHHHHHHHHH
Confidence 67888888888888873
No 55
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=26.94 E-value=1.5e+02 Score=20.31 Aligned_cols=51 Identities=18% Similarity=0.362 Sum_probs=28.9
Q ss_pred EEEEEEeC--CeeEeeeeCCC---------CCH---HHHHHHHhccCCCCCCCeeEEEeCCEEEE
Q 031220 4 LFSLVARG--SVVLAECSATA---------TNA---SAIARQILDKIPGNNDSHVSYSQDRYIFH 54 (163)
Q Consensus 4 ~Y~~Iar~--~~iLae~~~~~---------~~~---~~~~~~vl~~i~~~~~~k~~~~~~~~~~h 54 (163)
+|+.|... +.+||.-+..+ +|. ..+...+.++.....-.+..|+.++|.||
T Consensus 36 iyAQvidd~~~~tl~saST~e~~~k~~~~~~n~~aa~~vG~~la~ra~~~gi~~vvfDrg~~~yh 100 (117)
T PRK05593 36 IYAQVIDDVKGKTLASASTLEKDVRAGLKGGNKEAAKKVGKLIAERAKAKGIKQVVFDRGGYKYH 100 (117)
T ss_pred EEEEEEECCCCEEEEEEecCcHhHhccccCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCCCccc
Confidence 68878765 36666666422 232 23333333443322245688888888887
No 56
>KOG3230 consensus Vacuolar assembly/sorting protein DID4 [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.65 E-value=79 Score=23.89 Aligned_cols=18 Identities=6% Similarity=-0.077 Sum_probs=13.4
Q ss_pred HhHHHHHHHHHhcHHHHH
Q 031220 132 GEMSQETRSASESRLGVS 149 (163)
Q Consensus 132 ~~v~evk~im~~NI~kvl 149 (163)
..++-+.++|-++||-.+
T Consensus 133 e~Mdm~~Emm~daIDdal 150 (224)
T KOG3230|consen 133 EIMDMKEEMMDDAIDDAL 150 (224)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 456678888999988655
No 57
>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=25.93 E-value=2.4e+02 Score=19.90 Aligned_cols=67 Identities=12% Similarity=0.240 Sum_probs=42.1
Q ss_pred CcccHHHHHHHHHHHHHhhhcccccccCCCCchhhhHHHHHHHHHHhcCCch---hhHH-HHHHHhHHHHHH
Q 031220 72 GRRIPFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSDDPN---ADRI-NRIKGEMSQETR 139 (163)
Q Consensus 72 ~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~~~~---~dki-~~i~~~v~evk~ 139 (163)
....|-.=+.+....|...|.........-+| ..+...|..+-.||++.++ .+|+ ..+.+|++++..
T Consensus 60 ~~~~a~~~ar~~indyvsrYRr~~~v~g~~SF-ttm~TALNsLAGHY~sy~~rPlPeklk~Rl~~El~~AE~ 130 (135)
T TIGR03044 60 NKSEAQAEARQLINDYISRYRRRPRVNGLSSF-TTMQTALNSLAGHYKSYANRPLPEKLKERLEKELKKAEK 130 (135)
T ss_pred cHHHHHHHHHHHHHHHHHHhcCCCCcCCcccH-HHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH
Confidence 34556667777888888888543222222233 3667889999999988542 2444 667777766543
No 58
>PF12277 DUF3618: Protein of unknown function (DUF3618); InterPro: IPR022062 This domain family is found in bacteria, and is approximately 50 amino acids in length.
Probab=25.23 E-value=1.4e+02 Score=16.87 Aligned_cols=24 Identities=8% Similarity=0.162 Sum_probs=19.7
Q ss_pred HHHHHHhHHHHHHHHHhcHHHHHh
Q 031220 127 INRIKGEMSQETRSASESRLGVSE 150 (163)
Q Consensus 127 i~~i~~~v~evk~im~~NI~kvle 150 (163)
..+|+.+|+.++.-|..+++.+-+
T Consensus 5 ~~~ie~dIe~tR~~La~tvd~L~~ 28 (49)
T PF12277_consen 5 PDEIERDIERTRAELAETVDELAA 28 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999886544
No 59
>PF14805 THDPS_N_2: Tetrahydrodipicolinate N-succinyltransferase N-terminal; PDB: 3EG4_A 3TDT_A 2TDT_A 1KGT_A 1TDT_A 1KGQ_A 3BXY_A 3GOS_A 3TK8_A.
