Query 031403
Match_columns 160
No_of_seqs 113 out of 773
Neff 8.8
Searched_HMMs 46136
Date Fri Mar 29 13:36:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031403.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031403hhsearch_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 7.4E-51 1.6E-55 290.9 16.9 153 4-158 1-154 (217)
2 KOG0862 Synaptobrevin/VAMP-lik 100.0 7.4E-31 1.6E-35 191.5 16.0 150 5-156 1-161 (216)
3 KOG0861 SNARE protein YKT6, sy 99.9 5.9E-26 1.3E-30 160.1 14.8 150 4-158 1-166 (198)
4 PF13774 Longin: Regulated-SNA 99.9 5.5E-22 1.2E-26 127.8 11.0 81 31-112 1-82 (83)
5 COG5143 SNC1 Synaptobrevin/VAM 99.8 1.6E-18 3.5E-23 125.2 12.4 149 5-158 2-158 (190)
6 KOG0860 Synaptobrevin/VAMP-lik 98.8 8.7E-09 1.9E-13 68.9 4.5 34 124-158 25-58 (116)
7 PF00957 Synaptobrevin: Synapt 98.4 4.9E-07 1.1E-11 58.6 4.0 28 129-156 3-30 (89)
8 PF04086 SRP-alpha_N: Signal r 95.3 0.048 1E-06 42.4 5.7 64 29-94 5-70 (279)
9 PF09426 Nyv1_N: Vacuolar R-SN 95.2 0.033 7.1E-07 38.4 3.9 60 28-87 42-110 (141)
10 KOG0781 Signal recognition par 93.9 0.29 6.2E-06 41.1 7.1 86 7-94 4-95 (587)
11 PF04099 Sybindin: Sybindin-li 91.6 3.4 7.4E-05 28.9 9.8 75 43-119 65-141 (142)
12 PF01217 Clat_adaptor_s: Clath 91.6 3.3 7.2E-05 28.7 12.3 88 5-94 1-96 (141)
13 KOG0938 Adaptor complexes medi 90.9 6.2 0.00013 31.9 10.8 125 7-138 5-132 (446)
14 smart00096 UTG Uteroglobin. 85.0 3.1 6.8E-05 25.5 4.6 42 114-155 21-62 (69)
15 PF01099 Uteroglobin: Uteroglo 84.4 2 4.3E-05 26.0 3.7 44 112-155 17-60 (67)
16 cd00633 Secretoglobin Secretog 83.6 3.9 8.4E-05 24.7 4.7 44 112-155 17-60 (67)
17 PF04628 Sedlin_N: Sedlin, N-t 69.8 33 0.00071 23.5 8.7 84 10-93 1-106 (132)
18 PF03164 Mon1: Trafficking pro 67.9 31 0.00067 28.6 7.3 98 28-125 37-142 (415)
19 PF11675 DUF3271: Protein of u 66.0 26 0.00057 26.8 5.9 52 3-55 28-79 (249)
20 PRK11546 zraP zinc resistance 63.0 51 0.0011 23.2 6.9 57 80-146 50-106 (143)
21 PF12277 DUF3618: Protein of u 59.5 23 0.0005 19.9 3.7 25 131-155 5-29 (49)
22 COG5143 SNC1 Synaptobrevin/VAM 58.0 4.6 9.9E-05 29.8 0.7 28 130-157 95-122 (190)
23 PF01649 Ribosomal_S20p: Ribos 46.3 75 0.0016 20.1 4.9 24 137-160 45-68 (84)
24 KOG3369 Transport protein part 45.2 1.2E+02 0.0026 22.2 9.5 82 35-119 110-196 (199)
25 COG3917 NahD 2-hydroxychromene 43.3 24 0.00053 26.0 2.5 21 139-159 156-176 (203)
26 PHA01811 hypothetical protein 43.2 33 0.00072 20.6 2.6 19 43-61 4-22 (78)
27 KOG3230 Vacuolar assembly/sort 42.6 70 0.0015 23.9 4.8 18 137-154 134-151 (224)
28 PF03607 DCX: Doublecortin; I 42.4 36 0.00079 19.9 2.8 48 25-72 8-58 (60)
29 PRK00239 rpsT 30S ribosomal pr 42.3 42 0.00092 21.5 3.3 24 137-160 46-69 (88)
30 TIGR01478 STEVOR variant surfa 42.1 33 0.00071 27.1 3.2 21 129-149 103-123 (295)
31 PF13463 HTH_27: Winged helix 41.6 23 0.00051 20.6 1.9 30 130-159 20-49 (68)
32 PF13076 DUF3940: Protein of u 40.7 19 0.00041 19.3 1.2 12 149-160 7-18 (38)
33 PTZ00370 STEVOR; Provisional 39.6 38 0.00083 26.7 3.2 23 129-151 102-124 (296)
34 COG4051 Uncharacterized protei 39.0 1.1E+02 0.0025 22.4 5.3 29 13-41 3-33 (202)
35 CHL00102 rps20 ribosomal prote 38.9 1.1E+02 0.0024 19.9 5.1 25 136-160 52-76 (93)
36 TIGR00029 S20 ribosomal protei 38.0 63 0.0014 20.7 3.6 24 137-160 46-69 (87)
37 COG5122 TRS23 Transport protei 37.8 1.3E+02 0.0028 20.4 9.6 82 34-118 45-131 (134)
38 KOG2740 Clathrin-associated pr 36.0 1.2E+02 0.0025 25.0 5.5 36 59-94 61-96 (418)
39 PF04079 DUF387: Putative tran 34.6 26 0.00057 25.0 1.6 25 135-159 99-124 (159)
40 cd01617 DCX Ubiquitin-like dom 33.8 92 0.002 19.3 3.8 49 25-73 25-78 (80)
41 PF12325 TMF_TATA_bd: TATA ele 33.1 78 0.0017 21.5 3.6 26 128-153 95-120 (120)
42 KOG3368 Transport protein part 32.6 1.7E+02 0.0038 20.4 9.5 54 32-87 45-102 (140)
43 PF05527 DUF758: Domain of unk 32.5 2.1E+02 0.0045 21.2 6.2 43 114-157 143-185 (186)
44 cd07634 BAR_GAP10-like The Bin 32.3 2.2E+02 0.0047 21.4 6.2 72 78-154 14-95 (207)
45 PF02520 DUF148: Domain of unk 31.9 1.5E+02 0.0033 19.4 7.2 61 84-155 2-62 (113)
46 PF11281 DUF3083: Protein of u 31.7 2.6E+02 0.0056 22.3 6.6 72 9-92 211-292 (316)
47 PF10504 DUF2452: Protein of u 31.1 43 0.00092 24.0 2.1 55 28-82 64-125 (159)
48 COG0268 RpsT Ribosomal protein 29.8 1.6E+02 0.0034 19.0 5.3 21 140-160 49-69 (88)
49 PF10112 Halogen_Hydrol: 5-bro 28.6 1.4E+02 0.003 21.8 4.6 43 112-154 136-181 (199)
50 PF12579 DUF3755: Protein of u 28.5 45 0.00097 17.5 1.4 18 129-146 17-34 (35)
51 TIGR00281 segregation and cond 28.1 42 0.0009 24.7 1.7 25 135-159 104-129 (186)
52 PF05542 DUF760: Protein of un 27.6 60 0.0013 20.6 2.2 26 130-155 14-40 (86)
53 PF07897 DUF1675: Protein of u 27.5 68 0.0015 25.3 2.9 26 49-74 237-262 (284)
54 PF08506 Cse1: Cse1; InterPro 27.2 68 0.0015 26.2 3.0 45 69-126 222-266 (370)
55 PF08900 DUF1845: Domain of un 27.0 2.7E+02 0.006 20.9 6.3 45 108-152 40-85 (217)
56 TIGR00828 EIID-AGA PTS system, 26.9 2.5E+02 0.0054 22.0 5.9 46 71-126 22-67 (271)
57 PF06008 Laminin_I: Laminin Do 26.8 2.9E+02 0.0063 21.1 6.7 15 77-91 157-171 (264)
58 cd00223 TOPRIM_TopoIIB_SPO TOP 25.6 91 0.002 22.0 3.1 26 64-89 25-50 (160)
59 cd07642 BAR_ASAP2 The Bin/Amph 25.5 3E+02 0.0065 20.8 6.0 47 108-154 40-91 (215)
60 cd07636 BAR_GRAF The Bin/Amphi 25.0 3E+02 0.0065 20.6 6.2 47 108-154 40-95 (207)
61 PF13228 DUF4037: Domain of un 24.8 2E+02 0.0044 18.7 5.3 44 108-156 23-66 (100)
62 KOG0972 Huntingtin interacting 24.8 1.8E+02 0.0039 23.2 4.7 68 77-147 245-326 (384)
63 PTZ00032 60S ribosomal protein 24.5 1.3E+02 0.0029 22.5 3.7 13 44-56 182-194 (211)
64 PRK09855 PTS system N-acetylga 24.5 2.6E+02 0.0056 21.8 5.6 45 72-126 25-69 (263)
65 COG2957 Peptidylarginine deimi 24.4 1.2E+02 0.0026 24.5 3.7 47 10-60 289-341 (346)
66 COG3355 Predicted transcriptio 24.3 1.3E+02 0.0028 20.7 3.5 43 112-159 31-73 (126)
67 PRK14891 50S ribosomal protein 24.2 90 0.0019 21.6 2.6 44 37-82 12-55 (131)
68 PRK00807 50S ribosomal protein 24.1 1.2E+02 0.0025 17.4 2.8 22 38-59 10-31 (52)
69 PF07792 Afi1: Docking domain 24.1 2.6E+02 0.0057 19.6 5.8 50 5-60 1-58 (145)
70 cd03164 CD53_like_LEL Tetraspa 24.0 1.4E+02 0.0031 18.1 3.5 9 113-121 14-22 (86)
71 cd07604 BAR_ASAPs The Bin/Amph 23.5 3.1E+02 0.0066 20.6 5.7 47 108-154 40-91 (215)
72 PF13747 DUF4164: Domain of un 23.3 2.1E+02 0.0046 18.2 4.2 28 128-155 62-89 (89)
73 cd03161 TM4SF2_6_like_LEL Tetr 22.9 1.1E+02 0.0023 19.3 2.8 14 110-123 11-24 (104)
74 PRK11103 PTS system mannose-sp 22.9 3E+02 0.0066 21.7 5.7 45 72-126 33-77 (282)
75 PF13851 GAS: Growth-arrest sp 22.7 2.4E+02 0.0053 20.9 5.0 38 110-148 7-46 (201)
76 TIGR03044 PS_II_psb27 photosys 22.4 2.8E+02 0.0061 19.4 7.4 66 74-141 60-128 (135)
77 PF12802 MarR_2: MarR family; 22.3 79 0.0017 17.8 1.9 30 130-159 23-52 (62)
78 PF11074 DUF2779: Domain of un 22.0 2.7E+02 0.0059 19.1 5.8 81 52-147 27-117 (130)
79 PF09114 MotA_activ: Transcrip 21.4 59 0.0013 21.1 1.2 22 139-160 43-64 (96)
80 PF11598 COMP: Cartilage oligo 21.4 1.7E+02 0.0036 16.3 3.8 22 130-151 9-30 (45)
81 PF03613 EIID-AGA: PTS system 21.2 2.9E+02 0.0064 21.5 5.3 45 71-126 22-66 (264)
82 cd03163 TM4SF8_like_LEL Tetras 21.2 1.6E+02 0.0034 18.7 3.4 12 111-122 13-24 (105)
83 PHA01351 putative minor struct 21.1 6.4E+02 0.014 23.0 8.2 77 75-159 419-498 (1070)
84 PF05073 Baculo_p24: Baculovir 21.0 3.1E+02 0.0067 20.1 5.0 22 128-149 107-128 (182)
85 cd00472 Ribosomal_L24e_L24 Rib 20.8 1.3E+02 0.0029 17.3 2.6 24 37-60 11-34 (54)
86 COG3716 ManZ Phosphotransferas 20.8 3.3E+02 0.0071 21.4 5.4 44 73-126 28-71 (269)
87 cd07603 BAR_ACAPs The Bin/Amph 20.6 3.6E+02 0.0078 19.9 5.9 46 108-153 40-88 (200)
88 PF12641 Flavodoxin_3: Flavodo 20.4 3E+02 0.0064 19.6 4.9 65 19-87 2-67 (160)
89 PF08360 TetR_C_5: QacR-like p 20.1 1.6E+02 0.0034 20.2 3.3 23 135-157 56-78 (131)
No 1
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=7.4e-51 Score=290.95 Aligned_cols=153 Identities=68% Similarity=1.017 Sum_probs=147.4
Q ss_pred cceEEEEEEeCCeeEEEEeccCCCHHHHHHHHhcCCCCC-CCeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHH
Q 031403 4 KSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFL 82 (160)
Q Consensus 4 ~~I~Ya~Iar~~~iLae~~~~~~n~~~~~~~vL~~i~~~-~~k~s~~~~~~~~h~l~~~~l~~~citd~~~~~~~af~fL 82 (160)
|+|+|+.||||++|||||++.+|||..++..+|+++|++ ++|.+|.+|+|+|||+.+||++|+||+|++.++++||.||
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 789999999999999999999999999999999999998 6799999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcccc
Q 031403 83 ERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVGMLCLF 158 (160)
Q Consensus 83 ~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL~Rg~~ 158 (160)
++|+++|.+.|+ ..++++.+|++|++|++.|++.|++|.++|. .|++.+++.|++|||+||.+|||++|+||-+
T Consensus 81 e~Ik~~F~k~YG-~~a~ta~AysmN~EFs~vL~qqm~y~s~~p~-id~lskvkaqv~evk~vM~eNIekvldRGek 154 (217)
T KOG0859|consen 81 ERIKEDFKKRYG-GGAHTAVAYSMNKEFSSVLKQQMQYCSEHPE-ISKLAKVKAQVTEVKGVMMENIEKVLDRGEK 154 (217)
T ss_pred HHHHHHHHHHhc-cchhHHHHhHhHHHHHHHHHHHHHHHHcCcc-hhHHHHHHHHHHHHHHHHHHHHHHHHhccCe
Confidence 999999999995 5578899999999999999999999999997 6999999999999999999999999999954
No 2
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=7.4e-31 Score=191.50 Aligned_cols=150 Identities=23% Similarity=0.410 Sum_probs=134.7
Q ss_pred ceEEEEEEeC--CeeEEEEec---cCCC----HHHHHHHHhcCCCCC-CCeeEEEeCCeEEEEEEeCCEEEEEEecCCCC
Q 031403 5 SLIYAFVARG--NVVLAEYTE---FSGN----FNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSG 74 (160)
Q Consensus 5 ~I~Ya~Iar~--~~iLae~~~---~~~n----~~~~~~~vL~~i~~~-~~k~s~~~~~~~~h~l~~~~l~~~citd~~~~ 74 (160)
||++++|+|. +.|||...+ .+++ +.+.++.+++++.+. ++|+|.+.++|.|||++++|++|+|+||.+||
