Query psy8727
Match_columns 300
No_of_seqs 171 out of 1529
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 17:41:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8727.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8727hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1471|consensus 100.0 1.1E-40 2.4E-45 305.8 18.2 240 15-260 2-260 (317)
2 KOG1470|consensus 100.0 1.4E-38 3E-43 283.4 17.7 196 56-259 46-245 (324)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 4.6E-31 9.9E-36 217.8 8.5 146 111-256 5-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 4.6E-28 1E-32 199.6 13.7 137 119-258 14-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 1.7E-26 3.7E-31 188.7 12.1 143 113-256 9-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.4 1.6E-13 3.5E-18 112.2 5.0 137 116-260 5-147 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 98.9 2E-09 4.4E-14 72.7 5.4 48 36-83 1-55 (55)
8 KOG4406|consensus 98.1 2.6E-05 5.6E-10 72.0 10.3 131 105-244 71-206 (467)
9 PF14555 UBA_4: UBA-like domai 87.5 2.4 5.2E-05 26.6 5.3 35 37-80 2-36 (43)
10 smart00546 CUE Domain that may 81.8 5.2 0.00011 24.9 5.0 38 36-81 3-40 (43)
11 PF02845 CUE: CUE domain; Int 78.4 7.3 0.00016 24.1 4.8 38 37-82 3-40 (42)
12 PF06972 DUF1296: Protein of u 73.1 14 0.00031 24.9 5.2 43 32-82 2-44 (60)
13 PF14213 DUF4325: Domain of un 66.2 22 0.00049 24.9 5.6 51 166-221 17-69 (74)
14 cd04750 Commd2 COMM_Domain con 63.6 82 0.0018 26.0 9.3 139 15-157 13-159 (166)
15 PF03474 DMA: DMRTA motif; In 60.0 18 0.00039 22.3 3.4 24 57-80 15-38 (39)
16 PF00627 UBA: UBA/TS-N domain; 53.7 23 0.0005 21.1 3.3 23 58-80 15-37 (37)
17 cd00194 UBA Ubiquitin Associat 51.5 25 0.00055 20.8 3.2 24 57-80 13-36 (38)
18 smart00165 UBA Ubiquitin assoc 49.9 27 0.0006 20.5 3.2 24 57-80 13-36 (37)
19 PF04079 DUF387: Putative tran 48.1 70 0.0015 26.3 6.3 111 20-133 15-142 (159)
20 smart00804 TAP_C C-terminal do 45.4 97 0.0021 21.2 5.8 27 57-83 25-51 (63)
21 PF08938 HBS1_N: HBS1 N-termin 43.7 3.7 8E-05 29.5 -1.7 43 34-82 27-69 (79)
22 cd07322 PriL_PriS_Eukaryotic E 42.7 1.4E+02 0.0031 28.3 8.3 46 36-83 225-270 (390)
23 PF04378 RsmJ: Ribosomal RNA s 41.7 19 0.00041 31.8 2.1 32 202-233 203-234 (245)
24 PF05344 DUF746: Domain of Unk 40.6 42 0.00092 23.2 3.2 29 20-48 15-43 (65)
25 PF11964 SpoIIAA-like: SpoIIAA 40.4 1.1E+02 0.0023 22.6 5.9 76 140-226 11-87 (109)
26 COG2961 ComJ Protein involved 39.4 24 0.00053 31.3 2.4 27 205-231 237-263 (279)
27 COG0466 Lon ATP-dependent Lon 35.0 1.4E+02 0.0031 30.7 7.2 31 61-91 316-346 (782)
28 PRK00117 recX recombination re 34.3 1.6E+02 0.0035 23.6 6.5 68 13-84 87-154 (157)
29 PRK14136 recX recombination re 34.0 1.6E+02 0.0034 27.0 6.7 65 14-83 238-302 (309)
30 PHA02570 dexA exonuclease; Pro 32.9 1.5E+02 0.0032 25.8 6.1 59 24-88 75-135 (220)
31 TIGR02886 spore_II_AA anti-sig 32.5 1.8E+02 0.004 21.2 6.1 51 167-223 40-90 (106)
32 cd01886 EF-G Elongation factor 32.1 1.4E+02 0.0031 26.6 6.3 58 30-91 187-244 (270)
33 PF03641 Lysine_decarbox: Poss 32.0 62 0.0013 25.5 3.5 38 206-243 86-128 (133)
34 TIGR02364 dha_pts dihydroxyace 31.6 1.3E+02 0.0029 23.5 5.3 52 165-228 60-111 (125)
35 PF04838 Baculo_LEF5: Baculovi 30.4 34 0.00074 27.7 1.7 48 189-237 17-68 (159)
36 PRK14137 recX recombination re 30.2 3.1E+02 0.0066 23.3 7.6 70 15-88 115-184 (195)
37 KOG2005|consensus 30.0 1.1E+02 0.0025 31.1 5.5 66 12-81 35-108 (878)
38 cd07042 STAS_SulP_like_sulfate 27.5 1.6E+02 0.0035 21.1 5.1 50 167-222 42-91 (107)
39 KOG3923|consensus 26.8 27 0.00059 31.9 0.7 43 165-220 182-224 (342)
40 KOG2267|consensus 26.2 1.4E+02 0.003 28.3 5.1 48 36-85 288-335 (475)
41 smart00151 SWIB SWI complex, B 26.0 2.4E+02 0.0052 19.8 6.3 66 14-84 5-75 (77)