Probab=24.81 E-value=76 Score=19.68 Aligned_cols=17 Identities=24% Similarity=0.114 Sum_probs=10.9
Q ss_pred HHhcHHHHHhhhhcCCC
Q 031220 141 ASESRLGVSEAQYGGET 157 (163)
Q Consensus 141 m~~NI~kvle~l~RGe~ 157 (163)
..+.|..++++|++|+-
T Consensus 26 ~~~av~~~i~~Ld~G~l 42 (70)
T PF14805_consen 26 LRDAVEEVIELLDSGEL 42 (70)
T ss_dssp HHHHHHHHHHHHHTTSS
T ss_pred HHHHHHHHHHHhcCCCe
Confidence 34445556677889974
No 60
>PHA02557 22 prohead core protein; Provisional
Probab=24.25 E-value=3.7e+02 Score=21.36 Aligned_cols=74 Identities=12% Similarity=0.099 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHhhhcccccccCCCCchhhhHHHHHHHHHHhcC-Cch--hhHHHHHHHhHHHHHHHHHhcHHHHH
Q 031220 76 PFAFLEDIHQRFVKTYGRAVLSAQAYGMNDEFSRVLSQQMEYYSD-DPN--ADRINRIKGEMSQETRSASESRLGVS 149 (163)
Q Consensus 76 af~fL~~i~~~F~~~~~~~~~~~~~~~~~~~F~~~l~~~~~~yn~-~~~--~dki~~i~~~v~evk~im~~NI~kvl 149 (163)
+-.||+.+-.+|...............+..+|-.-|+.+....|= -|. .|-+..+..+|++-+.-...-++...
T Consensus 89 vd~~l~~~~~eW~~ENk~Av~~~IKaem~Es~l~GLK~lF~Ehnv~vpee~vdvV~em~~~L~E~e~~~~~l~~en~ 165 (271)
T PHA02557 89 ADKYLDHLAKEWLAENKLAVDRGIKAELFESFLGGLKELFVEHNVVVPEEKVDVVAEMEEELDEMEEELNELFEENV 165 (271)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCcHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999876544433334444445666677887665553 343 57888888888887766665555433
No 61
>PF15457 HopW1-1: Type III T3SS secreted effector HopW1-1/HopPmaA
Probab=24.20 E-value=1.4e+02 Score=23.52 Aligned_cols=47 Identities=17% Similarity=0.174 Sum_probs=38.6
Q ss_pred HHHHHHHHHhcCCchhhHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCCCccc
Q 031220 109 RVLSQQMEYYSDDPNADRINRIKGEMSQETRSASESRLGVSEAQYGGETSSS 160 (163)
Q Consensus 109 ~~l~~~~~~yn~~~~~dki~~i~~~v~evk~im~~NI~kvle~l~RGe~~~~ 160 (163)
..|..+.+...|.+..+.+..+.+..-+.-+-+++| ++|-|-|-+||
T Consensus 235 ~aLaaLtEnCpD~pt~~dLr~Lae~aG~LLq~LR~~-----~lLp~~eeis~ 281 (320)
T PF15457_consen 235 GALAALTENCPDTPTQNDLRSLAEVAGELLQQLREH-----DLLPRSEEISS 281 (320)
T ss_pred HHHHHHHhcCCCCchhHHHHHHHHHHHHHHHHHHHc-----CCcCchhhhcc
Confidence 457788888888888888888888888888888888 77888888776
No 62
>PF10158 LOH1CR12: Tumour suppressor protein; InterPro: IPR018780 This entry represents a region of 130 amino acids that is the most conserved part of some hypothetical proteins involved in loss of heterozygosity, and thus, tumour suppression []. The exact function of these proteins is not known.