T Consensus 1 mi~~T~I~RV~DGLPLa~s~d~~e~~~~s~~e~r~q~K~L~kkLs~~s~~r~Sietg~f~fHfli~~~Vcylvicd~~yP 80 (216)
T KOG0862|consen 1 MILLTLIARVRDGLPLAASTDDNEQSGDSLLEYRQQAKSLFKKLSQQSPTRCSIETGPFVFHFLIESGVCYLVICDKSYP 80 (216)
T ss_pred CceeEEEEEecCCcccccccCcccCCCchHHHHHHHHHHHHHhccCCCCcccccccCCeEEEEEecCCEEEEEEecCCCc
Confidence 6899999994 699997644 2343 467899999999987 89999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHhhhCCCCCC-CCCCCccchhhHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 031403 75 RQIPMAFLERVKDEFVSKYGGGKAA-TAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVG 153 (160)
Q Consensus 75 ~~~af~fL~~i~~~F~~~~~~~~~~-~~~~~~l~~~f~~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL 153 (160)
+.+||.||+++.++|.+.++.+... .++||++ -+|++.|++.-+.|| |++..+.+.++..++.+|+.||.+||+.+|
T Consensus 81 ~kLAF~YLedL~~EF~~~~~~~~~~~~~RPY~F-ieFD~~IQk~Kk~yn-d~r~~~n~~~~n~el~~v~~im~~niedvl 158 (216)
T KOG0862|consen 81 RKLAFSYLEDLAQEFDKSYGKNIIQPASRPYAF-IEFDTFIQKTKKRYN-DTRSQRNLLKLNQELQDVQRIMVENLEDVL 158 (216)
T ss_pred HHHHHHHHHHHHHHHHHhcccccCCccCCCeeE-EehhHHHHHHHHHhc-CcHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 9999999999999999999644333 6789999 899999999999996 777679999999999999999999999999
Q ss_pred hcc
Q 031403 154 MLC 156 (160)
Q Consensus 154 ~Rg 156 (160)
.||
T Consensus 159 ~rg 161 (216)
T KOG0862|consen 159 QRG 161 (216)
T ss_pred hhc
Confidence 998
No 3
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.94 E-value=5.9e-26 Score=160.06 Aligned_cols=150 Identities=19% Similarity=0.241 Sum_probs=123.2
Q ss_pred cceEEEEEEeCC----eeEEEEeccC-------CC---H-HHHHHHHhcCCCCCCCeeEEEeCCeEEEEEEe-CCEEEEE
Q 031403 4 KSLIYAFVARGN----VVLAEYTEFS-------GN---F-NSIAYQCLQKLPASNNKFTYNCDAHTFNYLVD-NGYTYCV 67 (160)
Q Consensus 4 ~~I~Ya~Iar~~----~iLae~~~~~-------~n---~-~~~~~~vL~~i~~~~~k~s~~~~~~~~h~l~~-~~l~~~c 67 (160)
|.|++..|.+.. .+|+.-++-+ ++ | .-+++.+.+|.+|+ +|++++++.|.+|.... +|++++|
T Consensus 1 Mki~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F~sktvaeRt~~g-~rqsvk~~~Y~~h~yvrndgL~~V~ 79 (198)
T KOG0861|consen 1 MKIYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTFISKTVAERTGPG-QRQSVKHEEYLVHVYVRNDGLCGVL 79 (198)
T ss_pred CceEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHHHHHHHHHhcCcc-cccccccceeEEEEEEecCCeeEEE
Confidence 667888888752 4666433311 23 3 33778899999994 99999999999997655 6999999
Q ss_pred EecCCCCcccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHH
Q 031403 68 VADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMME 147 (160)
Q Consensus 68 itd~~~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~ 147 (160)
++|.+||.|+||.+|+++.++|....++.+|....+..+ --|.|...+..| +||.+.|+|.++|++++|+|.||++
T Consensus 80 ~~D~eYP~rvA~tLL~kvld~~~~k~~~~~W~~~~~~~~---~~~~L~~~l~ky-qdP~ead~l~kvQ~EldETKiiLhk 155 (198)
T KOG0861|consen 80 IADDEYPVRVAFTLLNKVLDEFTTKVPATQWPVGETADL---SYPYLDTLLSKY-QDPAEADPLLKVQNELDETKIILHK 155 (198)
T ss_pred EecCcCchhHHHHHHHHHHHHHhhcCcccccCcCCCcCC---CchhHHHHHHHh-cChhhhChHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999988877888884433322 237899999999 8999999999999999999999999
Q ss_pred hHHHHHhcccc
Q 031403 148 NIEKVGMLCLF 158 (160)
Q Consensus 148 Nid~iL~Rg~~ 158 (160)
+|+.+|+||=+
T Consensus 156 TiesVL~RgEK 166 (198)
T KOG0861|consen 156 TIESVLERGEK 166 (198)
T ss_pred HHHHHHHccch
Confidence 99999999954
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=5.5e-22 Score=127.76 Aligned_cols=81 Identities=33% Similarity=0.705 Sum_probs=73.5
Q ss_pred HHHHHhcCCCCCC-CeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchh
Q 031403 31 IAYQCLQKLPASN-NKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKE 109 (160)
Q Consensus 31 ~~~~vL~~i~~~~-~k~s~~~~~~~~h~l~~~~l~~~citd~~~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~ 109 (160)
+|+.||+++++.+ +|.+++.++|.||+++++|++|+||||++||+++||.||++|+++|.++++.+++..+.|+++ .+
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 5889999999765 899999999999999999999999999999999999999999999999996578888889999 88
Q ss_pred hHH
Q 031403 110 FGP 112 (160)
Q Consensus 110 f~~ 112 (160)
|++
T Consensus 80 F~~ 82 (83)
T PF13774_consen 80 FDS 82 (83)
T ss_dssp HHH
T ss_pred cCC
Confidence 876
No 5
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=99.80 E-value=1.6e-18 Score=125.16 Aligned_cols=149 Identities=19% Similarity=0.238 Sum_probs=112.6
Q ss_pred ceEEEEEEeCC--eeEEE-EeccCCCH--HHHHHHHhcCCCCC-CCeeEEEeCCeEEEEEEe-CCEEEEEEecCCCCccc
Q 031403 5 SLIYAFVARGN--VVLAE-YTEFSGNF--NSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVD-NGYTYCVVADESSGRQI 77 (160)
Q Consensus 5 ~I~Ya~Iar~~--~iLae-~~~~~~n~--~~~~~~vL~~i~~~-~~k~s~~~~~~~~h~l~~-~~l~~~citd~~~~~~~ 77 (160)
.++|..+..+. .+|++ ++..+..| ...+..+|.++.|- .++.+.+.++|.|||+.. +|++|+|+|+++||.++
T Consensus 2 ~s~~~~~~~~~~~~~~~~~~s~~~~~ff~~~~v~~~l~~~~~~~a~~~~ies~~~~~~~~~~s~gi~y~~~~~~e~p~~l 81 (190)
T COG5143 2 ASISLFRVKGEPLRTLSDAESLSSFSFFHRSKVKEVLRFLSKTSASRASIESGDYFFHYLKMSSGIVYVPISDKEYPNKL 81 (190)
T ss_pred ceEEEEeecCCcceeeccccccCcccccccchHHHHHHHhcccccchhccccCceEEEEEecCCCceeEEecccccchhh
Confidence 45666666663 45553 33323233 34667777777664 457888889999999865 59999999999999999
Q ss_pred HHHHHHHHHHHHHhhhCCCCCCCCC-CCccchhhHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcc
Q 031403 78 PMAFLERVKDEFVSKYGGGKAATAP-ANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVGMLC 156 (160)
Q Consensus 78 af~fL~~i~~~F~~~~~~~~~~~~~-~~~l~~~f~~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL~Rg 156 (160)
||..|+++..+|........|.... ++.+ .+|++.+++ .| ++|...|++.+++.+++|||.+|++||+++|+||
T Consensus 82 a~~~~~~~~~~~~~s~~~~~~~d~~~~~~~-~~~d~~~e~---~y-~d~s~~D~~d~l~~el~e~K~~l~k~ie~~l~R~ 156 (190)
T COG5143 82 AYGYLNSIATEFLKSSALEQLIDDTVGIMR-VNIDKVIEK---GY-RDPSIQDKLDQLQQELEETKRVLNKNIEKVLYRD 156 (190)
T ss_pred hhHHHHhhccHhhhhhhHhhcccCccchhh-hhHHHHHHh---hc-CCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 9999999999998877544444332 3333 567777665 26 6888889999999999999999999999999999
Q ss_pred cc
Q 031403 157 LF 158 (160)
Q Consensus 157 ~~ 158 (160)
.+
T Consensus 157 ek 158 (190)
T COG5143 157 EK 158 (190)
T ss_pred ch
Confidence 75
No 6
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.79 E-value=8.7e-09 Score=68.94 Aligned_cols=34 Identities=38% Similarity=0.362 Sum_probs=30.4
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcccc
Q 031403 124 HPEEISKLAKVKAQVSEVKGVMMENIEKVGMLCLF 158 (160)
Q Consensus 124 ~p~~~dki~~i~~~v~evk~im~~Nid~iL~Rg~~ 158 (160)
++.+ +++.++|+|++||++||++||+|+||||-+
T Consensus 25 ~~~~-~k~~~tq~QvdeVv~IMr~NV~KVlER~ek 58 (116)
T KOG0860|consen 25 NTAN-DKLQQTQAQVDEVVDIMRENVEKVLERGEK 58 (116)
T ss_pred chhh-HHHHHHHHHHHHHHHHHHHhHHHHHHhcch
Confidence 4434 999999999999999999999999999954
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=98.37 E-value=4.9e-07 Score=58.65 Aligned_cols=28 Identities=43% Similarity=0.535 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHhcc
Q 031403 129 SKLAKVKAQVSEVKGVMMENIEKVGMLC 156 (160)
Q Consensus 129 dki~~i~~~v~evk~im~~Nid~iL~Rg 156 (160)
|++.++++++++|+++|.+||+++++||
T Consensus 3 dkl~~i~~~v~~v~~im~~Ni~~ll~Rg 30 (89)
T PF00957_consen 3 DKLEQIQEQVEEVKNIMRENIDKLLERG 30 (89)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 8999999999999999999999999998
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=95.30 E-value=0.048 Score=42.44 Aligned_cols=64 Identities=25% Similarity=0.377 Sum_probs=39.9
Q ss_pred HHHHHHHhcCCCCCCCeeEEEeCCeEEEEEEeC--CEEEEEEecCCCCcccHHHHHHHHHHHHHhhhC
Q 031403 29 NSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDN--GYTYCVVADESSGRQIPMAFLERVKDEFVSKYG 94 (160)
Q Consensus 29 ~~~~~~vL~~i~~~~~k~s~~~~~~~~h~l~~~--~l~~~citd~~~~~~~af~fL~~i~~~F~~~~~ 94 (160)
..+++.||-.=.. ...+|.+++|..+|...| +|+||+|=..-..-.-.=.||+.|+..|...|.
T Consensus 5 n~LI~~vlleeR~--~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~ 70 (279)
T PF04086_consen 5 NALIRDVLLEERS--GNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYK 70 (279)
T ss_dssp HHHHHHTGGG---------------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTH
T ss_pred HHHHHHhheeecc--CCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHh
Confidence 4566666543222 445689999999998765 699999988887766666899999999999994
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=95.20 E-value=0.033 Score=38.40 Aligned_cols=60 Identities=17% Similarity=0.299 Sum_probs=38.6
Q ss_pred HHHHH-HHHhcCCCCC-C---CeeEEE-eCCeEEEEEE---eCCEEEEEEecCCCCcccHHHHHHHHHH
Q 031403 28 FNSIA-YQCLQKLPAS-N---NKFTYN-CDAHTFNYLV---DNGYTYCVVADESSGRQIPMAFLERVKD 87 (160)
Q Consensus 28 ~~~~~-~~vL~~i~~~-~---~k~s~~-~~~~~~h~l~---~~~l~~~citd~~~~~~~af~fL~~i~~ 87 (160)
|-.++ ..|+.++-|- + +|+|.. .+||-++|.. +++-+++|+|..+.|+-+|...|.+++.
T Consensus 42 FH~Li~dmVlPkVV~v~GNKVTK~S~~lIDGyDCYYTT~~~d~~~vlVCFt~~~vPKILPiRlLSeLK~ 110 (141)
T PF09426_consen 42 FHKLIHDMVLPKVVPVEGNKVTKMSMHLIDGYDCYYTTEDNDDNKVLVCFTRVDVPKILPIRLLSELKG 110 (141)
T ss_dssp HHHHHHHTTGGG----SS-SSEE--S--SSSEEEEE---SS-TTEEEEEEEETTS-SSHHHHHHHHHTT
T ss_pred HHHHHhhccccceEEccCCeEEEEEeecccccceeeecccCCCCeEEEEEEecCCcceecHHHHHhhcc
Confidence 43333 4467776653 2 455555 5899999987 4689999999999999999999999864
No 10
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.90 E-value=0.29 Score=41.13 Aligned_cols=86 Identities=23% Similarity=0.334 Sum_probs=63.8
Q ss_pred EEEEEEeCCeeEEEEeccCCCH----HHHHHHHhcCCCCCCCeeEEEeCCeEEEEEEe--CCEEEEEEecCCCCcccHHH
Q 031403 7 IYAFVARGNVVLAEYTEFSGNF----NSIAYQCLQKLPASNNKFTYNCDAHTFNYLVD--NGYTYCVVADESSGRQIPMA 80 (160)
Q Consensus 7 ~Ya~Iar~~~iLae~~~~~~n~----~~~~~~vL~~i~~~~~k~s~~~~~~~~h~l~~--~~l~~~citd~~~~~~~af~ 80 (160)
.++.+.+|..||+.|....-+| ..+++.+|-.=. .+-.+++.+.|+.-|-.+ -+++|+|+-..-..-.-+-.