42 KOG1838|consensus 25.4 6.1E+02 0.013 24.3 9.7 85 122-220 122-213 (409)
43 PF11339 DUF3141: Protein of u 24.4 3.5E+02 0.0076 26.9 7.6 79 124-218 100-179 (581)
44 PF13466 STAS_2: STAS domain 24.3 2.3E+02 0.0051 19.4 5.2 51 167-223 27-77 (80)
45 TIGR00281 segregation and cond 23.7 4.4E+02 0.0094 22.2 7.4 108 24-133 23-147 (186)
46 PF03943 TAP_C: TAP C-terminal 23.4 1.2E+02 0.0025 19.7 3.0 26 57-82 13-38 (51)
47 PF13950 Epimerase_Csub: UDP-g 22.8 1.3E+02 0.0028 20.3 3.3 32 20-51 28-60 (62)
48 PF01740 STAS: STAS domain; I 22.4 97 0.0021 23.2 3.0 49 167-221 49-97 (117)
49 TIGR03824 FlgM_jcvi flagellar 22.3 1.3E+02 0.0027 22.2 3.5 35 14-48 41-77 (95)
50 PF14053 DUF4248: Domain of un 21.6 95 0.0021 21.6 2.5 29 22-52 10-38 (69)
51 KOG4119|consensus 21.4 1.5E+02 0.0032 20.9 3.3 30 20-49 15-44 (71)
52 PF02954 HTH_8: Bacterial regu 21.2 1.2E+02 0.0025 18.6 2.6 24 58-81 6-29 (42)
53 PRK14484 phosphotransferase ma 20.7 3.5E+02 0.0076 21.2 5.8 49 165-227 58-106 (124)
54 TIGR00377 ant_ant_sig anti-ant 20.3 3.5E+02 0.0075 19.6 6.3 53 165-223 42-94 (108)
No 1
>KOG1471|consensus
Probab=100.00 E-value=1.1e-40 Score=305.77 Aligned_cols=240 Identities=28% Similarity=0.342 Sum_probs=202.6
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHhhcc-cc
Q psy8727 15 SVSKQGLQIAKAELREDESTREDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERYILLRNTYG-DL 93 (300)
Q Consensus 15 ~~~~~~~~~~~~el~e~~e~~~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~~~~R~~~~-d~ 93 (300)
+.++.+...+.+++++.++..++.++.+| |+.++|+++....||.+|+|||||++||+++|++++.+++.||.++. |+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~i~~lr-~~~~~~~l~~~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~ 80 (317)
T KOG1471|consen 2 SLSPMLAKVAKEELNEITESEEAVIAQLR-WLLQKPHLPNKYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDE 80 (317)
T ss_pred CcccccccccccccCCCcHHHHHHHHHHH-HHhhccCCCCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCcc
Confidence 35667778889999999999999999999 99999999854689999999999999999999999999999999998 78
Q ss_pred ccccCCCCCHHHHHHHHcCceeeCCCCCCCCCEEEEEecCCCCCCCC----CHHHH--------HHHHHHHHHHhhcccC
Q psy8727 94 AFSKLDPKNPTMQELLKLGYLFATPKRDKLGRRVIIARPGVFNPHKY----TNSHM--------LQIHGMTYETLMEDEE 161 (300)
Q Consensus 94 ~~~~~~~~~~~~~~~l~~g~~~~l~g~Dk~GrpV~~~~~~~~~~~~~----~~~~~--------~r~~~~~le~~~~~~~ 161 (300)
++.+.+.. .++.. -+....+|.|+.|+||.+.+.|..+.+.. ...+. .+.+.+.++......+
T Consensus 81 i~~~~~~~-~~~~~----~~~~~~~~~~~~g~~v~~~~~g~~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~ 155 (317)
T KOG1471|consen 81 IFEDFEED-DELLK----YYPQGLHGVDKEGRPVYIERLGKIDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGE 155 (317)
T ss_pred Hhhccccc-hhhhh----hccccccccCCCCCEEEEeccCCCCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 88763322 12222 22334568999999999999999877654 44444 4444455555554446
Q ss_pred ceeccEEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHHHHHhhhcCHhhhcceE-Ee-c
Q psy8727 162 NQVRGFVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFGLNLVSEKIRKRIK-VS-V 239 (300)
Q Consensus 162 ~~~~g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~likpfl~~~t~~Ki~-~~-~ 239 (300)
.+++|+++|+|++|++++|+++..++.+++++..+|++||++++++||||+|++|+++|+++||||+++|++||+ ++ +
T Consensus 156 ~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~~ 235 (317)
T KOG1471|consen 156 RQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHSK 235 (317)
T ss_pred CCcceeEEEEECCCCcchhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCCC
Confidence 789999999999999999999999999999999999999999999999999999999999999999999999999 55 4
Q ss_pred ccccc--ccchhh--hcCCCCCchh
Q psy8727 240 IVNAR--FLLRFL--RSKKFSVPMA 260 (300)
Q Consensus 240 ~~~~L--~i~~~~--~eyGG~~~~~ 260 (300)
+.++| +||+++ ++|||+++..