Probab=24.08 E-value=2.3e+02 Score=19.81 Aligned_cols=25 Identities=8% Similarity=0.247 Sum_probs=20.7
Q ss_pred hhHHHHHHHhHHHHHHHHHhcHHHH
Q 031220 124 ADRINRIKGEMSQETRSASESRLGV 148 (163)
Q Consensus 124 ~dki~~i~~~v~evk~im~~NI~kv 148 (163)
..++.++..++..++..+.+++..+
T Consensus 86 L~kv~els~~L~~~~~lL~~~v~~i 110 (131)
T PF10158_consen 86 LEKVNELSQQLSRCQSLLNQTVPSI 110 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678888999999999999987643
No 63
>PRK05244 Der GTPase activator; Provisional
Probab=24.07 E-value=64 Score=23.90 Aligned_cols=16 Identities=25% Similarity=0.152 Sum_probs=13.3
Q ss_pred HHHHHhhhhcCCCccc
Q 031220 145 RLGVSEAQYGGETSSS 160 (163)
Q Consensus 145 I~kvle~l~RGe~~~~ 160 (163)
++.+||.|+-||.||.
T Consensus 109 L~~LLdrLE~Ge~Ls~ 124 (177)
T PRK05244 109 LNALLDRLEAGETLSA 124 (177)
T ss_pred HHHHHHHHHCCCcCCH
Confidence 6668889999999874
No 64
>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=24.05 E-value=83 Score=25.12 Aligned_cols=25 Identities=4% Similarity=0.402 Sum_probs=20.6
Q ss_pred eCCEEEEEEEeCCEEEEEEecCCCC
Q 031220 48 QDRYIFHVKRTDGLTVLCMADDTAG 72 (163)
Q Consensus 48 ~~~~~~h~l~~~~~~~~~itd~~~~ 72 (163)
.+||+|-|-..+++..+|||.-.+-
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 4678888866789999999998774
No 65
>PF03231 Bunya_NS-S_2: Bunyavirus non-structural protein NS-S; InterPro: IPR004915 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein (NSs). The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the segment S non-structural protein, NSs. This protein is present in infected cells, but absent from purified virus particles [, ]. It is not essential for virus replication, but contributes substantially to pathogenesis []. This may be due to the capacity of NSs to interfere with the host immune response; it has been shown to inhibit the production of alpha/beta interferons, and to inhibit interferon regulatory factor-mediated cell death [, ]. Studies indicate that NSs suppresses host mRNA synthesis by sequestering subunits of the basal transcription factor TFIIH, explaining the dramatic drop in RNA synthesis observed upon infection [].
Probab=23.99 E-value=41 Score=28.50 Aligned_cols=31 Identities=19% Similarity=0.387 Sum_probs=25.0
Q ss_pred CCEEEEEEecCCCCcccHHHHHHHHHHHHHhh
Q 031220 59 DGLTVLCMADDTAGRRIPFAFLEDIHQRFVKT 90 (163)
Q Consensus 59 ~~~~~~~itd~~~~~~~af~fL~~i~~~F~~~ 90 (163)
-|++-+|-+|++||+++|..+|+ ++.+|...
T Consensus 333 ~g~v~~~~~DpnynqiIv~~Ll~-vHt~fA~~ 363 (444)
T PF03231_consen 333 SGIVDFVDSDPNYNQIIVHSLLS-VHTSFAQK 363 (444)
T ss_pred cceeecccCCCCccHHHHHHHHH-HHHHHHHH
Confidence 37788999999999999999885 66666543
No 66
>PF13068 DUF3932: Protein of unknown function (DUF3932)
Probab=22.31 E-value=79 Score=19.40 Aligned_cols=20 Identities=10% Similarity=0.223 Sum_probs=14.2
Q ss_pred HHHHHHHHHHhcCCchhhHH
Q 031220 108 SRVLSQQMEYYSDDPNADRI 127 (163)
Q Consensus 108 ~~~l~~~~~~yn~~~~~dki 127 (163)
...|++++.+|-....+|.+
T Consensus 32 wttlkeliheytt~htn~tl 51 (81)
T PF13068_consen 32 WTTLKELIHEYTTSHTNQTL 51 (81)
T ss_pred hhHHHHHHHHHhccccccch
Confidence 57788888888766555544
No 67
>PF05542 DUF760: Protein of unknown function (DUF760); InterPro: IPR008479 This entry contains uncharacterised proteins.