T Consensus 4 ~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~er--~~~~~~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~yv~~ 81 (587)
T KOG0781|consen 4 QFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLSER--GGVNSFTFEAYTLKYQLDNQYSLVFVVVFQKILTLTYVDK 81 (587)
T ss_pred eeeeecCCcEEEEEecccchhccchHHHHHHHHHHHhh--cCcccCchhheeEeeeecCCccEEEEEEEeccchhhhHHH
Confidence 5788889999999998755554 445555443311 222337888888877654 47999999988888788889
Q ss_pred HHHHHHHHHHhhhC
Q 031403 81 FLERVKDEFVSKYG 94 (160)
Q Consensus 81 fL~~i~~~F~~~~~ 94 (160)
+|+++.+.|+..|.
T Consensus 82 ll~~v~~~f~e~~~ 95 (587)
T KOG0781|consen 82 LLNDVLNLFREKYD 95 (587)
T ss_pred HHHHHHHHHHHHhc
Confidence 99999999999884
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=91.65 E-value=3.4 Score=28.93 Aligned_cols=75 Identities=11% Similarity=0.158 Sum_probs=41.7
Q ss_pred CCeeEEEeCCeEEEEEE-eCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhCCCCC-CCCCCCccchhhHHHHHHHHH
Q 031403 43 NNKFTYNCDAHTFNYLV-DNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKA-ATAPANGLNKEFGPKLKELMQ 119 (160)
Q Consensus 43 ~~k~s~~~~~~~~h~l~-~~~l~~~citd~~~~~~~af~fL~~i~~~F~~~~~~~~~-~~~~~~~l~~~f~~~l~~~m~ 119 (160)
..-.+++-+.|..|++. -.|+-|+++||+..+. ..-.+++.+.+-|..-...+-. .-..|-. ...|+..|.++++
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 35678888999999885 5899999999999863 3444555555555553322211 1112222 2456666665553
No 12
>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=91.58 E-value=3.3 Score=28.66 Aligned_cols=88 Identities=17% Similarity=0.269 Sum_probs=61.6
Q ss_pred ceEEEEEEe--CCeeEEEEecc-CC-----CHHHHHHHHhcCCCCCCCeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcc
Q 031403 5 SLIYAFVAR--GNVVLAEYTEF-SG-----NFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQ 76 (160)
Q Consensus 5 ~I~Ya~Iar--~~~iLae~~~~-~~-----n~~~~~~~vL~~i~~~~~k~s~~~~~~~~h~l~~~~l~~~citd~~~~~~ 76 (160)
||...+|.. |.++++-|-.. +. -++...+.+..+-+. .--.+..+++.+-|..-+++.++++++.+...-
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~~~--~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel 78 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRNSK--QSPIFEHDNYRIVYKRYSDLYFVVVGDENENEL 78 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSSSS--STSEEEETTEEEEEEEETTEEEEEEESSTSBHH
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhcccc--cceeeecccceeeeEeeccEEEEEEeecccchH
Confidence 455555655 45777766432 21 144444455544322 223466888888888889999999999999999
Q ss_pred cHHHHHHHHHHHHHhhhC
Q 031403 77 IPMAFLERVKDEFVSKYG 94 (160)
Q Consensus 77 ~af~fL~~i~~~F~~~~~ 94 (160)
..+.||..+-+.+..-++
T Consensus 79 ~~~e~l~~~v~~l~~~~~ 96 (141)
T PF01217_consen 79 LLLEFLHRLVEVLDDYFG 96 (141)
T ss_dssp HHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHhhhhhhhhhc
Confidence 999999999999888773
No 13
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.94 E-value=6.2 Score=31.86 Aligned_cols=125 Identities=14% Similarity=0.259 Sum_probs=76.8
Q ss_pred EEEEEEeCCeeEEEE-e-ccCCCHHHHHHH-HhcCCCCCCCeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHH
Q 031403 7 IYAFVARGNVVLAEY-T-EFSGNFNSIAYQ-CLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLE 83 (160)
Q Consensus 7 ~Ya~Iar~~~iLae~-~-~~~~n~~~~~~~-vL~~i~~~~~k~s~~~~~~~~h~l~~~~l~~~citd~~~~~~~af~fL~ 83 (160)
+|..=.||.++++-. . +-.++..++-+- ++....- .--..+.++.+||+...+++=.++||.........|.||.
T Consensus 5 lfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~d~--r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl~ 82 (446)
T KOG0938|consen 5 LFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNLDV--RSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFLY 82 (446)
T ss_pred EEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhcccc--CCCeeEecceeEEEEeeccEEEEEEecCCCchhhHHHHHH
Confidence 344456888888854 3 345666554443 3333221 1124467899999999999999999999999999999999
Q ss_pred HHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChHHHHHHHHHHHHH
Q 031403 84 RVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQV 138 (160)
Q Consensus 84 ~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~~~dki~~i~~~v 138 (160)
++-+-+..-++ .....+....+-- .-..|.++|. | .-|.+ .....++.++
T Consensus 83 kl~avm~aYfg-k~~Eeaiknnf~l-I~ElLDemld-~-G~pqn-te~~al~~~i 132 (446)
T KOG0938|consen 83 KLDAVMNAYFG-KDREEAIKNNFVL-IYELLDEMLD-F-GIPQN-TEPNALKAQI 132 (446)
T ss_pred HHHHHHHHHhc-ccchhhhhhceEe-HHHHHHHHHh-c-CCCcc-CChhHHHhhh
Confidence 99999888774 3222333322211 1134666666 3 35543 2333344433
No 14
>smart00096 UTG Uteroglobin.
Probab=84.97 E-value=3.1 Score=25.51 Aligned_cols=42 Identities=17% Similarity=0.141 Sum_probs=32.3
Q ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhc
Q 031403 114 LKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVGML 155 (160)
Q Consensus 114 l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL~R 155 (160)
...-++.||.+|...+...++++-+|....-=..||-++|++
T Consensus 21 Y~~~l~~y~~~~~~~ea~~~lK~cvD~L~~~~k~~i~~ll~k 62 (69)
T smart00096 21 YEASLKQFKPDPDMLEAGRQLKKLVDTLPQETRENILKLTEK 62 (69)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 445568898888888999999999998766666666666654
No 15
>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=84.42 E-value=2 Score=26.02 Aligned_cols=44 Identities=25% Similarity=0.206 Sum_probs=33.0
Q ss_pred HHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhc
Q 031403 112 PKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVGML 155 (160)
Q Consensus 112 ~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL~R 155 (160)
+..+..++.||.+|.......++++-++....-=..||.++|++
T Consensus 17 ~~Y~~~l~~y~~~~~~~~A~~~lK~C~d~ls~e~~~~i~~~l~~ 60 (67)
T PF01099_consen 17 EEYKESLQKYNPPPEAVEAKLELKQCVDKLSNETRENILKLLEK 60 (67)
T ss_dssp HHHHHHHHCC---HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 45677788998888777999999999998888888888888765
No 16
>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=83.63 E-value=3.9 Score=24.66 Aligned_cols=44 Identities=25% Similarity=0.178 Sum_probs=34.5
Q ss_pred HHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhc
Q 031403 112 PKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVGML 155 (160)
Q Consensus 112 ~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL~R 155 (160)
..+..-++.||.+|...+...++|+-+++...-=..|+-++|+.
T Consensus 17 ~~y~~~L~~f~~~~~~~~A~~~lK~C~d~~~~e~k~~~~~~m~~ 60 (67)
T cd00633 17 EEYKAELEKFNATPEAVEAKEKLKQCVDEQSLETKENIAKLLEK 60 (67)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCHhHHHHHHHHHHH
Confidence 35667778999888888999999999998866666677666653
No 17
>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=69.80 E-value=33 Score=23.50 Aligned_cols=84 Identities=13% Similarity=0.175 Sum_probs=49.5
Q ss_pred EEEeCCeeEEEEec--cCCC--------HHH---HHHHHhcCCC-C-C-C--CeeEEEeCCeEEE-EEEeCCEEEEEEec
Q 031403 10 FVARGNVVLAEYTE--FSGN--------FNS---IAYQCLQKLP-A-S-N--NKFTYNCDAHTFN-YLVDNGYTYCVVAD 70 (160)
Q Consensus 10 ~Iar~~~iLae~~~--~~~n--------~~~---~~~~vL~~i~-~-~-~--~k~s~~~~~~~~h-~l~~~~l~~~citd 70 (160)
.|++.+.+|-+++- .+.. +.- .+..+++... . . + =+..+..+++..+ |+...++=++.+++
T Consensus 1 IIg~~n~PLy~~~~~~~~~~~~~~~~~l~~~~~h~sLD~iee~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~ 80 (132)
T PF04628_consen 1 IIGPNNNPLYIRSFPSEKESSSSDARHLYQFIAHSSLDVIEEKLWKSSSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHD 80 (132)
T ss_dssp EE-TTS-EEEEEEE--ST-CGHHHHHHHHHHHHHHHHHHHHHCCHCSSSCSEEEEEEEETTEEEEEEETTT--EEEEEEC
T ss_pred CCCCCCcceEEEecCCCcccccchHHHHHHHHHHHHHHHHHHHHhhcccccccCceehhhhHHHHhhhccCceeEEEEEe
Confidence 37788888887652 2221 222 3334444322 2 1 1 2566677887755 77778888888888
Q ss_pred ---CCCCcccHHHHHHHHHHHHHhhh
Q 031403 71 ---ESSGRQIPMAFLERVKDEFVSKY 93 (160)
Q Consensus 71 ---~~~~~~~af~fL~~i~~~F~~~~ 93 (160)
........-.|+.+++..|.+..
T Consensus 81 ~~~~~~~d~~ik~fF~~vh~~Y~~~~ 106 (132)
T PF04628_consen 81 MSDNSIRDEDIKQFFKEVHELYVKAL 106 (132)
T ss_dssp GGG-S--HHHHHHHHHHHHHHHHHHH
T ss_pred cccCCcchHHHHHHHHHHHHHHHHHc
Confidence 56667778899999999999877
No 18
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=67.89 E-value=31 Score=28.62 Aligned_cols=98 Identities=10% Similarity=0.100 Sum_probs=66.9
Q ss_pred HHHHHHHHhcCCCCC-CCeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhCCCC----CCCCC
Q 031403 28 FNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGK----AATAP 102 (160)
Q Consensus 28 ~~~~~~~vL~~i~~~-~~k~s~~~~~~~~h~l~~~~l~~~citd~~~~~~~af~fL~~i~~~F~~~~~~~~----~~~~~ 102 (160)
+..+.+.++.-.... +.-.++..++..|.|+..+.+.++||+..+-+...-..-|+-+........+... .....
T Consensus 37 ~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly~qils~lt~~~l~~~f~~r~ 116 (415)
T PF03164_consen 37 LMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLYSQILSILTKPQLERIFEKRP 116 (415)
T ss_pred HHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHHHHHHHhccHHHHHHHhccCC
Confidence 555666666655433 4556778899999999999999999999999988888889999888887664211 22223
Q ss_pred CCccc---hhhHHHHHHHHHHhcCCh
Q 031403 103 ANGLN---KEFGPKLKELMQYCVDHP 125 (160)
Q Consensus 103 ~~~l~---~~f~~~l~~~m~~yn~~p 125 (160)
.+++. ..-+..+..++..++.+|
T Consensus 117 n~DlR~lL~gtd~~~~~~~~~~~~~~ 142 (415)
T PF03164_consen 117 NFDLRRLLGGTDRFLDSLLDSMNRSP 142 (415)
T ss_pred CcchhhhccchHHHHHHHHHHhcCCh
Confidence 34431 112345666666666555
No 19
>PF11675 DUF3271: Protein of unknown function (DUF3271); InterPro: IPR021689 This family of proteins with unknown function appears to be restricted to Plasmodium.
Probab=65.95 E-value=26 Score=26.79 Aligned_cols=52 Identities=15% Similarity=0.227 Sum_probs=39.6
Q ss_pred ccceEEEEEEeCCeeEEEEeccCCCHHHHHHHHhcCCCCCCCeeEEEeCCeEE
Q 031403 3 QKSLIYAFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTF 55 (160)
Q Consensus 3 ~~~I~Ya~Iar~~~iLae~~~~~~n~~~~~~~vL~~i~~~~~k~s~~~~~~~~ 55 (160)
|.+|-|+.||.-+..+.........+-.++..++..-+.+ .|..++.++|.|
T Consensus 28 pk~i~y~sv~qpt~~f~~~~k~h~~YLdiIN~il~~eSeN-~Kyayeg~nYHw 79 (249)
T PF11675_consen 28 PKPIAYISVAQPTATFEHDEKKHTKYLDIINDILRDESEN-IKYAYEGGNYHW 79 (249)
T ss_pred CCceeEEeccCceEEEeecCccchhHHHHHHHHHhccccc-cceeeeCCceEE
Confidence 5689999999886666665555566888999999887774 787887777665
No 20
>PRK11546 zraP zinc resistance protein; Provisional
Probab=63.04 E-value=51 Score=23.25 Aligned_cols=57 Identities=14% Similarity=0.271 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHH
Q 031403 80 AFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMM 146 (160)
Q Consensus 80 ~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~ 146 (160)
.-++.|.++|..... .- + . .+ -.-...|+.++.. +.|.. .+|.++.+||.+++.-|.