T Consensus 236 ~~~~L~k~i~~~~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 236 DKESLLKYIPPEVLPEEYGGTCGDL 260 (317)
T ss_pred chhhhhhhCCHhhCccccCCCcccc
Confidence 56777 999994 9999999886
No 2
>KOG1470|consensus
Probab=100.00 E-value=1.4e-38 Score=283.44 Aligned_cols=196 Identities=18% Similarity=0.166 Sum_probs=173.5
Q ss_pred CCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHhhccccccccCCCCCHHHHHHHHcCceeeCCCCCCCCCEEEEEecCCC
Q psy8727 56 RLDARFLLRFLRSKKFSVPMAEEALERYILLRNTYGDLAFSKLDPKNPTMQELLKLGYLFATPKRDKLGRRVIIARPGVF 135 (300)
Q Consensus 56 ~~dd~~llRFLra~~~dv~~A~~~l~~~~~~R~~~~d~~~~~~~~~~~~~~~~l~~g~~~~l~g~Dk~GrpV~~~~~~~~ 135 (300)
..+|.+++|||||+||||.+|.+++.+++.||+.++ . .. .....++...++.|.++.+ |+|++||||+|+++..+
T Consensus 46 ~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~-~--~~-~~~~~Ev~~e~~tGK~yi~-G~D~~gRPVl~~~~~~~ 120 (324)
T KOG1470|consen 46 WCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFG-P--EE-VIEADEVAAELETGKAYIL-GHDKDGRPVLYLRPRPH 120 (324)
T ss_pred cCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcC-C--cc-ccCHHHHHHHhhcCcEEEe-cccCCCCeEEEEecCCC
Confidence 468999999999999999999999999999999987 1 11 1223458889999999888 79999999999988888
Q ss_pred CCCCCCHHHHHHHHHHHHHHhhcccCceeccEEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChH
Q psy8727 136 NPHKYTNSHMLQIHGMTYETLMEDEENQVRGFVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPS 215 (300)
Q Consensus 136 ~~~~~~~~~~~r~~~~~le~~~~~~~~~~~g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~ 215 (300)
.++..+..+..|+++|++|.++.....+++++++++|++|+|++| ++.+..+.+++++|+||||||+..+++|+||+
T Consensus 121 ~qn~~t~~~~~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs~sN---~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~i 197 (324)
T KOG1470|consen 121 RQNTKTQKELERLLVYTLENAILFLPPGQEQFVWLFDLTGFSMSN---PDIKFLKELLHILQDHYPERLGKALLVNAPWI 197 (324)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHhCCCCcceEEEEEecccCcccC---CCcHHHHHHHHHHHHhChHHhhhhhhcCChHH
Confidence 888889999999999999999743333568899999999999995 57999999999999999999999999999999
Q ss_pred HHHHHHHHhhhcCHhhhcceEEecccccc--ccchh-h-hcCCCCCch
Q psy8727 216 VKYALDFGLNLVSEKIRKRIKVSVIVNAR--FLLRF-L-RSKKFSVPM 259 (300)
Q Consensus 216 f~~~w~likpfl~~~t~~Ki~~~~~~~~L--~i~~~-~-~eyGG~~~~ 259 (300)
|..+|+++||||+++|++||.|..+.+.+ |||++ + ..|||+...
T Consensus 198 F~~~wkiikpflDp~t~~Kv~F~~~~~~l~~~~d~~~l~s~~GG~~~~ 245 (324)
T KOG1470|consen 198 FQPFWKIIKPFLDPKTASKVKFVEPKDDLSEYFDESQLPSLFGGKLLF 245 (324)
T ss_pred HHHHHHHhhhccChhhhceeEEecChhHHHhhCCccccchhhCCCccc
Confidence 99999999999999999999999655556 99999 5 999997743
No 3
>PF00650 CRAL_TRIO: CRAL/TRIO domain; InterPro: IPR001251 This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1OLM_E 1O6U_E 3Q8G_A 3B7Q_B 3B7Z_A ....
Probab=99.97 E-value=4.6e-31 Score=217.84 Aligned_cols=146 Identities=23% Similarity=0.238 Sum_probs=119.6
Q ss_pred cCceeeCCCCCCCCCEEEEEecCCCCCCCCCHHHHHHHHHHHHHHhh-cccC-ceeccEEEEEeCCCCCcccccCCCHHH
Q psy8727 111 LGYLFATPKRDKLGRRVIIARPGVFNPHKYTNSHMLQIHGMTYETLM-EDEE-NQVRGFVHFNDGAGVSFPHLTLFTPKE 188 (300)
Q Consensus 111 ~g~~~~l~g~Dk~GrpV~~~~~~~~~~~~~~~~~~~r~~~~~le~~~-~~~~-~~~~g~v~IiD~~g~s~~~~~~~~~~~ 188 (300)
.+...+++|+|++||||+++++++++++.++.+++++++++++|.++ ..+. .++.|+++|+|++|++++++...+.+.