Probab=22.20 E-value=75 Score=20.36 Aligned_cols=28 Identities=11% Similarity=0.176 Sum_probs=19.1
Q ss_pred hHHHHHHHh-HHHHHHHHHhcHHHHHhhh
Q 031220 125 DRINRIKGE-MSQETRSASESRLGVSEAQ 152 (163)
Q Consensus 125 dki~~i~~~-v~evk~im~~NI~kvle~l 152 (163)
+.+.++.+. =.||.++|.++|..++-.+
T Consensus 13 e~~~~l~~~~s~ev~e~m~~~v~~llG~l 41 (86)
T PF05542_consen 13 ERIQQLSEPASPEVLEAMKQHVSGLLGNL 41 (86)
T ss_pred HHHHHhhccCCHHHHHHHHHHHHHHHcCC
Confidence 344444443 3579999999999988644
No 68
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=22.19 E-value=2e+02 Score=21.85 Aligned_cols=49 Identities=18% Similarity=0.171 Sum_probs=36.2
Q ss_pred hhHHHHHHHHHH-hcCCchh-hHHHHHHHhHHHHHHHHHhcHHHHHhhhhc
Q 031220 106 EFSRVLSQQMEY-YSDDPNA-DRINRIKGEMSQETRSASESRLGVSEAQYG 154 (163)
Q Consensus 106 ~F~~~l~~~~~~-yn~~~~~-dki~~i~~~v~evk~im~~NI~kvle~l~R 154 (163)
.|...+..+-.- -+|+|-+ ..+.+++++|+++++.|.+-++.+.+++..
T Consensus 41 ~~~~~~~~i~~~a~~DdPyAD~~L~~iEe~i~~~~~~l~~~~~~l~~~l~~ 91 (217)
T PF08900_consen 41 GFASRLNRIWRDARQDDPYADWWLLRIEEKINEARQELQELIARLDALLAE 91 (217)
T ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 666666665432 2345545 567999999999999999999988777766
No 69
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=21.85 E-value=2.8e+02 Score=19.09 Aligned_cols=43 Identities=9% Similarity=0.182 Sum_probs=30.8
Q ss_pred hhHHHHHHHHHHhcCCc-----hhhHHHHHHHhHHHHHHHHHhcHHHH
Q 031220 106 EFSRVLSQQMEYYSDDP-----NADRINRIKGEMSQETRSASESRLGV 148 (163)
Q Consensus 106 ~F~~~l~~~~~~yn~~~-----~~dki~~i~~~v~evk~im~~NI~kv 148 (163)
.....++++=.+|+..- ....+..++.+|.++|+.+..=|+.+
T Consensus 72 ~L~~el~~l~~ry~t~LellGEK~E~veEL~~Dv~DlK~myr~Qi~~l 119 (120)
T PF12325_consen 72 ELEQELEELQQRYQTLLELLGEKSEEVEELRADVQDLKEMYREQIDQL 119 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34455666666776532 35788889999999999998887653
No 70
>PF11867 DUF3387: Domain of unknown function (DUF3387); InterPro: IPR021810 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with PF04851 from PFAM, PF04313 from PFAM.
Probab=21.79 E-value=2.1e+02 Score=23.11 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=15.3
Q ss_pred hhhHHHHHHHHHHhcCC
Q 031220 105 DEFSRVLSQQMEYYSDD 121 (163)
Q Consensus 105 ~~F~~~l~~~~~~yn~~ 121 (163)
..|+.-|.+++++||+.