T Consensus 50 a~~q~I~~~f~~~t~-~L-R---q-qL-~aKr~ELnALl~~--~~pD~-~kI~aL~kEI~~Lr~kL~ 106 (143)
T PRK11546 50 AAWQKIHNDFYAQTS-AL-R---Q-QL-VSKRYEYNALLTA--NPPDS-SKINAVAKEMENLRQSLD 106 (143)
T ss_pred HHHHHHHHHHHHHHH-HH-H---H-HH-HHHHHHHHHHHcC--CCCCH-HHHHHHHHHHHHHHHHHH
Confidence 456777777776552 10 0 0 01 0111245555444 33443 788889899888887654
No 21
>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=59.53 E-value=23 Score=19.93 Aligned_cols=25 Identities=4% Similarity=0.279 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHhc
Q 031403 131 LAKVKAQVSEVKGVMMENIEKVGML 155 (160)
Q Consensus 131 i~~i~~~v~evk~im~~Nid~iL~R 155 (160)
...|+.+|+.++.-|-.++|.|-.|
T Consensus 5 ~~~ie~dIe~tR~~La~tvd~L~~r 29 (49)
T PF12277_consen 5 PDEIERDIERTRAELAETVDELAAR 29 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4688999999999999999988765
No 22
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=58.02 E-value=4.6 Score=29.81 Aligned_cols=28 Identities=25% Similarity=0.293 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHhccc
Q 031403 130 KLAKVKAQVSEVKGVMMENIEKVGMLCL 157 (160)
Q Consensus 130 ki~~i~~~v~evk~im~~Nid~iL~Rg~ 157 (160)
+...++..++.++.+|..|+|+.++||.
T Consensus 95 ~s~~~~~~~d~~~~~~~~~~d~~~e~~y 122 (190)
T COG5143 95 KSSALEQLIDDTVGIMRVNIDKVIEKGY 122 (190)
T ss_pred hhhhHhhcccCccchhhhhHHHHHHhhc
Confidence 5677888899999999999999999963
No 23
>PF01649 Ribosomal_S20p: Ribosomal protein S20; InterPro: IPR002583 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1I94_T 1FJG_T 4DH9_T 3KNJ_T 3TVG_W 3UYF_W 3V28_T 3KIS_t 3HUY_T 1HNX_T ....
Probab=46.32 E-value=75 Score=20.13 Aligned_cols=24 Identities=21% Similarity=0.273 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHhHHHHHhccccCC
Q 031403 137 QVSEVKGVMMENIEKVGMLCLFHK 160 (160)
Q Consensus 137 ~v~evk~im~~Nid~iL~Rg~~~~ 160 (160)
+..+.-.....-||+...+|++|+
T Consensus 45 ~a~~~l~~a~s~iDka~~kgiihk 68 (84)
T PF01649_consen 45 EAKELLRKAYSAIDKAAKKGIIHK 68 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHHSSSTT
T ss_pred HHHHHHHHHHHHHHHHHHcCCcch
Confidence 355556677788999999999996
No 24
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.19 E-value=1.2e+02 Score=22.23 Aligned_cols=82 Identities=16% Similarity=0.168 Sum_probs=48.0
Q ss_pred HhcCCCCC---CCeeEEEeCCeEEEEEE-eCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhCCCCCCC-CCCCccchh
Q 031403 35 CLQKLPAS---NNKFTYNCDAHTFNYLV-DNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAAT-APANGLNKE 109 (160)
Q Consensus 35 vL~~i~~~---~~k~s~~~~~~~~h~l~-~~~l~~~citd~~~~~~~af~fL~~i~~~F~~~~~~~~~~~-~~~~~l~~~ 109 (160)
+..++.|. .......-+.+..|+.. -.|+-|++||++.. ..|=.+|+.|..-|..-...+-+-+ .-|-.. ..
T Consensus 110 I~~qlsp~~ksSGie~LetdtF~l~~~QTlTG~KFVvis~~~~--~~aD~lLrKiYelYsDyvlKNPfYSlEMPIRc-~l 186 (199)
T KOG3369|consen 110 ISTQLSPEPKSSGIEVLETDTFTLHIFQTLTGTKFVVIAEPGT--QGADSLLRKIYELYSDYVLKNPFYSLEMPIRC-EL 186 (199)
T ss_pred eeeccCCCCCCCceEEEEeccEEEEEEEccCCcEEEEEecCCc--hhHHHHHHHHHHHHHHHhhcCCccCcccceeH-HH
Confidence 34455543 23455666888888764 58999999999887 4566777777766554322221111 112222 45
Q ss_pred hHHHHHHHHH
Q 031403 110 FGPKLKELMQ 119 (160)
Q Consensus 110 f~~~l~~~m~ 119 (160)
|++.|+.+++
T Consensus 187 FDe~lk~~le 196 (199)
T KOG3369|consen 187 FDEKLKFLLE 196 (199)
T ss_pred hhHHHHHHHh
Confidence 6766666553
No 25
>COG3917 NahD 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=43.32 E-value=24 Score=25.99 Aligned_cols=21 Identities=19% Similarity=0.213 Sum_probs=19.1
Q ss_pred HHHHHHHHHhHHHHHhccccC
Q 031403 139 SEVKGVMMENIEKVGMLCLFH 159 (160)
Q Consensus 139 ~evk~im~~Nid~iL~Rg~~~ 159 (160)
+++|+-.+.|.+..++||+|-
T Consensus 156 ~eik~~l~a~~~~a~srGvfG 176 (203)
T COG3917 156 DEIKARLKANTAEAVSRGVFG 176 (203)
T ss_pred HHHHHHHHhhHHHHHhcCccC
Confidence 678999999999999999983
No 26
>PHA01811 hypothetical protein
Probab=43.23 E-value=33 Score=20.61 Aligned_cols=19 Identities=21% Similarity=0.394 Sum_probs=15.0
Q ss_pred CCeeEEEeCCeEEEEEEeC
Q 031403 43 NNKFTYNCDAHTFNYLVDN 61 (160)
Q Consensus 43 ~~k~s~~~~~~~~h~l~~~ 61 (160)
+.-.+....||.+||+-++
T Consensus 4 ddivtlrvkgyi~hyldd~ 22 (78)
T PHA01811 4 DDIVTLRVKGYILHYLDDD 22 (78)
T ss_pred ccEEEEEEeeEEEEEEcCc
Confidence 3556788899999999764
No 27
>KOG3230 consensus Vacuolar assembly/sorting protein DID4 [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.61 E-value=70 Score=23.87 Aligned_cols=18 Identities=11% Similarity=0.032 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHhHHHHHh
Q 031403 137 QVSEVKGVMMENIEKVGM 154 (160)
Q Consensus 137 ~v~evk~im~~Nid~iL~ 154 (160)
.++...+.|.++||..|+
T Consensus 134 ~Mdm~~Emm~daIDdal~ 151 (224)
T KOG3230|consen 134 IMDMKEEMMDDAIDDALG 151 (224)
T ss_pred HHHHHHHHHHHHHHHhhc
Confidence 466778899999999985
No 28
>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=42.44 E-value=36 Score=19.89 Aligned_cols=48 Identities=17% Similarity=0.265 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHhcCCCCC-CCeeEEEeCCeEEEEEE--eCCEEEEEEecCC
Q 031403 25 SGNFNSIAYQCLQKLPAS-NNKFTYNCDAHTFNYLV--DNGYTYCVVADES 72 (160)
Q Consensus 25 ~~n~~~~~~~vL~~i~~~-~~k~s~~~~~~~~h~l~--~~~l~~~citd~~ 72 (160)
-.+|+.+...+-+++... +-|..|+.+|...+=+. ++|-.|+|...+.
T Consensus 8 ~~s~e~lL~~it~~v~l~~gVr~lyt~~G~~V~~l~~l~dg~~yVa~g~e~ 58 (60)
T PF03607_consen 8 FRSFEQLLDEITEKVQLPSGVRKLYTLDGKRVKSLDELEDGGSYVASGREP 58 (60)
T ss_dssp HSSHHHHHHHHHHSSSSTTS-SEEEETTSSEESSGGGS-TTEEEEEESSSS
T ss_pred hcCHHHHHHHHHhhcCCCcccceEECCCCCEeCCHHHHCCCCEEEEEcCCc
Confidence 357888888888888754 47888888886665442 4888899986654
No 29
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=42.32 E-value=42 Score=21.51 Aligned_cols=24 Identities=21% Similarity=0.238 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHhHHHHHhccccCC
Q 031403 137 QVSEVKGVMMENIEKVGMLCLFHK 160 (160)
Q Consensus 137 ~v~evk~im~~Nid~iL~Rg~~~~ 160 (160)
+..+.-.....-||+....|++||
T Consensus 46 ~a~~~~~~a~s~iDka~~KgiiHk 69 (88)
T PRK00239 46 AAEEALKAAQSKIDKAASKGVIHK 69 (88)
T ss_pred HHHHHHHHHHHHHHHHHHCCCcch
Confidence 344555667788999999999996
No 30
>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=42.13 E-value=33 Score=27.07 Aligned_cols=21 Identities=10% Similarity=0.170 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhH
Q 031403 129 SKLAKVKAQVSEVKGVMMENI 149 (160)
Q Consensus 129 dki~~i~~~v~evk~im~~Ni 149 (160)
+.+.+++.|+-|.=+-|.-+=
T Consensus 103 e~~~klEKel~e~~~~~fg~e 123 (295)
T TIGR01478 103 EPMSTIEKELLEKYEEMFGDE 123 (295)
T ss_pred chhhHHHHHHHHHHHHHhCCc
Confidence 344555555555554444433
No 31
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=41.57 E-value=23 Score=20.61 Aligned_cols=30 Identities=13% Similarity=0.121 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHhccccC
Q 031403 130 KLAKVKAQVSEVKGVMMENIEKVGMLCLFH 159 (160)
Q Consensus 130 ki~~i~~~v~evk~im~~Nid~iL~Rg~~~ 159 (160)
.+..|-+.+.--+.-+...|+++.++||..
T Consensus 20 t~~~l~~~~~~~~~~vs~~i~~L~~~glv~ 49 (68)
T PF13463_consen 20 TQSDLAERLGISKSTVSRIIKKLEEKGLVE 49 (68)
T ss_dssp EHHHHHHHTT--HHHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 447777777778888899999999999974
No 32
>PF13076 DUF3940: Protein of unknown function (DUF3940)
Probab=40.74 E-value=19 Score=19.34 Aligned_cols=12 Identities=33% Similarity=0.409 Sum_probs=9.8
Q ss_pred HHHHHhccccCC
Q 031403 149 IEKVGMLCLFHK 160 (160)
Q Consensus 149 id~iL~Rg~~~~ 160 (160)
|+++|+.|++++
T Consensus 7 I~~Li~~Giyk~ 18 (38)
T PF13076_consen 7 IEKLIQSGIYKK 18 (38)
T ss_pred HHHHHHcCCcCc
Confidence 789999998863
No 33
>PTZ00370 STEVOR; Provisional
Probab=39.64 E-value=38 Score=26.71 Aligned_cols=23 Identities=9% Similarity=0.172 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHH
Q 031403 129 SKLAKVKAQVSEVKGVMMENIEK 151 (160)
Q Consensus 129 dki~~i~~~v~evk~im~~Nid~ 151 (160)
+...+++.|+-|.=+-|.-+=..
T Consensus 102 e~k~klEKel~e~~ee~fg~~~~ 124 (296)
T PTZ00370 102 EPMSTLEKELLETYEEMFGDESD 124 (296)
T ss_pred chhHHHHHHHHHHHHHHhcCccc
Confidence 44666666666665555544444
No 34
>COG4051 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.04 E-value=1.1e+02 Score=22.41 Aligned_cols=29 Identities=24% Similarity=0.446 Sum_probs=21.6
Q ss_pred eCCeeEEEEeccCCC--HHHHHHHHhcCCCC
Q 031403 13 RGNVVLAEYTEFSGN--FNSIAYQCLQKLPA 41 (160)
Q Consensus 13 r~~~iLae~~~~~~n--~~~~~~~vL~~i~~ 41 (160)
+|.+|++++++.+|. +..+++..|.-+.-
T Consensus 3 ~g~~ivV~~~dk~gae~Y~kIir~al~dL~L 33 (202)
T COG4051 3 SGETIVVECADKSGAEFYRKIIRDALADLKL 33 (202)
T ss_pred CCceEEEEecChhhhHHHHHHHHHHHHHhcc
Confidence 467899999886664 67788888876554
No 35
>CHL00102 rps20 ribosomal protein S20
Probab=38.87 E-value=1.1e+02 Score=19.87 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHhHHHHHhccccCC
Q 031403 136 AQVSEVKGVMMENIEKVGMLCLFHK 160 (160)
Q Consensus 136 ~~v~evk~im~~Nid~iL~Rg~~~~ 160 (160)
++..+.-.....-||+...+|++|+
T Consensus 52 ~~a~~~l~~a~s~iDkaa~KGviHk 76 (93)
T CHL00102 52 KKVQETLSSVYSKIDKAVKKGVFHK 76 (93)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcch
Confidence 3455566677788999999999996
No 36
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=37.99 E-value=63 Score=20.68 Aligned_cols=24 Identities=13% Similarity=0.221 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHhHHHHHhccccCC
Q 031403 137 QVSEVKGVMMENIEKVGMLCLFHK 160 (160)
Q Consensus 137 ~v~evk~im~~Nid~iL~Rg~~~~ 160 (160)
+..+.-.....-||+....|++|+
T Consensus 46 ~a~~~l~~a~s~iDkaa~KgviHk 69 (87)
T TIGR00029 46 KAQEAFKEAAKKLDRAARKGIIHK 69 (87)
T ss_pred HHHHHHHHHHHHHHHHHHCCCcch
Confidence 344455667788999999999996
No 37
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=37.79 E-value=1.3e+02 Score=20.43 Aligned_cols=82 Identities=11% Similarity=0.148 Sum_probs=43.4
Q ss_pred HHhcCCCC---CCCeeEEEeCCeEEEEEE-eCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhCCCCCCC-CCCCccch
Q 031403 34 QCLQKLPA---SNNKFTYNCDAHTFNYLV-DNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYGGGKAAT-APANGLNK 108 (160)
Q Consensus 34 ~vL~~i~~---~~~k~s~~~~~~~~h~l~-~~~l~~~citd~~~~~~~af~fL~~i~~~F~~~~~~~~~~~-~~~~~l~~ 108 (160)
.++.++.| ...+.....+.+..|+.. ..|.-|+.++++. +...+|+ |+.+..-|..-...+...+ .-|-.. .