T Consensus 5 ~~~~~~~~g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~~~~ 84 (159)
T PF00650_consen 5 KSGPFYLHGRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFSLSNFDWWPISF 84 (159)
T ss_dssp TTSCEEEEEE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT--HHHHHCHHHHH
T ss_pred CCeeEEECCCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCceEeccccchhhh
Confidence 34455667999999999999999999999999999999999999987 3333 688999999999999999887555899
Q ss_pred HHHHHHHhhcccCceeceEEEEeCChHHHHHHHHHhhhcCHhhhcceEEecc--c-ccc--ccchh-h-hcCCCC
Q psy8727 189 AVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFGLNLVSEKIRKRIKVSVI--V-NAR--FLLRF-L-RSKKFS 256 (300)
Q Consensus 189 ~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~likpfl~~~t~~Ki~~~~~--~-~~L--~i~~~-~-~eyGG~ 256 (300)
++.+++++|++||+|++++|+||+|++|+++|+++++|++++|++||+++++ + ++| +||++ + ++|||+
T Consensus 85 ~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~~GG~ 159 (159)
T PF00650_consen 85 LKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVEYGGT 159 (159)
T ss_dssp HHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGGGTSS
T ss_pred hhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchhcCCC
Confidence 9999999999999999999999999999999999999999999999999943 3 456 99999 5 999996
No 4
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.95 E-value=4.6e-28 Score=199.63 Aligned_cols=137 Identities=21% Similarity=0.214 Sum_probs=127.7
Q ss_pred CCCCCCCEEEEEecCCCCCCCCCHHHHHHHHHHHHHHhhcc--cCceeccEEEEEeCCCCCcccccCCCHHHHHHHHHHh
Q psy8727 119 KRDKLGRRVIIARPGVFNPHKYTNSHMLQIHGMTYETLMED--EENQVRGFVHFNDGAGVSFPHLTLFTPKEAVRIVKNG 196 (300)
Q Consensus 119 g~Dk~GrpV~~~~~~~~~~~~~~~~~~~r~~~~~le~~~~~--~~~~~~g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~l 196 (300)
|+|++||||+++++++++++..+.+++++++++++|.++.. ++.++.|+++|+|++|++++| ++++.+|.+++++
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~i~D~~~~~~~~---~~~~~lk~~~~~~ 90 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQREKKTGGIEGFTVIFDLKGLSMSN---PDLSVLRKILKIL 90 (158)
T ss_pred CCCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHHHhcCCCeeeEEEEEECCCCCccc---ccHHHHHHHHHHH
Confidence 79999999999999999999999999999999999998854 567899999999999999987 5789999999999
Q ss_pred hcccCceeceEEEEeCChHHHHHHHHHhhhcCHhhhcceEEecc--cccc--ccchh-h-hcCCCCCc
Q psy8727 197 ERTLPMRHKEIHIINCHPSVKYALDFGLNLVSEKIRKRIKVSVI--VNAR--FLLRF-L-RSKKFSVP 258 (300)
Q Consensus 197 q~~yP~rl~~i~ivN~P~~f~~~w~likpfl~~~t~~Ki~~~~~--~~~L--~i~~~-~-~eyGG~~~ 258 (300)
+++||+|++++||||+|++++++|+++++|+++++++||+++++ .+.| +||++ + .+|||++.
T Consensus 91 ~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~L~~~i~~~~lP~~~GG~~~ 158 (158)
T smart00516 91 QDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGNDSKEELLEYIDPEQLPEELGGTLD 158 (158)
T ss_pred HHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCCCHHHHHhhCCHhhCcHhhCCCCC
Confidence 99999999999999999999999999999999999999999954 6677 99999 5 99999873
No 5
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.94 E-value=1.7e-26 Score=188.72 Aligned_cols=143 Identities=29% Similarity=0.289 Sum_probs=126.9
Q ss_pred ceeeCCCCCCCCCEEEEEecCCCCCCC-CCHHHHHHHHHHHHHHhhcccCceeccEEEEEeCCCCCcccccCCCHHHHHH
Q psy8727 113 YLFATPKRDKLGRRVIIARPGVFNPHK-YTNSHMLQIHGMTYETLMEDEENQVRGFVHFNDGAGVSFPHLTLFTPKEAVR 191 (300)
Q Consensus 113 ~~~~l~g~Dk~GrpV~~~~~~~~~~~~-~~~~~~~r~~~~~le~~~~~~~~~~~g~v~IiD~~g~s~~~~~~~~~~~~k~ 191 (300)
.+.+.+|+|++||||+++++++.++.. .+.++.+++.++.+|.++..+..+..|+++|+|++|++++++. .+.+.+|+
T Consensus 9 ~~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~i~D~~~~~~~~~~-~~~~~~k~ 87 (157)
T cd00170 9 KVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQEDDEQVEGFVVIIDLKGLSLSHLL-PDPSLLKK 87 (157)
T ss_pred cccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhhhhhcccceEEEEECCCCChhccc-hhHHHHHH
Confidence 445565689999999999999655544 3559999999999999986665556799999999999999886 67899999
Q ss_pred HHHHhhcccCceeceEEEEeCChHHHHHHHHHhhhcCHhhhcceEEecc-cccc--ccchh-h-hcCCCC
Q psy8727 192 IVKNGERTLPMRHKEIHIINCHPSVKYALDFGLNLVSEKIRKRIKVSVI-VNAR--FLLRF-L-RSKKFS 256 (300)
Q Consensus 192 ~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~likpfl~~~t~~Ki~~~~~-~~~L--~i~~~-~-~eyGG~ 256 (300)
++++++++||++++++||||+|++|+++|+++++|+++++++||+++++ .++| +||++ + .+|||+
T Consensus 88 ~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 88 ILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSDKEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred HHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCCHHHHHhhCChhhCcHhhCCC
Confidence 9999999999999999999999999999999999999999999999966 7888 99999 5 999996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.42 E-value=1.6e-13 Score=112.16 Aligned_cols=137 Identities=18% Similarity=0.100 Sum_probs=93.9
Q ss_pred eCCCCCCCCCEEEEEecCCCCCCCCCHHHHHHHHHHHHHHhhcccCceeccEEEEEeCCCCCcccccCCCHHHHHHHHHH
Q psy8727 116 ATPKRDKLGRRVIIARPGVFNPHKYTNSHMLQIHGMTYETLMEDEENQVRGFVHFNDGAGVSFPHLTLFTPKEAVRIVKN 195 (300)
Q Consensus 116 ~l~g~Dk~GrpV~~~~~~~~~~~~~~~~~~~r~~~~~le~~~~~~~~~~~g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~ 195 (300)
...|+|++|+||+++...+. ++.. ++-+.+.|++..+... ....++++|+|++|++..+ ..+...++++...