T Consensus 197 ~~fsErLe~iI~~Y~~~ 213 (335)
T PF11867_consen 197 KKFSERLEEIIEKYNNR 213 (335)
T ss_pred HHHHHHHHHHHHHHHcc
Confidence 58999999999999885
No 71
>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=21.75 E-value=2.1e+02 Score=17.78 Aligned_cols=50 Identities=12% Similarity=0.095 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHhccCCC-CCCCeeEEEeCC-EEEEEE--EeCCEEEEEEecCCC
Q 031220 22 ATNASAIARQILDKIPG-NNDSHVSYSQDR-YIFHVK--RTDGLTVLCMADDTA 71 (163)
Q Consensus 22 ~~~~~~~~~~vl~~i~~-~~~~k~~~~~~~-~~~h~l--~~~~~~~~~itd~~~ 71 (163)
-.+|+.+...+-+++.+ +..-+..|+.++ ....-+ .++|-.|+|...+.+
T Consensus 25 ~~sfd~lL~~lt~~l~l~~~~Vr~lyt~~g~~~v~~~~~l~~g~~yVa~g~e~f 78 (80)
T cd01617 25 FKSFDALLDDLTEKVQLDPGAVRKLYTLDGGHRVSLLDELEDGGVYVASGREPF 78 (80)
T ss_pred hCCHHHHHHHHHHHhCCCCCcEEEEEcCCCCeEeccHHHhcCCCEEEEECCCCC
Confidence 47898888888888875 246688888877 555433 357899999876654
No 72
>PF00191 Annexin: Annexin; InterPro: IPR018502 The annexins (or lipocortins) are a family of proteins that bind to phospholipids in a calcium-dependent manner []. They are distributed ubiquitously in different tissues and cell types of higher and lower eukaryotes, including mammals, fish, birds, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Caenorhabditis elegans , Dictyostelium discoideum (Slime mold) and Neurospora crassa [, ]. Annexins are absent from yeasts and prokaryotes []. The plant annexins are somewhat distinct from those found in other taxa []. Most eukaryotic species have 1-20 annexin (ANX) genes. All annexins share a core domain made up of four similar repeats, each approximately 70 amino acids long []. Each individual annexin repeat (sometimes referred to as endonexin folds) is folded into five alpha-helices, and in turn are wound into a right-handed super-helix; they usually contain a characteristic 'type 2' motif for binding calcium ions with the sequence 'GxGT-[38 residues]-D/E'. Animal and fungal annexins also have variable amino-terminal domains. The core domains of most vertebrate annexins have been analysed by X-ray crystallography, revealing conservation of their secondary and tertiary structures despite only 45-55% amino-acid identity among individual members. The four repeats pack into a structure that resembles a flattened disc, with a slightly convex surface on which the Ca 2+ -binding loops are located and a concave surface at which the amino and carboxyl termini come into close apposition. Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. The famiy has been linked with inhibition of phospholipase activity, exocytosis and endoctyosis, signal transduction, organisation of the extracellular matrix, resistance to reactive oxygen species and DNA replication [].; GO: 0005509 calcium ion binding, 0005544 calcium-dependent phospholipid binding; PDB: 1N44_A 1BC1_A 2IE6_A 2H0M_A 1A8B_A 2H0K_A 1BCW_A 1BCZ_A 1N42_A 1BC0_A ....
Probab=21.73 E-value=67 Score=18.82 Aligned_cols=10 Identities=40% Similarity=0.697 Sum_probs=4.1
Q ss_pred HHHHHHHhhh
Q 031220 82 DIHQRFVKTY 91 (163)
Q Consensus 82 ~i~~~F~~~~ 91 (163)
.|.+.|...|
T Consensus 34 ~i~~~Y~~~~ 43 (66)
T PF00191_consen 34 AIKQAYKKKY 43 (66)
T ss_dssp HHHHHHHHHH
T ss_pred eeehhhhhhh
Confidence 3444444444
No 73
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=21.36 E-value=62 Score=23.49 Aligned_cols=32 Identities=19% Similarity=0.197 Sum_probs=25.3
Q ss_pred hHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCCC
Q 031220 125 DRINRIKGEMSQETRSASESRLGVSEAQYGGET 157 (163)
Q Consensus 125 dki~~i~~~v~evk~im~~NI~kvle~l~RGe~ 157 (163)
.....+++++++|+.-..+.|+.|.. |++-++
T Consensus 27 ~E~~~l~~EL~evk~~v~~~I~evD~-Le~~er 58 (159)
T PF05384_consen 27 QEYERLRKELEEVKEEVSEVIEEVDK-LEKRER 58 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH
Confidence 56778899999999999999998854 554443
No 74
>smart00335 ANX Annexin repeats.