T Consensus 45 aI~tq~~p~~gssg~~~l~~~~f~m~I~qT~TG~kFV~~~~k~-t~na~~q-l~kiY~lYsdYV~knPfys~EMPI~c-~ 121 (134)
T COG5122 45 AILTQTIPLPGSSGRLVLYFRNFVMTIFQTTTGTKFVFVAEKR-TVNALFQ-LQKIYSLYSDYVTKNPFYSPEMPIQC-S 121 (134)
T ss_pred hhhhhcccCCCCCceEEEEeccEEEEEEEecCCcEEEEEecCC-chhHHHH-HHHHHHHHHHHhhcCCCCCcccceeh-h
Confidence 34444443 246777778899988764 5899999999443 3344555 3333333332111111111 112222 4
Q ss_pred hhHHHHHHHH
Q 031403 109 EFGPKLKELM 118 (160)
Q Consensus 109 ~f~~~l~~~m 118 (160)
.|++.++++.
T Consensus 122 lFde~lkrm~ 131 (134)
T COG5122 122 LFDEHLKRMF 131 (134)
T ss_pred hhhHHHHHHh
Confidence 5777777554
No 38
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.99 E-value=1.2e+02 Score=25.03 Aligned_cols=36 Identities=22% Similarity=0.444 Sum_probs=31.3
Q ss_pred EeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhC
Q 031403 59 VDNGYTYCVVADESSGRQIPMAFLERVKDEFVSKYG 94 (160)
Q Consensus 59 ~~~~l~~~citd~~~~~~~af~fL~~i~~~F~~~~~ 94 (160)
.++++.+++++.-+.|--.++.||..|-+-|..-|+
T Consensus 61 ~~~~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg 96 (418)
T KOG2740|consen 61 YRDLIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFG 96 (418)
T ss_pred eccCcEEEEEEeccCCChhHHHHHHHHHHHHHHHhc
Confidence 467888888888888999999999999999998775
No 39
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=34.63 E-value=26 Score=25.05 Aligned_cols=25 Identities=24% Similarity=0.420 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHh-HHHHHhccccC
Q 031403 135 KAQVSEVKGVMMEN-IEKVGMLCLFH 159 (160)
Q Consensus 135 ~~~v~evk~im~~N-id~iL~Rg~~~ 159 (160)
+.+|++++++=.++ |+++++|||..
T Consensus 99 r~eIe~IRGv~s~~~i~~L~e~glI~ 124 (159)
T PF04079_consen 99 RAEIEEIRGVNSDSVIKTLLERGLIE 124 (159)
T ss_dssp HHHHHHHHTS--HCHHHHHHHTTSEE
T ss_pred HHHHHHHcCCChHHHHHHHHHCCCEE
Confidence 57888998887766 89999999963
No 40
>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=33.85 E-value=92 Score=19.28 Aligned_cols=49 Identities=18% Similarity=0.314 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHhcCCCC--CCCeeEEEeCC-eEEEEE--EeCCEEEEEEecCCC
Q 031403 25 SGNFNSIAYQCLQKLPA--SNNKFTYNCDA-HTFNYL--VDNGYTYCVVADESS 73 (160)
Q Consensus 25 ~~n~~~~~~~vL~~i~~--~~~k~s~~~~~-~~~h~l--~~~~l~~~citd~~~ 73 (160)
-.+|+.+...+-+.+.+ ..-+..|+.++ ....-+ .++|-.|+|...+.+
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 46899999888888874 45688888887 554443 358999999877654
No 41
>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=33.10 E-value=78 Score=21.55 Aligned_cols=26 Identities=19% Similarity=0.406 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHH
Q 031403 128 ISKLAKVKAQVSEVKGVMMENIEKVG 153 (160)
Q Consensus 128 ~dki~~i~~~v~evk~im~~Nid~iL 153 (160)
...+..++.+|.|+|+.+..=|+.++
T Consensus 95 ~E~veEL~~Dv~DlK~myr~Qi~~lv 120 (120)
T PF12325_consen 95 SEEVEELRADVQDLKEMYREQIDQLV 120 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 37899999999999999999888764
No 42
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.62 E-value=1.7e+02 Score=20.36 Aligned_cols=54 Identities=13% Similarity=0.291 Sum_probs=40.5
Q ss_pred HHHHhcCCCCC---CCeeEEEeCCeEEEEEEe-CCEEEEEEecCCCCcccHHHHHHHHHH
Q 031403 32 AYQCLQKLPAS---NNKFTYNCDAHTFNYLVD-NGYTYCVVADESSGRQIPMAFLERVKD 87 (160)
Q Consensus 32 ~~~vL~~i~~~---~~k~s~~~~~~~~h~l~~-~~l~~~citd~~~~~~~af~fL~~i~~ 87 (160)
.+.+.+++.|+ ++-.+++-+.|-.||... .|+=++-+||+.... --..|..|.+
T Consensus 45 lkS~v~Kls~~d~k~~f~sy~Ts~YklhfyeTptglk~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 45 LKSFVSKLSPGDVKDGFLSYKTSKYKLHFYETPTGLKFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred HHHHHHhcCCCCcccCeeEEeeceeEEEEEEcCCCcEEEEecCCCccc--HHHHHHHHHH
Confidence 45667788876 455677888999998854 899999999987763 2356666666
No 43
>PF05527 DUF758: Domain of unknown function (DUF758) ; InterPro: IPR008477 This is a family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor.; PDB: 3F4M_A.
Probab=32.55 E-value=2.1e+02 Score=21.18 Aligned_cols=43 Identities=12% Similarity=0.209 Sum_probs=27.9
Q ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccc
Q 031403 114 LKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVGMLCL 157 (160)
Q Consensus 114 l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL~Rg~ 157 (160)
|+.....| .+|.=.|.+-.-+.+..+.-.-+.+-++++||+|-
T Consensus 143 i~~vF~~f-~~~efL~~lf~~~~~~~~~L~~i~~~Lnklld~g~ 185 (186)
T PF05527_consen 143 IDHVFNFF-SDPEFLDALFSPDEEYRDHLGKICDGLNKLLDEGS 185 (186)
T ss_dssp HHHHHHHH-T-HHHHHHHTSG--GGHHHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHhh-CChHHHHHHhCcccchHHHHHHHHHHHHHHHhCCC
Confidence 55555666 56654455555556677777788899999999983
No 44
>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=32.29 E-value=2.2e+02 Score=21.40 Aligned_cols=72 Identities=14% Similarity=0.276 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHhhhCCCCCCCCCCCcc-chhhHHHHHHHHHHhcCCh---------HHHHHHHHHHHHHHHHHHHHHH
Q 031403 78 PMAFLERVKDEFVSKYGGGKAATAPANGL-NKEFGPKLKELMQYCVDHP---------EEISKLAKVKAQVSEVKGVMME 147 (160)
Q Consensus 78 af~fL~~i~~~F~~~~~~~~~~~~~~~~l-~~~f~~~l~~~m~~yn~~p---------~~~dki~~i~~~v~evk~im~~ 147 (160)
+..||++|-........+. ..++. +..|...|.++-.++..++ ....+..+.-++|++-+.+|.+
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 TNKFIKELIKDGSLLIGAL-----RNLSMAVQKFSQSLQDFQFECIGDAETDDEISIAQSLKEFARLLIAVEEERRRLIQ 88 (207)
T ss_pred HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHhhccCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4577777777665544211 11111 3567777777665554444 2346778888888888999999
Q ss_pred hHHHHHh
Q 031403 148 NIEKVGM 154 (160)
Q Consensus 148 Nid~iL~ 154 (160)
|++..+-
T Consensus 89 ~~~~~l~ 95 (207)
T cd07634 89 NANDVLI 95 (207)
T ss_pred HHHHHHH
Confidence 9887664
No 45
>PF02520 DUF148: Domain of unknown function DUF148; InterPro: IPR003677 This entry represents the domain DUF148, which has no known function.
Probab=31.87 E-value=1.5e+02 Score=19.44 Aligned_cols=61 Identities=20% Similarity=0.159 Sum_probs=39.2
Q ss_pred HHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhc
Q 031403 84 RVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVGML 155 (160)
Q Consensus 84 ~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL~R 155 (160)
+.+++|...+. +. .... .+....+.+..+.|+ . .+.+.....++..-+.-+.+|+..++.+
T Consensus 2 ea~~ef~~I~~-n~-----~lt~-~e~~~~l~~Wa~~~~-v---~~~~~~f~~~~~~~~~~~~~~~~~vi~~ 62 (113)
T PF02520_consen 2 EARKEFFQIFQ-NP-----NLTK-AEIEEQLDEWAEKYG-V---QDQYNEFKAQVQAQKEEVRKNVTAVISN 62 (113)
T ss_pred hHHHHHHHHHc-CC-----CCCH-HHHHHHHHHHHHHCC-c---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56778887773 21 1111 445556666666664 2 2788888888888888888888777653
No 46
>PF11281 DUF3083: Protein of unknown function (DUF3083); InterPro: IPR021433 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=31.73 E-value=2.6e+02 Score=22.34 Aligned_cols=72 Identities=15% Similarity=0.257 Sum_probs=44.2
Q ss_pred EEEEeCCeeEEEEeccCCCHHHHHHHHhcCCCCCC--CeeEEE----eCCeEEEEEEe---CCEEEEEEecCCCCcccHH
Q 031403 9 AFVARGNVVLAEYTEFSGNFNSIAYQCLQKLPASN--NKFTYN----CDAHTFNYLVD---NGYTYCVVADESSGRQIPM 79 (160)
Q Consensus 9 a~Iar~~~iLae~~~~~~n~~~~~~~vL~~i~~~~--~k~s~~----~~~~~~h~l~~---~~l~~~citd~~~~~~~af 79 (160)
|.||.|-++|+-++... ++..++ ++.+|. ..++..||-.+ +-+-|+.++++.-.....|
T Consensus 211 AmvANGl~PiVRnsk~d------------~~~~~~Elqmlgfdp~~~~~q~~~~w~~~kLVet~~fvi~A~~~d~~~~gy 278 (316)
T PF11281_consen 211 AMVANGLTPIVRNSKDD------------QVEGNGELQMLGFDPNAEEPQFICHWDADKLVETVHFVIVAGKQDKTDHGY 278 (316)
T ss_pred hhhhcCCcceeeccccc------------cccccceeEEEecCcccCCcceeeeeccceeeeeEEEEEEecCcccccccH
Confidence 57888888888776422 111110 122222 12455566433 5677888888888888888
Q ss_pred -HHHHHHHHHHHhh
Q 031403 80 -AFLERVKDEFVSK 92 (160)
Q Consensus 80 -~fL~~i~~~F~~~ 92 (160)
.|+.++.+.....
T Consensus 279 GrFmNqvE~Al~~~ 292 (316)
T PF11281_consen 279 GRFMNQVEDALRSF 292 (316)
T ss_pred HHHHHHHHHHHHHH
Confidence 6888888776553
No 47
>PF10504 DUF2452: Protein of unknown function (DUF2452); InterPro: IPR019534 This entry contains proteins that have no known function.
Probab=31.06 E-value=43 Score=24.05 Aligned_cols=55 Identities=18% Similarity=0.336 Sum_probs=34.9
Q ss_pred HHHHHHHHhcCCCCC----CCeeEEEe-CCeEEEEE-EeCCEEEEEEecC-CCCcccHHHHH
Q 031403 28 FNSIAYQCLQKLPAS----NNKFTYNC-DAHTFNYL-VDNGYTYCVVADE-SSGRQIPMAFL 82 (160)
Q Consensus 28 ~~~~~~~vL~~i~~~----~~k~s~~~-~~~~~h~l-~~~~l~~~citd~-~~~~~~af~fL 82 (160)
+...|++|+++...+ +.++.|.- =|.+||.. .++|-.|+.+..+ +.+.+.++.||
T Consensus 64 Lq~QA~~ile~~~~~~~l~~A~cnF~pipG~iYhLY~r~~G~~ylSmisP~EWg~~~p~~fl 125 (159)
T PF10504_consen 64 LQEQARKILEEAERNEELHHAKCNFEPIPGQIYHLYRRENGQDYLSMISPEEWGGSCPHEFL 125 (159)
T ss_pred HHHHHHHHHHHHHHhHHHhhcccCceecCCCEEEEEECCCCCEEEEeeCHHHhCCCCCcCEE
Confidence 455677788876654 67888884 47788844 5677766666554 44555555443
No 48
>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]
Probab=29.83 E-value=1.6e+02 Score=18.98 Aligned_cols=21 Identities=19% Similarity=0.197 Sum_probs=16.3
Q ss_pred HHHHHHHHhHHHHHhccccCC
Q 031403 140 EVKGVMMENIEKVGMLCLFHK 160 (160)
Q Consensus 140 evk~im~~Nid~iL~Rg~~~~ 160 (160)
+.-..+..-||+.-.+|++||
T Consensus 49 ~~l~~a~~~idkaa~KGvihk 69 (88)
T COG0268 49 AALKEAQKKIDKAASKGVIHK 69 (88)
T ss_pred HHHHHHHHHHHHHHHcCcccc
Confidence 344556677899999999997
No 49
>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=28.65 E-value=1.4e+02 Score=21.84 Aligned_cols=43 Identities=14% Similarity=0.212 Sum_probs=24.5
Q ss_pred HHHHHHHHHhc---CChHHHHHHHHHHHHHHHHHHHHHHhHHHHHh
Q 031403 112 PKLKELMQYCV---DHPEEISKLAKVKAQVSEVKGVMMENIEKVGM 154 (160)
Q Consensus 112 ~~l~~~m~~yn---~~p~~~dki~~i~~~v~evk~im~~Nid~iL~ 154 (160)
|...++++.|. +.|...+.+.+...+++++-+.+.+++++.++
T Consensus 136 p~~~~l~~kY~~l~~~~~~~~~~~~~l~e~~~~L~~l~~~f~~~~~ 181 (199)
T PF10112_consen 136 PTAVKLLEKYAELESQPVKSEEIKQSLEEIEETLDTLNQAFEKDLD 181 (199)
T ss_pred hHHHHHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666776664 12322355666666666666666666665554
No 50
>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=28.51 E-value=45 Score=17.52 Aligned_cols=18 Identities=11% Similarity=0.425 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 031403 129 SKLAKVKAQVSEVKGVMM 146 (160)
Q Consensus 129 dki~~i~~~v~evk~im~ 146 (160)
|.|..+..++.++-+||.