T Consensus 5 ~~gG~d~~g~pV~~~~~~~~-~~~~---~~~~ll~yl~~~l~~~--~~~~~f~vVid~~~~~~~~--~~~~~~l~~~~~~ 76 (149)
T PF13716_consen 5 YPGGRDREGRPVVVFIASRL-PSSD---DLERLLLYLLSTLSEE--VVDKPFSVVIDHTGFSRSS--EPSLSWLKQLYKL 76 (149)
T ss_dssp EEEEEBTTS-EEEEEEGGG--C-TT---HHHHHHHHHHHHH-TT--TTTS-EEEEEE-TT--GGG-----HHHHHHTTTS
T ss_pred EecccCCCcCEEEEEECCcC-cchh---hHHHHHHHHHHhhhHH--hcCCCEEEEEEcCCCcccc--CCchHHHHHHHHH
Confidence 34589999999999997777 4333 6666666666655322 2346799999999998754 3467889999999
Q ss_pred hhcccCceeceEEEEeCChHHHHHH-HHHhhhcCHhh-hcceEEecccccc--ccchh-h-hcCCCCCchh
Q psy8727 196 GERTLPMRHKEIHIINCHPSVKYAL-DFGLNLVSEKI-RKRIKVSVIVNAR--FLLRF-L-RSKKFSVPMA 260 (300)
Q Consensus 196 lq~~yP~rl~~i~ivN~P~~f~~~w-~likpfl~~~t-~~Ki~~~~~~~~L--~i~~~-~-~eyGG~~~~~ 260 (300)
+...|+..+++++|||++++++.++ .+.+++.+.+. ..||.+.++..+| +||++ + .+.||+.+..
T Consensus 77 l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~sl~~L~~~i~~~qL~~~lp~~~~~d 147 (149)
T PF13716_consen 77 LPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSSLSELSKHIDPSQLPESLPGVLQYD 147 (149)
T ss_dssp S-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESSTCGGGGTSGGGG------HHH---
T ss_pred HHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECCHHHHHhhCCHHHhcccCCCEEecC
Confidence 9999999999999999999999999 66678889998 8999999889998 99998 5 8999876543
No 7
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=98.93 E-value=2e-09 Score=72.69 Aligned_cols=48 Identities=35% Similarity=0.478 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHhC-------CCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHH
Q psy8727 36 EDALIQLRQWITKN-------SRIQTCRLDARFLLRFLRSKKFSVPMAEEALERY 83 (300)
Q Consensus 36 ~~~l~~Lr~~l~~~-------p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~ 83 (300)
++++++|++.+... ++......+|.+++|||||++|||++|.++|.++
T Consensus 1 k~~l~~l~~~l~~~~~~~~~~~~~~~~~~~d~~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 1 KQKLKQLREHLSELDEKAPGLWDDEKEDHDDNFLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp HHHHHHHHHHHHH--GGGTHHHTTHTSS-SHHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhccchhcccccccCCCCHHHHHHHHHHccCCHHHHHHHHHhC
Confidence 47889999999874 1222236899999999999999999999999875
No 8
>KOG4406|consensus
Probab=98.09 E-value=2.6e-05 Score=72.00 Aligned_cols=131 Identities=13% Similarity=0.119 Sum_probs=93.6
Q ss_pred HHHHHHc--CceeeCCC-CCCCCCEEEEEecCCCCCCCCCHHH--HHHHHHHHHHHhhcccCceeccEEEEEeCCCCCcc
Q psy8727 105 MQELLKL--GYLFATPK-RDKLGRRVIIARPGVFNPHKYTNSH--MLQIHGMTYETLMEDEENQVRGFVHFNDGAGVSFP 179 (300)
Q Consensus 105 ~~~~l~~--g~~~~l~g-~Dk~GrpV~~~~~~~~~~~~~~~~~--~~r~~~~~le~~~~~~~~~~~g~v~IiD~~g~s~~ 179 (300)
+-..+.+ +.+.+..+ .|+.||.|+++-+.++-+. ..+++ ++++.++.+|..++.. ++.++=-.|+...