Probab=21.27 E-value=76 Score=17.72 Aligned_cols=15 Identities=40% Similarity=0.784 Sum_probs=9.4
Q ss_pred HHHHHHHHHhhhccc
Q 031220 80 LEDIHQRFVKTYGRA 94 (163)
Q Consensus 80 L~~i~~~F~~~~~~~ 94 (163)
+..|...|...|+..
T Consensus 19 ~~~i~~~Y~~~~~~~ 33 (53)
T smart00335 19 LQAIKQAYKKRYGKD 33 (53)
T ss_pred HHHHHHHHHHHhCcc
Confidence 456677777666543
No 75
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=20.63 E-value=1.4e+02 Score=27.11 Aligned_cols=20 Identities=10% Similarity=0.195 Sum_probs=14.1
Q ss_pred CcccHHHHHHHHHHHHHhhh
Q 031220 72 GRRIPFAFLEDIHQRFVKTY 91 (163)
Q Consensus 72 ~~~~af~fL~~i~~~F~~~~ 91 (163)
+..-.++||.+--+.|+..|
T Consensus 533 ~~~E~l~lL~~a~~vlreeY 552 (717)
T PF10168_consen 533 SPQECLELLSQATKVLREEY 552 (717)
T ss_pred CCHHHHHHHHHHHHHHHHHH
Confidence 45567777777777777665
No 76
>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins.
Probab=20.48 E-value=52 Score=31.58 Aligned_cols=41 Identities=24% Similarity=0.615 Sum_probs=28.5
Q ss_pred CCeeEEE-----e-CCEEEE-EEEeCC-EEEEEEecCCCCcccHHHHHH
Q 031220 41 DSHVSYS-----Q-DRYIFH-VKRTDG-LTVLCMADDTAGRRIPFAFLE 81 (163)
Q Consensus 41 ~~k~~~~-----~-~~~~~h-~l~~~~-~~~~~itd~~~~~~~af~fL~ 81 (163)
.+|.+|. + +.|..+ |..++| ++.++++.+.-+..+.|.|++
T Consensus 53 ~~rksF~~yYLP~~nSyIIYEY~R~~G~~~~vvl~~~s~g~~V~YRFId 101 (1201)
T PF12128_consen 53 SGRKSFDDYYLPYSNSYIIYEYQREDGQLCCVVLSRKSDGRGVQYRFID 101 (1201)
T ss_pred chhhhHHHHcCCCCCceEEEeeeccCCceeEEEEeecCCCCceeeeecc
Confidence 3566664 2 567766 777778 666666657667788898887
No 77
>PF09537 DUF2383: Domain of unknown function (DUF2383); InterPro: IPR019052 This entry represents a functionally uncharacterised ferritin like domain.; PDB: 3FSE_B.
Probab=20.31 E-value=1.7e+02 Score=19.07 Aligned_cols=53 Identities=9% Similarity=0.102 Sum_probs=18.0
Q ss_pred hhHHHHHHHHHHhcCCch--hhHHHHHHHhHHHHHHHHHhcHHH-HHhhhhcCCCc
Q 031220 106 EFSRVLSQQMEYYSDDPN--ADRINRIKGEMSQETRSASESRLG-VSEAQYGGETS 158 (163)
Q Consensus 106 ~F~~~l~~~~~~yn~~~~--~dki~~i~~~v~evk~im~~NI~k-vle~l~RGe~~ 158 (163)
.+...|+..+..+...|. ..-.-.+.+-.-.++..+..+=+. +++.+.|||+.