T Consensus 17 ~NI~~il~~m~~mpgim~ 34 (35)
T PF12579_consen 17 DNILAILNDMNDMPGIMS 34 (35)
T ss_pred HHHHHHHHHHHcchhhhc
Confidence 777778888888777774
No 51
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=28.13 E-value=42 Score=24.72 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=19.7
Q ss_pred HHHHHHHHHH-HHHhHHHHHhccccC
Q 031403 135 KAQVSEVKGV-MMENIEKVGMLCLFH 159 (160)
Q Consensus 135 ~~~v~evk~i-m~~Nid~iL~Rg~~~ 159 (160)
+.+|++++++ -..-|.++++|||..
T Consensus 104 r~eIe~IRGv~s~~~l~~L~ergLI~ 129 (186)
T TIGR00281 104 RARINEIRGVKSYQIVDDLVEKGLVV 129 (186)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCCeE
Confidence 5668888777 567789999999973
No 52
>PF05542 DUF760: Protein of unknown function (DUF760); InterPro: IPR008479 This entry contains uncharacterised proteins.
Probab=27.57 E-value=60 Score=20.57 Aligned_cols=26 Identities=12% Similarity=0.143 Sum_probs=18.2
Q ss_pred HHHHHHHH-HHHHHHHHHHhHHHHHhc
Q 031403 130 KLAKVKAQ-VSEVKGVMMENIEKVGML 155 (160)
Q Consensus 130 ki~~i~~~-v~evk~im~~Nid~iL~R 155 (160)
.+..+.+. =.||.++|.++|..+|..
T Consensus 14 ~~~~l~~~~s~ev~e~m~~~v~~llG~ 40 (86)
T PF05542_consen 14 RIQQLSEPASPEVLEAMKQHVSGLLGN 40 (86)
T ss_pred HHHHhhccCCHHHHHHHHHHHHHHHcC
Confidence 44444443 357899999999998853
No 53
>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=27.54 E-value=68 Score=25.31 Aligned_cols=26 Identities=12% Similarity=0.070 Sum_probs=21.6
Q ss_pred EeCCeEEEEEEeCCEEEEEEecCCCC
Q 031403 49 NCDAHTFNYLVDNGYTYCVVADESSG 74 (160)
Q Consensus 49 ~~~~~~~h~l~~~~l~~~citd~~~~ 74 (160)
++++++|-|-..+++.++|+|.-.+-
T Consensus 237 ~i~g~ly~y~~~~~v~i~c~chg~~~ 262 (284)
T PF07897_consen 237 RIEGFLYKYGKGEEVRIVCVCHGSFL 262 (284)
T ss_pred eeeEEEEEecCCCeEEEEEEecCCCC
Confidence 46788888866789999999998875
No 54
>PF08506 Cse1: Cse1; InterPro: IPR013713 The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments. This domain is found in exportin Cse1 (also known as importin-alpha re-exporter). Exportin Cse1 mediates nuclear transport of importin-alpha back into the cytosol, where importin-alpha functions as a transporter of proteins carrying nuclear localisation signals (NLS) from the cytoplasm into the nucleus [, , ]. This domain contains HEAT repeats. More information about these proteins can be found at Protein of the Month: Importins [].; GO: 0006886 intracellular protein transport; PDB: 1Z3H_B 1WA5_C.
Probab=27.22 E-value=68 Score=26.23 Aligned_cols=45 Identities=18% Similarity=0.330 Sum_probs=31.7
Q ss_pred ecCCCCcccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChH
Q 031403 69 ADESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPE 126 (160)
Q Consensus 69 td~~~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~ 126 (160)
+|-+.+++.|-.||..+.+.|.+... .-+...+..++..|+++|.
T Consensus 222 sd~~TrR~AA~dfl~~L~~~~~~~v~-------------~i~~~~i~~~l~~y~~~~~ 266 (370)
T PF08506_consen 222 SDSDTRRRAACDFLRSLCKKFEKQVT-------------SILMQYIQQLLQQYASNPS 266 (370)
T ss_dssp S---SHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHH-TT
T ss_pred cccCCcHHHHHHHHHHHHHHHhHHHH-------------HHHHHHHHHHHHHHhhCCc
Confidence 56678899999999999998876542 3456678888888877764
No 55
>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=27.00 E-value=2.7e+02 Score=20.86 Aligned_cols=45 Identities=18% Similarity=0.304 Sum_probs=33.0
Q ss_pred hhhHHHHHHHHH-HhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q 031403 108 KEFGPKLKELMQ-YCVDHPEEISKLAKVKAQVSEVKGVMMENIEKV 152 (160)
Q Consensus 108 ~~f~~~l~~~m~-~yn~~p~~~dki~~i~~~v~evk~im~~Nid~i 152 (160)
..|-..++.+-. .-++||-+...+.+++++|+++++.|.+-++++
T Consensus 40 ~~~~~~~~~i~~~a~~DdPyAD~~L~~iEe~i~~~~~~l~~~~~~l 85 (217)
T PF08900_consen 40 PGFASRLNRIWRDARQDDPYADWWLLRIEEKINEARQELQELIARL 85 (217)
T ss_pred HHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666666553 344678766889999999999999888877665
No 56
>TIGR00828 EIID-AGA PTS system, mannose/fructose/sorbose family, IID component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IID subunits of this family of PTS transporters.
Probab=26.87 E-value=2.5e+02 Score=22.01 Aligned_cols=46 Identities=15% Similarity=0.197 Sum_probs=29.9
Q ss_pred CCCCcccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChH
Q 031403 71 ESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPE 126 (160)
Q Consensus 71 ~~~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~ 126 (160)
-+|.+-.+..|.--+.-...+.|+.+ ..+..+.+++-+++||.+|.
T Consensus 22 ~NyErmQ~~gf~~~m~P~L~KlY~~d----------~e~~~~Alkrhl~fFNT~p~ 67 (271)
T TIGR00828 22 FNFERMQALGFCYAMIPAIKKLYPDD----------KAGRSAALKRHLEFFNTHPN 67 (271)
T ss_pred ccHHHHhhHhHHHHHHHHHHHHcCCC----------HHHHHHHHHHHHHHHCCCch
Confidence 34555566666666666666666211 13556788899999998884
No 57
>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells. Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex
Probab=26.81 E-value=2.9e+02 Score=21.12 Aligned_cols=15 Identities=27% Similarity=0.288 Sum_probs=7.4
Q ss_pred cHHHHHHHHHHHHHh
Q 031403 77 IPMAFLERVKDEFVS 91 (160)
Q Consensus 77 ~af~fL~~i~~~F~~ 91 (160)
.|..+|++|+..|..
T Consensus 157 ~A~~LL~~v~~~~~~ 171 (264)
T PF06008_consen 157 EAEDLLSRVQKWFQK 171 (264)
T ss_pred HHHHHHHHHHHHHhh
Confidence 444555555555543
No 58
>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=25.60 E-value=91 Score=21.95 Aligned_cols=26 Identities=15% Similarity=0.355 Sum_probs=23.7
Q ss_pred EEEEEecCCCCcccHHHHHHHHHHHH
Q 031403 64 TYCVVADESSGRQIPMAFLERVKDEF 89 (160)
Q Consensus 64 ~~~citd~~~~~~~af~fL~~i~~~F 89 (160)
.++.||.++||.+....||..+.+..
T Consensus 25 ~~ilit~kG~P~~~tr~~l~~L~~~~ 50 (160)
T cd00223 25 NCILITGKGYPDRATRRFLRRLHEEL 50 (160)
T ss_pred CEEEEEcCCcCCHHHHHHHHHHHHhh
Confidence 57899999999999999999999875
No 59
>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=25.54 E-value=3e+02 Score=20.83 Aligned_cols=47 Identities=13% Similarity=0.359 Sum_probs=31.5
Q ss_pred hhhHHHHHHHHHH--hcCChH---HHHHHHHHHHHHHHHHHHHHHhHHHHHh
Q 031403 108 KEFGPKLKELMQY--CVDHPE---EISKLAKVKAQVSEVKGVMMENIEKVGM 154 (160)
Q Consensus 108 ~~f~~~l~~~m~~--yn~~p~---~~dki~~i~~~v~evk~im~~Nid~iL~ 154 (160)
..|...|.++=.. ++.||. ...++.+++.++.....+..+|++.++.
T Consensus 40 ~~f~~~L~~LG~~~l~~dd~~~~~~l~kf~~~~~El~~l~~~L~~~~~~~I~ 91 (215)
T cd07642 40 EQYTQALEKFGSNCVCRDDPDLGSAFLKFSVFTKELTALFKNLVQNMNNIIT 91 (215)
T ss_pred HHHHHHHHHHhhcccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566677766655 555552 3467777888888877777777776654
No 60
>cd07636 BAR_GRAF The Bin/Amphiphysin/Rvs (BAR) domain of GTPase Regulator Associated with Focal adhesion kinase. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. GTPase Regulator Associated with Focal adhesion kinase (GRAF), also called Rho GTPase activating protein 26 (ARHGAP26), is a GAP with activity towards RhoA and Cdc42 and is only weakly active towards Rac1. It influences Rho-mediated cytoskeletal rearrangements and binds focal adhesion kinase (FAK), which is a critical component of integrin signaling. GRAF 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 domain of GRAF directly interacts with its Rho GAP domain and inhibits its activity. Autoinhibited GRAF is capable o
Probab=24.99 E-value=3e+02 Score=20.65 Aligned_cols=47 Identities=21% Similarity=0.425 Sum_probs=28.4
Q ss_pred hhhHHHHHHHHHHhcCCh---------HHHHHHHHHHHHHHHHHHHHHHhHHHHHh
Q 031403 108 KEFGPKLKELMQYCVDHP---------EEISKLAKVKAQVSEVKGVMMENIEKVGM 154 (160)
Q Consensus 108 ~~f~~~l~~~m~~yn~~p---------~~~dki~~i~~~v~evk~im~~Nid~iL~ 154 (160)
..|...|+++-.++..++ ....+...+-++|++-+.+|.++.+..|-
T Consensus 40 ~~Fa~sL~~f~~~~~gd~~~dDe~~I~~~L~kF~~~L~ei~~~r~~L~~qa~~~l~ 95 (207)
T cd07636 40 RKFADSLNEFKFQCIGDAETDDEICIARSLQEFAAVLRNLEDERTRMIENASEVLI 95 (207)
T ss_pred HHHHHHHHHHHhhcCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666665554544343 22345566677777778888888766553
No 61
>PF13228 DUF4037: Domain of unknown function (DUF4037)
Probab=24.85 E-value=2e+02 Score=18.65 Aligned_cols=44 Identities=20% Similarity=0.235 Sum_probs=30.3
Q ss_pred hhhHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcc
Q 031403 108 KEFGPKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVGMLC 156 (160)
Q Consensus 108 ~~f~~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL~Rg 156 (160)
..|++.-+++ ..| |.. =....+..+...+.+-..-|+.+.++||
T Consensus 23 G~~~~~R~~l-~~Y---P~d-l~~~~ia~~~~~~~qa~~~n~~ra~~R~ 66 (100)
T PF13228_consen 23 GEFTALRERL-AYY---PED-LRLNKIARNLMLLAQAGQYNLGRALKRG 66 (100)
T ss_pred chHHHHHHHH-HHC---hHH-HHHHHHHHHHHHhhhhhHHHHHHHHHCC
Confidence 3455543444 665 654 4666777778877777778999999997
No 62
>KOG0972 consensus Huntingtin interacting protein 1 (Hip1) interactor Hippi [Signal transduction mechanisms]
Probab=24.77 E-value=1.8e+02 Score=23.25 Aligned_cols=68 Identities=18% Similarity=0.265 Sum_probs=37.0
Q ss_pred cHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHH----------HHHHHHHhcCCh----HHHHHHHHHHHHHHHHH
Q 031403 77 IPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPK----------LKELMQYCVDHP----EEISKLAKVKAQVSEVK 142 (160)
Q Consensus 77 ~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~----------l~~~m~~yn~~p----~~~dki~~i~~~v~evk 142 (160)
-+=.||+.++++|..... . ..++..++|+++.+. +.++-..|++.. .....+..+..+++.+|
T Consensus 245 ~~~~~Ldklh~eit~~LE-k--I~SREK~lNnqL~~l~q~fr~a~~~lse~~e~y~q~~~gv~~rT~~L~eVm~e~E~~K 321 (384)
T KOG0972|consen 245 NVGPYLDKLHKEITKALE-K--IASREKSLNNQLASLMQKFRRATDTLSELREKYKQASVGVSSRTETLDEVMDEIEQLK 321 (384)
T ss_pred chhHHHHHHHHHHHHHHH-H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHH
Confidence 345789999999988662 1 112233343333332 333444554332 12256667777777777
Q ss_pred HHHHH
Q 031403 143 GVMME 147 (160)
Q Consensus 143 ~im~~ 147 (160)
+-|.+
T Consensus 322 qemEe 326 (384)
T KOG0972|consen 322 QEMEE 326 (384)
T ss_pred HHHHH
Confidence 76653
No 63
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=24.49 E-value=1.3e+02 Score=22.54 Aligned_cols=13 Identities=8% Similarity=0.276 Sum_probs=11.8
Q ss_pred CeeEEEeCCeEEE
Q 031403 44 NKFTYNCDAHTFN 56 (160)
Q Consensus 44 ~k~s~~~~~~~~h 56 (160)
++.+|..++|.||
T Consensus 182 ~kVvFDRgGy~YH 194 (211)
T PTZ00032 182 SKVRFDRAHYKYA 194 (211)
T ss_pred CEEEEeCCCCeeh
Confidence 6799999999998
No 64
>PRK09855 PTS system N-acetylgalactosamine-specific transporter subunit IID; Provisional
Probab=24.48 E-value=2.6e+02 Score=21.80 Aligned_cols=45 Identities=13% Similarity=0.206 Sum_probs=26.6
Q ss_pred CCCcccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChH
Q 031403 72 SSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPE 126 (160)
Q Consensus 72 ~~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~ 126 (160)
+|.+-.+..|.-.+.-...+.|..+ +.+..+.+++-+++||.+|.