T Consensus 71 fyd~~~H~~ei~qvi~~~~D~~gr~iivv~a~rlp~~-~eld~~~li~~~v~~id~~Ve~D------Yt~vYfh~gl~s~ 143 (467)
T KOG4406|consen 71 FYDIARHEREILQVIGDAKDKQGRKIIVVYACRLPSS-SELDDIRLISYLVYTIDKYVEND------YTLVYFHHGLPSD 143 (467)
T ss_pred HHHHHHhhhheeeeccCcccccCCeeEEEEEecCCch-hhhhhHHHHHHHHHHHHHHHhcc------ceeeehhcCCccc
Confidence 4445544 66666655 6999999999998887543 23444 7888899999887443 5556655666544
Q ss_pred cccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHHHHHhhhcCHhhhcceEEecccccc
Q psy8727 180 HLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFGLNLVSEKIRKRIKVSVIVNAR 244 (300)
Q Consensus 180 ~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~likpfl~~~t~~Ki~~~~~~~~L 244 (300)
+- ...+.+.+...-+-.+|---++.+|+|.+-|+..++|+++|||++.|..+||+-.+.+.+|
T Consensus 144 nk--p~l~~l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n~lseL 206 (467)
T KOG4406|consen 144 NK--PYLQLLFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFNSLSEL 206 (467)
T ss_pred cc--chHHHHHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEeehHHHH
Confidence 32 2344444444444446778899999999999999999999999999999999877555444
No 9
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=87.46 E-value=2.4 Score=26.56 Aligned_cols=35 Identities=14% Similarity=0.298 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHH
Q psy8727 37 DALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEAL 80 (300)
Q Consensus 37 ~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l 80 (300)
+.|.+|.+... .++.....||.+++||++.|...+
T Consensus 2 e~i~~F~~iTg---------~~~~~A~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 2 EKIAQFMSITG---------ADEDVAIQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp HHHHHHHHHH----------SSHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHC---------cCHHHHHHHHHHcCCCHHHHHHHH
Confidence 45666666553 366889999999999999998865
No 10
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=81.79 E-value=5.2 Score=24.88 Aligned_cols=38 Identities=21% Similarity=0.254 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHH
Q psy8727 36 EDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALE 81 (300)
Q Consensus 36 ~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~ 81 (300)
.+.++.|++. -|+ +++..+.+.|+++++|++.|...|.
T Consensus 3 ~~~v~~L~~m---FP~-----l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 3 DEALHDLKDM---FPN-----LDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred HHHHHHHHHH---CCC-----CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3456666653 233 5778999999999999999998775
No 11
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=78.42 E-value=7.3 Score=24.13 Aligned_cols=38 Identities=24% Similarity=0.283 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHH
Q psy8727 37 DALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALER 82 (300)
Q Consensus 37 ~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~ 82 (300)
+.|+.|++.. | ..+...+..-|.++++|++.|...|-.
T Consensus 3 ~~v~~L~~mF---P-----~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMF---P-----DLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHS---S-----SS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHC---C-----CCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 4556666532 3 367899999999999999999998754
No 12
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=73.10 E-value=14 Score=24.93 Aligned_cols=43 Identities=7% Similarity=0.088 Sum_probs=33.4
Q ss_pred hhHHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHH
Q psy8727 32 ESTREDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALER 82 (300)
Q Consensus 32 ~e~~~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~ 82 (300)
|.....-|+.+++.... .+|.-+.--|+-|+.|++.|.++|..
T Consensus 2 P~~~rk~VQ~iKEiv~~--------hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 2 PAASRKTVQSIKEIVGC--------HSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred ChHHHHHHHHHHHHhcC--------CCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 34456677777776543 36778999999999999999999875
No 13
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=66.21 E-value=22 Score=24.89 Aligned_cols=51 Identities=20% Similarity=0.089 Sum_probs=36.8
Q ss_pred cEEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccC--ceeceEEEEeCChHHHHHHH
Q psy8727 166 GFVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLP--MRHKEIHIINCHPSVKYALD 221 (300)
Q Consensus 166 g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP--~rl~~i~ivN~P~~f~~~w~ 221 (300)
|-.+++|++|++. ++.+++-.++.-+...|| +.-+++.++|+......+.+
T Consensus 17 ~~~V~lDF~gv~~-----~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I~ 69 (74)
T PF14213_consen 17 GEKVVLDFEGVES-----ITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMIK 69 (74)
T ss_pred CCeEEEECCCccc-----ccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHHH
Confidence 3448899999964 467788888877777777 44567888888776655543
No 14
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=63.64 E-value=82 Score=25.99 Aligned_cols=139 Identities=18% Similarity=0.171 Sum_probs=89.3
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHhhccccc
Q psy8727 15 SVSKQGLQIAKAELREDESTREDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERYILLRNTYGDLA 94 (300)
Q Consensus 15 ~~~~~~~~~~~~el~e~~e~~~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~~~~R~~~~d~~ 94 (300)
...+...+.+.+.++-+++..++.++.|-..+..-- +...++..+..-|..-+|+-+.+....+.|.+-|.... ..