T Consensus 45 ~~~~~L~~~i~~~Gg~p~~~gs~~g~~~r~~~~ik~~~~~~d~~aiL~~~~~gE~~ 100 (111)
T PF09537_consen 45 QHAEELQAEIQELGGEPEESGSFKGALHRAWMDIKSALGGDDDEAILEECERGEDM 100 (111)
T ss_dssp HHHHHHHHHHHHTT--H----HHCHHHH-TTTHHHHS-----H-------------
T ss_pred HHHHHHHHHHHHcCCCcCcccCHHHHHHHHHHHHHHHhcCCCccchhhhhhhhhhh
Confidence 444556666666654432 233345566666788877777554 88889999984
No 78
>PF08028 Acyl-CoA_dh_2: Acyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR013107 Acyl Co-A dehydrogenases (1.3.99.3 from EC) are enzymes that catalyse the first step in each cycle of beta-oxidation in mitochondion. Acyl-CoA dehydrogenases [, , ] catalyze the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD. Reoxidation of the flavin involves transfer of electrons to ETF (electron transfering flavoprotein). These enzymes are homodimers containing one molecule of FAD. The monomeric enzyme is folded into three domains of approximately equal size. The N-terminal and the C-terminal are mainly alpha-helices packed together, and the middle domain consists of two orthogonal beta-sheets. The flavin ring is buried in the crevise between two alpha-helical domains and the beta-sheet of one subunit, and the adenosine pyrophosphate moiety is stretched into the subunit junction with one formed by two C-terminal domains []. The C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3AFE_C 3AFF_A 2JBT_D 2JBS_C 2JBR_B 2RFQ_B 2OR0_B.
Probab=20.20 E-value=1.9e+02 Score=19.44 Aligned_cols=36 Identities=14% Similarity=0.130 Sum_probs=26.3
Q ss_pred hhHHHHHHHhHHHHHHHHHhcHHHHHhhhhcCCCcc
Q 031220 124 ADRINRIKGEMSQETRSASESRLGVSEAQYGGETSS 159 (163)
Q Consensus 124 ~dki~~i~~~v~evk~im~~NI~kvle~l~RGe~~~ 159 (163)
...+.+....++..+..+.++.+.+.+..++|+.++
T Consensus 41 q~~lgea~~~~~aa~~~l~~~~~~~~~~~~~g~~~~ 76 (134)
T PF08028_consen 41 QARLGEAAARLDAARALLYRAARRLWEAADAGEELT 76 (134)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCC
Confidence 357777888888888899999888887788888764
No 79
>cd07642 BAR_ASAP2 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP2 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2) is also known as DDEF2 (Development and Differentiation Enhancing Factor 2), AMAP2, centaurin beta-3, or PAG3. ASAP2 mediates the functions of Arf GTPases vial dual mechanisms: it exhibits GTPase activating protein (GAP) activity towards class I (Arf1) and II (Arf5) Arfs; and binds class III Arfs (GTP-Arf6) stably without GAP activity. It binds paxillin and is implicated in Fcgamma receptor-mediated phagocytosis in macrophages and in cell migration. ASAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, i
Probab=20.04 E-value=4.1e+02 Score=20.35 Aligned_cols=44 Identities=11% Similarity=0.239 Sum_probs=27.4
Q ss_pred hhhHHHHHHHHHH--hcCCch----hhHHHHHHHhHHHHHHHHHhcHHHH
Q 031220 105 DEFSRVLSQQMEY--YSDDPN----ADRINRIKGEMSQETRSASESRLGV 148 (163)
Q Consensus 105 ~~F~~~l~~~~~~--yn~~~~----~dki~~i~~~v~evk~im~~NI~kv 148 (163)
..|...|.++-.+ +++.+. -.+..+++.+|..-..+..+|+.++
T Consensus 40 ~~f~~~L~~LG~~~l~~dd~~~~~~l~kf~~~~~El~~l~~~L~~~~~~~ 89 (215)
T cd07642 40 EQYTQALEKFGSNCVCRDDPDLGSAFLKFSVFTKELTALFKNLVQNMNNI 89 (215)
T ss_pred HHHHHHHHHHhhcccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666666554 544432 2566777777777777777776654
Done!