T Consensus 25 NyErmq~~gf~~~m~P~L~KlY~~~----------~e~~~~Al~rHl~ffNT~p~ 69 (263)
T PRK09855 25 NYERMQAGGFTWAMLPILKKIYKDD----------KPGLSAAMKDNLEFINTHPN 69 (263)
T ss_pred CHHHHhhHhHHHHHHHHHHHHcCCC----------HHHHHHHHHHHHHHHCCCch
Confidence 3444455555555544444445211 14556788888899998874
No 65
>COG2957 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]
Probab=24.35 E-value=1.2e+02 Score=24.46 Aligned_cols=47 Identities=13% Similarity=0.318 Sum_probs=32.1
Q ss_pred EEEeCCeeEEEEeccCCCHHHHHHHHhcCCCCC------CCeeEEEeCCeEEEEEEe
Q 031403 10 FVARGNVVLAEYTEFSGNFNSIAYQCLQKLPAS------NNKFTYNCDAHTFNYLVD 60 (160)
Q Consensus 10 ~Iar~~~iLae~~~~~~n~~~~~~~vL~~i~~~------~~k~s~~~~~~~~h~l~~ 60 (160)
+|+.+.+|.-.|.+.+ ..+|.++|++.=|. +.|..+ .++-++|++..
T Consensus 289 lI~N~avIvP~y~D~~---D~~a~~~L~~~fP~reVVGVp~r~il-~ggGs~HCiTq 341 (346)
T COG2957 289 LIINGAVIVPQYDDPN---DALALDVLQQAFPGREVVGVPAREIL-LGGGSLHCITQ 341 (346)
T ss_pred EEecCeEEeeccCCcc---hHHHHHHHHHhCCCCeEeccccHHhe-ecCCceEEEee
Confidence 6788888888887655 66788888877663 233333 35668888765
No 66
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=24.33 E-value=1.3e+02 Score=20.70 Aligned_cols=43 Identities=9% Similarity=0.193 Sum_probs=32.3
Q ss_pred HHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccccC
Q 031403 112 PKLKELMQYCVDHPEEISKLAKVKAQVSEVKGVMMENIEKVGMLCLFH 159 (160)
Q Consensus 112 ~~l~~~m~~yn~~p~~~dki~~i~~~v~evk~im~~Nid~iL~Rg~~~ 159 (160)
..+..+++. ++|. .+..+-+.++--+.-....++++++.||.-
T Consensus 31 ~v~~~LL~~--~~~~---tvdelae~lnr~rStv~rsl~~L~~~GlV~ 73 (126)
T COG3355 31 EVYKALLEE--NGPL---TVDELAEILNRSRSTVYRSLQNLLEAGLVE 73 (126)
T ss_pred HHHHHHHhh--cCCc---CHHHHHHHHCccHHHHHHHHHHHHHcCCee
Confidence 356677763 5674 345555678888999999999999999974
No 67
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=24.15 E-value=90 Score=21.60 Aligned_cols=44 Identities=5% Similarity=0.058 Sum_probs=27.5
Q ss_pred cCCCCCCCeeEEEeCCeEEEEEEeCCEEEEEEecCCCCcccHHHHH
Q 031403 37 QKLPASNNKFTYNCDAHTFNYLVDNGYTYCVVADESSGRQIPMAFL 82 (160)
Q Consensus 37 ~~i~~~~~k~s~~~~~~~~h~l~~~~l~~~citd~~~~~~~af~fL 82 (160)
.+|.|++.+..+..++.+|+|+....-..+ --.--|+++.+.-+
T Consensus 12 ~kIyPG~G~~fVR~DGkvf~FcssKC~k~f--~~kRnPRKlkWT~~ 55 (131)
T PRK14891 12 EEIEPGTGTMFVRKDGTVLHFVDSKCEKNY--DLGREARDLEWTEA 55 (131)
T ss_pred CcccCCCCcEEEecCCCEEEEecHHHHHHH--HccCCCccchhHHH
Confidence 467888888888889999999864211000 12334666666544
No 68
>PRK00807 50S ribosomal protein L24e; Validated
Probab=24.13 E-value=1.2e+02 Score=17.35 Aligned_cols=22 Identities=9% Similarity=0.190 Sum_probs=16.6
Q ss_pred CCCCCCCeeEEEeCCeEEEEEE
Q 031403 38 KLPASNNKFTYNCDAHTFNYLV 59 (160)
Q Consensus 38 ~i~~~~~k~s~~~~~~~~h~l~ 59 (160)
+|.|++.+..+..|+..|+|+.
T Consensus 10 ~I~pg~G~~~vr~Dgkv~~Fcs 31 (52)
T PRK00807 10 EIEPGTGKMYVKKDGTILYFCS 31 (52)
T ss_pred eEcCCCCeEEEEeCCcEEEEeC
Confidence 4566667777888888888875
No 69
>PF07792 Afi1: Docking domain of Afi1 for Arf3 in vesicle trafficking; InterPro: IPR012860 This domain occurs at the N terminus of Afi1, a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3. Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity. Although Arf3 is the homologue of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalisation. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localisation and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth.
Probab=24.12 E-value=2.6e+02 Score=19.63 Aligned_cols=50 Identities=20% Similarity=0.261 Sum_probs=31.2
Q ss_pred ceEEEEEEe-----CCeeEEEEecc-CC--CHHHHHHHHhcCCCCCCCeeEEEeCCeEEEEEEe
Q 031403 5 SLIYAFVAR-----GNVVLAEYTEF-SG--NFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVD 60 (160)
Q Consensus 5 ~I~Ya~Iar-----~~~iLae~~~~-~~--n~~~~~~~vL~~i~~~~~k~s~~~~~~~~h~l~~ 60 (160)
+|-|.++|. |.++-.+|... .| +-..+|..+|. -+ .-...++++++||..
T Consensus 1 ~veyIL~AEFDid~Gp~l~hQYP~~i~g~~de~~LAelMLP---Dg---~h~r~~DwTvFfL~~ 58 (145)
T PF07792_consen 1 HVEYILLAEFDIDKGPVLKHQYPSPIPGLEDEHMLAELMLP---DG---AHKRSEDWTVFFLNR 58 (145)
T ss_pred CeeEEEEEEEecCcCCEEEEeCCCCccCCccHHHHHHhhCC---cc---cccccCCEEEEEEcc
Confidence 367888876 67888888753 23 55666666652 22 112345888888864
No 70
>cd03164 CD53_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), CD53_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". CD53 is a tetraspanin of the lymphoid-myeloid lineage and has been implicated in apoptosis protection. It associates with integrin alpha4beta1. Some of the cellular responses modulated by CD53 may be mediated by JNK activation and/or via the AKT pathway.
Probab=23.99 E-value=1.4e+02 Score=18.12 Aligned_cols=9 Identities=11% Similarity=0.220 Sum_probs=3.4
Q ss_pred HHHHHHHHh
Q 031403 113 KLKELMQYC 121 (160)
Q Consensus 113 ~l~~~m~~y 121 (160)
.+.+.|+.|
T Consensus 14 ~~~~~~~~y 22 (86)
T cd03164 14 GLTDSLEQY 22 (86)
T ss_pred HHHHHHHHh
Confidence 333333333
No 71
>cd07604 BAR_ASAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ASAPs (ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) with similarity to ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins) in that they contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and ankyrin (ANK) repeats. However, ASAPs contain an additional C-terminal SH3 domain. ASAPs function in regulating cell growth, migration, and invasion. Vertebrates contain at least three members, ASAP1, ASAP2, and ASAP3. ASAP1 and ASAP2 shows GTPase activating protein (GAP) activity towards Arf1 and Arf5. They do not show GAP activity towards Arf6, but is able to mediate
Probab=23.55 E-value=3.1e+02 Score=20.63 Aligned_cols=47 Identities=15% Similarity=0.264 Sum_probs=28.4
Q ss_pred hhhHHHHHHHHHHhcC--Ch---HHHHHHHHHHHHHHHHHHHHHHhHHHHHh
Q 031403 108 KEFGPKLKELMQYCVD--HP---EEISKLAKVKAQVSEVKGVMMENIEKVGM 154 (160)
Q Consensus 108 ~~f~~~l~~~m~~yn~--~p---~~~dki~~i~~~v~evk~im~~Nid~iL~ 154 (160)
..|...|+++-..+.. +| ....+...+.++|.+-+.+|.+|++.+|-
T Consensus 40 ~~F~~aL~~~g~~~~~~~~~~i~~~l~kF~~~l~El~~~~~~L~~~~~~~i~ 91 (215)
T cd07604 40 LQFAEALEKLGSKALSREEEDLGAAFLKFSVFTKELAALFKNLMQNLNNIIM 91 (215)
T ss_pred HHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666655544321 11 23466777777788777777777776653
No 72
>PF13747 DUF4164: Domain of unknown function (DUF4164)
Probab=23.26 E-value=2.1e+02 Score=18.24 Aligned_cols=28 Identities=21% Similarity=0.177 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHhc
Q 031403 128 ISKLAKVKAQVSEVKGVMMENIEKVGML 155 (160)
Q Consensus 128 ~dki~~i~~~v~evk~im~~Nid~iL~R 155 (160)
.+++...+.+|..=-...+++|..+|+|
T Consensus 62 ~~~Le~~~~Evs~rL~~a~e~Ir~vL~r 89 (89)
T PF13747_consen 62 ANRLEEANREVSRRLDSAIETIRAVLDR 89 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3788888888888888888899988887
No 73
>cd03161 TM4SF2_6_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF2_6_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This subfamily contaions transmembrane 4 superfamily 2 (TM4SF2) or Tspan-7, transmembrane 4 superfamily 6 (TM4SF6) or Tspan-6, and related proteins. TM4SF2 has been identified as involved in some forms of X-linked mental retardation.
Probab=22.94 E-value=1.1e+02 Score=19.33 Aligned_cols=14 Identities=14% Similarity=0.069 Sum_probs=6.7
Q ss_pred hHHHHHHHHHHhcC
Q 031403 110 FGPKLKELMQYCVD 123 (160)
Q Consensus 110 f~~~l~~~m~~yn~ 123 (160)
+...|.+.++.|+.
T Consensus 11 l~~~l~~~i~~y~~ 24 (104)
T cd03161 11 FLRTYNEAVSNYNG 24 (104)
T ss_pred HHHHHHHHHHHhcC
Confidence 34445555555543
No 74
>PRK11103 PTS system mannose-specific transporter subunit IID; Provisional
Probab=22.92 E-value=3e+02 Score=21.68 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=25.9
Q ss_pred CCCcccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChH
Q 031403 72 SSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPE 126 (160)
Q Consensus 72 ~~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~ 126 (160)
+|.+-.+..|+-.+.-...+.|+.+ ..+..+.+++-+++||..|.
T Consensus 33 NyErmQ~~gf~~sm~P~LkKlY~~d----------~e~~~~Al~Rhl~fFNT~p~ 77 (282)
T PRK11103 33 NFERMQALGFCFSMVPAIRRLYPEN----------NEARKQAIKRHLEFFNTHPY 77 (282)
T ss_pred CHHHHhhHhHHHHHHHHHHHHcCCC----------HHHHHHHHHHHHHHHCCCch
Confidence 3444444455545444444444211 14566788888899998874
No 75
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=22.67 E-value=2.4e+02 Score=20.85 Aligned_cols=38 Identities=16% Similarity=0.283 Sum_probs=24.9
Q ss_pred hHHHHHHHHHHhcCCh--HHHHHHHHHHHHHHHHHHHHHHh
Q 031403 110 FGPKLKELMQYCVDHP--EEISKLAKVKAQVSEVKGVMMEN 148 (160)
Q Consensus 110 f~~~l~~~m~~yn~~p--~~~dki~~i~~~v~evk~im~~N 148 (160)
-...+.++-.||| |- .+.+-|..++.+|.+.+.--..|
T Consensus 7 He~af~~iK~YYn-dIT~~NL~lIksLKeei~emkk~e~~~ 46 (201)
T PF13851_consen 7 HEKAFQEIKNYYN-DITLNNLELIKSLKEEIAEMKKKEERN 46 (201)
T ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456667778886 43 35678888888888876544433
No 76
>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=22.45 E-value=2.8e+02 Score=19.36 Aligned_cols=66 Identities=8% Similarity=0.116 Sum_probs=39.6
Q ss_pred CcccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCCh---HHHHHHHHHHHHHHHH
Q 031403 74 GRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHP---EEISKLAKVKAQVSEV 141 (160)
Q Consensus 74 ~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p---~~~dki~~i~~~v~ev 141 (160)
.++.|-.=+.+..+.|...|.... ....--++ ......|..+--+|++.| -....-.+|.+|++++
T Consensus 60 ~~~~a~~~ar~~indyvsrYRr~~-~v~g~~SF-ttm~TALNsLAGHY~sy~~rPlPeklk~Rl~~El~~A 128 (135)
T TIGR03044 60 NKSEAQAEARQLINDYISRYRRRP-RVNGLSSF-TTMQTALNSLAGHYKSYANRPLPEKLKERLEKELKKA 128 (135)
T ss_pred cHHHHHHHHHHHHHHHHHHhcCCC-CcCCcccH-HHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHH
Confidence 345666777788888888884321 11222233 455567888888887654 2224556777777665
No 77
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=22.31 E-value=79 Score=17.84 Aligned_cols=30 Identities=7% Similarity=0.120 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHhccccC
Q 031403 130 KLAKVKAQVSEVKGVMMENIEKVGMLCLFH 159 (160)
Q Consensus 130 ki~~i~~~v~evk~im~~Nid~iL~Rg~~~ 159 (160)
.+.+|-+.+.--+.-+...|+++.++||..