T Consensus 13 g~n~~~~~~~A~~l~i~~~~vk~~v~aL~~ll~~a~---K~~l~~~~~~~~L~~l~~~~e~~~~l~~~y~~~~~~l~-~~ 88 (166)
T cd04750 13 GINQKKYEGAARKLEVEVETVQHGVEALVYLLIEST---KLKLSERDFQDSIEFLGFSDDLNEILLQLYESNRKEIR-NI 88 (166)
T ss_pred CCChHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH---hccCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH-HH
Confidence 456778889999999999999999999999886531 11467788888888899999998888887766666655 33
Q ss_pred cccCCCCCHHHHHH-HHcCceeeCCCCCCCCCEEEEEecCCCCCCC-------CCHHHHHHHHHHHHHHhh
Q psy8727 95 FSKLDPKNPTMQEL-LKLGYLFATPKRDKLGRRVIIARPGVFNPHK-------YTNSHMLQIHGMTYETLM 157 (300)
Q Consensus 95 ~~~~~~~~~~~~~~-l~~g~~~~l~g~Dk~GrpV~~~~~~~~~~~~-------~~~~~~~r~~~~~le~~~ 157 (300)
.....+.-|.+.++ ++-++........+.+.|++.+++.--+... -+-.+-++.+...++.++
T Consensus 89 l~~~~~~lp~l~dleWRvDv~isS~~l~~~~~P~i~mkL~l~~~~~~~~~~~l~td~~~l~~l~~eLe~Al 159 (166)
T cd04750 89 LKELSPDLPHYHNLEWRLDVQIASRSLRSQVKPVITMKLHLEDENKKIETHLLQTDPANLVHLTQTLEQAL 159 (166)
T ss_pred HHhcCCCCccccCCceeEEeEEcchhhHhhcCceEEEEEEecCCCCcccceEEEeCHHHHHHHHHHHHHHH
Confidence 33333322222221 1222222222356678999999875333222 123344566666677665
No 15
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=59.98 E-value=18 Score=22.28 Aligned_cols=24 Identities=21% Similarity=0.037 Sum_probs=20.6
Q ss_pred CCHHHHHHHHhhcCCCHHHHHHHH
Q psy8727 57 LDARFLLRFLRSKKFSVPMAEEAL 80 (300)
Q Consensus 57 ~dd~~llRFLra~~~dv~~A~~~l 80 (300)
.....|-.-|++|++||-+|.+.+
T Consensus 15 ~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 15 QKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CChHHHHHHHHHcCCcHHHHHHHh
Confidence 456789999999999999998865
No 16
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=53.70 E-value=23 Score=21.11 Aligned_cols=23 Identities=22% Similarity=0.013 Sum_probs=18.7
Q ss_pred CHHHHHHHHhhcCCCHHHHHHHH
Q psy8727 58 DARFLLRFLRSKKFSVPMAEEAL 80 (300)
Q Consensus 58 dd~~llRFLra~~~dv~~A~~~l 80 (300)
+.....+-|+.+++|+++|..-|
T Consensus 15 ~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 15 SREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp -HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHhC
Confidence 45678999999999999998754
No 17
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=51.48 E-value=25 Score=20.83 Aligned_cols=24 Identities=25% Similarity=0.135 Sum_probs=20.6
Q ss_pred CCHHHHHHHHhhcCCCHHHHHHHH
Q psy8727 57 LDARFLLRFLRSKKFSVPMAEEAL 80 (300)
Q Consensus 57 ~dd~~llRFLra~~~dv~~A~~~l 80 (300)
.+.....+-|+.+++|+++|...|
T Consensus 13 f~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 13 FSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 456789999999999999998765
No 18
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=49.90 E-value=27 Score=20.55 Aligned_cols=24 Identities=29% Similarity=0.231 Sum_probs=19.9
Q ss_pred CCHHHHHHHHhhcCCCHHHHHHHH
Q psy8727 57 LDARFLLRFLRSKKFSVPMAEEAL 80 (300)
Q Consensus 57 ~dd~~llRFLra~~~dv~~A~~~l 80 (300)
.++....+-|+.+++|+++|..-|
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 456689999999999999997644
No 19
>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=48.08 E-value=70 Score=26.25 Aligned_cols=111 Identities=15% Similarity=0.214 Sum_probs=68.1
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHHHHhCCC-C--CC---------CCCCHHHHHHHHhh-cCCCHHHHHHHHHHHHHH
Q psy8727 20 GLQIAKAELREDESTREDALIQLRQWITKNSR-I--QT---------CRLDARFLLRFLRS-KKFSVPMAEEALERYILL 86 (300)
Q Consensus 20 ~~~~~~~el~e~~e~~~~~l~~Lr~~l~~~p~-l--~~---------~~~dd~~llRFLra-~~~dv~~A~~~l~~~~~~ 86 (300)
..+.+.+-++ +++..++.|++|++...+..+ + .. ...--.++.+|+.. ..-.+.+|.-.-...+..
T Consensus 15 s~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~~~~~~LS~aalEtLAiIAY 93 (159)
T PF04079_consen 15 SIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKKPKPPKLSQAALETLAIIAY 93 (159)
T ss_dssp -HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCTCCCHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccCccCCCCHHHHHHHHHHHh
Confidence 4456677777 788889999999999966532 1 00 01234568888877 344566666666677777
Q ss_pred Hhhcc----ccccccCCCCCHHHHHHHHcCceeeCCCCCCCCCEEEEEecC
Q psy8727 87 RNTYG----DLAFSKLDPKNPTMQELLKLGYLFATPKRDKLGRRVIIARPG 133 (300)
Q Consensus 87 R~~~~----d~~~~~~~~~~~~~~~~l~~g~~~~l~g~Dk~GrpV~~~~~~ 133 (300)
++-.. +++-+. + .+..++.+++.|++......|..|||++|.-..