T Consensus 23 t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 23 TQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 567777777778888999999999999864
No 78
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=21.99 E-value=2.7e+02 Score=19.07 Aligned_cols=81 Identities=17% Similarity=0.315 Sum_probs=42.8
Q ss_pred CeEEEEEEeCCE--------EEEEEecCCCCcc-cHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHH-HHHHHHHHh
Q 031403 52 AHTFNYLVDNGY--------TYCVVADESSGRQ-IPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGP-KLKELMQYC 121 (160)
Q Consensus 52 ~~~~h~l~~~~l--------~~~citd~~~~~~-~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~-~l~~~m~~y 121 (160)
++++|...++|+ .|++ .....|++ .+-.+++.|.... +. -...|..|.+ .|+++.+.+
T Consensus 27 Q~Slhi~~~~g~~~~~~~h~efL~-~~~~DPr~~~~~~L~~~i~~~~-----g~------ivvyN~sfE~~rL~ela~~~ 94 (130)
T PF11074_consen 27 QFSLHITDNDGIIYKELEHVEFLA-DPGEDPRRELIEALIKAIGSIY-----GS------IVVYNKSFEKTRLKELAELF 94 (130)
T ss_pred EEEEEEEcCCCcccCchhhHHHhc-cCCCCchHHHHHHHHHHhhhhc-----Ce------EEEechHHHHHHHHHHHHHh
Confidence 477888877773 3444 33344443 3334444443332 11 1123455775 456666664
Q ss_pred cCChHHHHHHHHHHHHHHHHHHHHHH
Q 031403 122 VDHPEEISKLAKVKAQVSEVKGVMME 147 (160)
Q Consensus 122 n~~p~~~dki~~i~~~v~evk~im~~ 147 (160)
|.-.+++..+.+.+-|.......
T Consensus 95 ---p~~~~~l~~I~~r~vDL~~~f~~ 117 (130)
T PF11074_consen 95 ---PDYAEKLNSIIERTVDLLDPFKN 117 (130)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHhh
Confidence 44347788877777766655443
No 79
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=21.41 E-value=59 Score=21.07 Aligned_cols=22 Identities=23% Similarity=0.063 Sum_probs=17.6
Q ss_pred HHHHHHHHHhHHHHHhccccCC
Q 031403 139 SEVKGVMMENIEKVGMLCLFHK 160 (160)
Q Consensus 139 ~evk~im~~Nid~iL~Rg~~~~ 160 (160)
+..+.....||.-+|..||..|
T Consensus 43 ~~~~~~V~SNIGvLIKkglIEK 64 (96)
T PF09114_consen 43 EMNKASVNSNIGVLIKKGLIEK 64 (96)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HhhhhHHHHhHHHHHHcCcccc
Confidence 4467788999999999999754
No 80
>PF11598 COMP: Cartilage oligomeric matrix protein; InterPro: IPR024665 Thrombospondins are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. Cartilage oligomeric matrix protein may play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as collagen and fibronectin [, ]. Thrombospondin 3 and 4 and cartilage oligomeric matrix proteins contain a five-stranded coiled-coil domain represented by this entry. This domain has a binding site between two internal rings formed by Leu37 and Thr40 [].; PDB: 1MZ9_D 1FBM_A 1VDF_E.
Probab=21.36 E-value=1.7e+02 Score=16.32 Aligned_cols=22 Identities=18% Similarity=0.466 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHHHHhHHH
Q 031403 130 KLAKVKAQVSEVKGVMMENIEK 151 (160)
Q Consensus 130 ki~~i~~~v~evk~im~~Nid~ 151 (160)
.+..+.+-+.|+|+.|.+.+..
T Consensus 9 ql~~l~~~l~elk~~l~~Q~kE 30 (45)
T PF11598_consen 9 QLSELNQMLQELKELLRQQIKE 30 (45)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444455556666555543
No 81
>PF03613 EIID-AGA: PTS system mannose/fructose/sorbose family IID component; InterPro: IPR004704 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IID subunits of this family of PTS transporters.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane
Probab=21.19 E-value=2.9e+02 Score=21.47 Aligned_cols=45 Identities=18% Similarity=0.207 Sum_probs=31.9
Q ss_pred CCCCcccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChH
Q 031403 71 ESSGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPE 126 (160)
Q Consensus 71 ~~~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~ 126 (160)
-+|.+-.+..|+--+.-...+.|+ + ..+..+.+++-+++||..|.
T Consensus 22 ~nyErmq~~gf~~~m~P~lkklY~-~----------~e~~~~al~rh~~fFNT~p~ 66 (264)
T PF03613_consen 22 WNYERMQGLGFAYSMLPALKKLYK-D----------KEELKEALKRHMEFFNTEPF 66 (264)
T ss_pred CCHHHHHhHhHHHHHHHHHHHHcC-C----------HHHHHHHHHHHHHHHCCCCh
Confidence 345566667777777777777673 1 25667889999999998884
No 82
>cd03163 TM4SF8_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF8_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This subfamily contaions transmembrane 4 superfamily 8 (TM4SF8) or Tspan-3 and related proteins. Tspan-3 has been reported to form a complex with integrin beta1 and OSP/claudin-11, which may be involved in oligodendrocyte proliferation and migration.
Probab=21.16 E-value=1.6e+02 Score=18.67 Aligned_cols=12 Identities=8% Similarity=0.332 Sum_probs=5.7
Q ss_pred HHHHHHHHHHhc
Q 031403 111 GPKLKELMQYCV 122 (160)
Q Consensus 111 ~~~l~~~m~~yn 122 (160)
...+++.++.|+
T Consensus 13 ~~~~~~~~~~y~ 24 (105)
T cd03163 13 NPSIDKVFNKYN 24 (105)
T ss_pred HHHHHHHHHHhc
Confidence 344455555453
No 83
>PHA01351 putative minor structural protein
Probab=21.15 E-value=6.4e+02 Score=23.05 Aligned_cols=77 Identities=17% Similarity=0.306 Sum_probs=55.1
Q ss_pred cccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChHHHHHHH---HHHHHHHHHHHHHHHhHHH
Q 031403 75 RQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPEEISKLA---KVKAQVSEVKGVMMENIEK 151 (160)
Q Consensus 75 ~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~~~dki~---~i~~~v~evk~im~~Nid~ 151 (160)
+|++-+||+.+.++=.+.|+ +||=--.=+++++.++.+.- +.|.+.+.+= --|+|+-+..+.+..-+++
T Consensus 419 qr~~rq~lrsllsralsnfg-------rpyid~~yl~st~~~lfkel-~~p~~v~~~f~~mi~qsqliq~nqll~~~l~s 490 (1070)
T PHA01351 419 QRIVRQFLRSLLSRALSNFG-------RPYLDFKYLDSTIAKLFKDL-GYPEEVRTVFDTMITQSQLIQTNQLLLRQLQQ 490 (1070)
T ss_pred HHHHHHHHHHHHHHHHHhCC-------CcceehHHHHHHHHHHHHHc-CCcHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 78888999999888887773 24411123567788888877 4787665543 3467788888888888889
Q ss_pred HHhccccC
Q 031403 152 VGMLCLFH 159 (160)
Q Consensus 152 iL~Rg~~~ 159 (160)
+++.|.+.
T Consensus 491 l~skGi~D 498 (1070)
T PHA01351 491 IVSLGIFD 498 (1070)
T ss_pred HHHccccc
Confidence 88888764
No 84
>PF05073 Baculo_p24: Baculovirus P24 capsid protein; InterPro: IPR007765 The Culex nigripalpus NPV (Culex nigripalpus nucleopolyhedrovirus) protein p24 is associated with nucleocapsids of budded and polyhedra-derived virions [, ].; GO: 0019028 viral capsid
Probab=21.03 E-value=3.1e+02 Score=20.15 Aligned_cols=22 Identities=23% Similarity=0.442 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhH
Q 031403 128 ISKLAKVKAQVSEVKGVMMENI 149 (160)
Q Consensus 128 ~dki~~i~~~v~evk~im~~Ni 149 (160)
.|.+..++.++..+++...+++
T Consensus 107 ~dpL~eIK~qLc~iqe~l~~~~ 128 (182)
T PF05073_consen 107 VDPLCEIKTQLCTIQECLNENN 128 (182)
T ss_pred HHHHHHHHHHHHHHHHHHhccc
Confidence 3666666666666666665544
No 85
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=20.80 E-value=1.3e+02 Score=17.34 Aligned_cols=24 Identities=17% Similarity=0.279 Sum_probs=18.3
Q ss_pred cCCCCCCCeeEEEeCCeEEEEEEe
Q 031403 37 QKLPASNNKFTYNCDAHTFNYLVD 60 (160)
Q Consensus 37 ~~i~~~~~k~s~~~~~~~~h~l~~ 60 (160)
.+|.|++.+.-+..|+-.|+|+..
T Consensus 11 ~~I~PG~G~~~Vr~Dgkv~~F~s~ 34 (54)
T cd00472 11 YKIYPGHGKMYVRNDGKVFRFCSS 34 (54)
T ss_pred CeecCCCccEEEecCCCEEEEECH
Confidence 357777778888888888888753
No 86
>COG3716 ManZ Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]
Probab=20.76 E-value=3.3e+02 Score=21.36 Aligned_cols=44 Identities=16% Similarity=0.327 Sum_probs=26.9
Q ss_pred CCcccHHHHHHHHHHHHHhhhCCCCCCCCCCCccchhhHHHHHHHHHHhcCChH
Q 031403 73 SGRQIPMAFLERVKDEFVSKYGGGKAATAPANGLNKEFGPKLKELMQYCVDHPE 126 (160)
Q Consensus 73 ~~~~~af~fL~~i~~~F~~~~~~~~~~~~~~~~l~~~f~~~l~~~m~~yn~~p~ 126 (160)
|.+-.+..|+-.+--...+.|+.+ ..+..+.+++-++.||..|.
T Consensus 28 yERmq~~G~~ysmlPalKKlY~~~----------k~~~~~AlkrHleFFNT~P~ 71 (269)
T COG3716 28 YERMQALGYLYAMLPALKKLYPDD----------KEDLKEALKRHLEFFNTHPH 71 (269)
T ss_pred HHHHhhhhHHHHHHHHHHHHcCCC----------cHHHHHHHHHHHHHhcCCch
Confidence 344445555555555555555311 15667888999999998884
No 87
>cd07603 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=20.60 E-value=3.6e+02 Score=19.94 Aligned_cols=46 Identities=13% Similarity=0.294 Sum_probs=25.7
Q ss_pred hhhHHHHHHHHHHhcCChH---HHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 031403 108 KEFGPKLKELMQYCVDHPE---EISKLAKVKAQVSEVKGVMMENIEKVG 153 (160)
Q Consensus 108 ~~f~~~l~~~m~~yn~~p~---~~dki~~i~~~v~evk~im~~Nid~iL 153 (160)
..|...|.++-..+..||. ...+....-+++..-+.+|.+|++.++
T Consensus 40 ~~F~~~L~~~~~~~~~d~~i~~~l~kF~~~l~el~~~~~~L~~q~~~~i 88 (200)
T cd07603 40 SLFVNSLNDLSDYFRDDSLVQNCLNKFIQALQEMNNFHTILLDQAQRTV 88 (200)
T ss_pred HHHHHHHHHHhcccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666666666654432 234445555566666666666665544
No 88
>PF12641 Flavodoxin_3: Flavodoxin domain
Probab=20.40 E-value=3e+02 Score=19.56 Aligned_cols=65 Identities=18% Similarity=0.225 Sum_probs=35.6
Q ss_pred EEEeccCCCHHHHHHHHhcCCCCCCCeeEEEeCCeEEEEEEeCCEEEEEE-ecCCCCcccHHHHHHHHHH
Q 031403 19 AEYTEFSGNFNSIAYQCLQKLPASNNKFTYNCDAHTFNYLVDNGYTYCVV-ADESSGRQIPMAFLERVKD 87 (160)
Q Consensus 19 ae~~~~~~n~~~~~~~vL~~i~~~~~k~s~~~~~~~~h~l~~~~l~~~ci-td~~~~~~~af~fL~~i~~ 87 (160)
.-|+...||-..+|..|.+.++.. .-..+..-.-. +.+-+++|++. ++.+.+....-.||..|+.
T Consensus 2 IvYsS~TGNTkkvA~aI~~~l~~~-~~~~~~~~~~~---~~~yD~i~lG~w~d~G~~d~~~~~fl~~l~~ 67 (160)
T PF12641_consen 2 IVYSSRTGNTKKVAEAIAEALGAK-DIVSVEEPPED---LEDYDLIFLGFWIDKGTPDKDMKEFLKKLKG 67 (160)
T ss_pred EEEECCCChHHHHHHHHHHHCCCc-eeEeccccccC---CCCCCEEEEEcCccCCCCCHHHHHHHHHccC
Confidence 347777899999999999988871 11222211100 22234444433 4455555555566665544
No 89
>PF08360 TetR_C_5: QacR-like protein, C-terminal region; InterPro: IPR013571 This entry represents the C-terminal domain found in the multidrug-binding transcription regulator QacR (P23217 from SWISSPROT) from Staphylococcus aureus, which is a member of the TetR (tetracycline-resistance) transcriptional regulator family of proteins. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (P23215 from SWISSPROT), a multidrug efflux pump []. The C-terminal region of QacR contains a multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites []. The C-terminal domains of QacR and TetR share a multi-helical, interlocking structure.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G0E_E 1JUM_A 1RPW_D 1QVT_B 2HQ5_D 1JT0_B 2DTZ_E 1JUP_D 1JT6_D 1JUS_E ....
Probab=20.09 E-value=1.6e+02 Score=20.18 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHhHHHHHhccc
Q 031403 135 KAQVSEVKGVMMENIEKVGMLCL 157 (160)
Q Consensus 135 ~~~v~evk~im~~Nid~iL~Rg~ 157 (160)
.+++.++..--.+-+.+||++|.
T Consensus 56 ~~~l~~i~~~~~~~~~~ileeGI 78 (131)
T PF08360_consen 56 LEKLNEIRRKYLEFFQKILEEGI 78 (131)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444555566666664
Done!