T Consensus 94 ~QPiTr~eIe~IRGv-~-s~~~i~~L~e~glI~~~gr~~~~Grp~ly~tT~ 142 (159)
T PF04079_consen 94 KQPITRAEIEEIRGV-N-SDSVIKTLLERGLIEEVGRKDTPGRPILYGTTD 142 (159)
T ss_dssp H-SEEHHHHHHHHTS----HCHHHHHHHTTSEEEEEE-TTTT--EEEEE-H
T ss_pred cCCcCHHHHHHHcCC-C-hHHHHHHHHHCCCEEecCcCCCCCCCeEeehhH
Confidence 76432 233322 2 234588999999998875567889999987643
No 20
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=45.42 E-value=97 Score=21.18 Aligned_cols=27 Identities=11% Similarity=0.209 Sum_probs=24.0
Q ss_pred CCHHHHHHHHhhcCCCHHHHHHHHHHH
Q psy8727 57 LDARFLLRFLRSKKFSVPMAEEALERY 83 (300)
Q Consensus 57 ~dd~~llRFLra~~~dv~~A~~~l~~~ 83 (300)
++..|-.++|..++||.+.|.+.+.+-
T Consensus 25 mn~~~s~~cLe~~~Wd~~~Al~~F~~l 51 (63)
T smart00804 25 MNAEYSQMCLEDNNWDYERALKNFTEL 51 (63)
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 567899999999999999999988764
No 21
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=43.70 E-value=3.7 Score=29.51 Aligned_cols=43 Identities=19% Similarity=0.101 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHH
Q psy8727 34 TREDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALER 82 (300)
Q Consensus 34 ~~~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~ 82 (300)
...+++.++|+.|... . . ++..|..-|+.++|||++|..-|.+
T Consensus 27 ~L~~~l~~vr~~Lg~~--~---~-~e~~i~eal~~~~fDvekAl~~Ll~ 69 (79)
T PF08938_consen 27 QLYSCLPQVREVLGDY--V---P-PEEQIKEALWHYYFDVEKALDYLLS 69 (79)
T ss_dssp HHCHHCCCHHHHCCCC--C------CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHHHHHHccc--C---C-CHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 3466777777776542 1 1 5567899999999999999998875
No 22
>cd07322 PriL_PriS_Eukaryotic Eukaryotic core primase: Large subunit, PriL. Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS) and a large subunit (PriL). In eukaryotic organisms, a heterotetrameric enzyme formed by DNA polymerase alpha, the B subunit and two primase subunits has primase activity. Although the catalytic activity resides within PriS, the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL such as stabilization of the PriS, involvement in synthesis initiation, improvement of primase processivity, determination of product size and transfer of
Probab=42.71 E-value=1.4e+02 Score=28.31 Aligned_cols=46 Identities=20% Similarity=0.098 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHH
Q psy8727 36 EDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERY 83 (300)
Q Consensus 36 ~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~ 83 (300)
.-++..|-+-+.+..||+- .....+--||.+.+.+++.|.+-++..
T Consensus 225 P~Cm~~l~~~l~~~~hL~h--~gR~ql~lFLk~iGl~~~e~l~~~~~~ 270 (390)
T cd07322 225 PLCMRQLHEALRKNHHLKH--GGRLQLGLFLKGIGLSLEEALKFWRSE 270 (390)
T ss_pred CHHHHHHHHHHhcCCCCCc--hhHHHHHHHHHhCCCCHHHHHHHHHHh
Confidence 3455666666777778873 678889999999999999999988765
No 23
>PF04378 RsmJ: Ribosomal RNA small subunit methyltransferase D, RsmJ; InterPro: IPR007473 This is a bacterial protein of unknown function, possibly secreted.; PDB: 2OO3_A.
Probab=41.65 E-value=19 Score=31.84 Aligned_cols=32 Identities=22% Similarity=0.187 Sum_probs=22.6
Q ss_pred ceeceEEEEeCChHHHHHHHHHhhhcCHhhhc
Q psy8727 202 MRHKEIHIINCHPSVKYALDFGLNLVSEKIRK 233 (300)
Q Consensus 202 ~rl~~i~ivN~P~~f~~~w~likpfl~~~t~~ 233 (300)
..=.+++|||+||-+....+-+-|+|.+...+
T Consensus 203 m~GSGm~iiNPPw~l~~~l~~~l~~L~~~L~~ 234 (245)
T PF04378_consen 203 MNGSGMLIINPPWTLDEELEEILPWLAETLAQ 234 (245)
T ss_dssp --EEEEEEES--TTHHHHHHHHHHHHHHHSST
T ss_pred eecceEEEEcCCccHHHHHHHHHHHHHHHhCc
Confidence 33468999999999999988888887765443
No 24
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=40.59 E-value=42 Score=23.17 Aligned_cols=29 Identities=24% Similarity=0.366 Sum_probs=26.4
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHHHHh
Q psy8727 20 GLQIAKAELREDESTREDALIQLRQWITK 48 (300)
Q Consensus 20 ~~~~~~~el~e~~e~~~~~l~~Lr~~l~~ 48 (300)
....|.+++|-++....+-+..+|+||-+
T Consensus 15 s~~~Aa~~lG~~~~~v~~wv~~fR~wll~ 43 (65)
T PF05344_consen 15 SVAQAADRLGTDPGTVRRWVRMFRQWLLQ 43 (65)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56678999999999999999999999976
No 25
>PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A.
Probab=40.35 E-value=1.1e+02 Score=22.59 Aligned_cols=76 Identities=13% Similarity=0.123 Sum_probs=49.9
Q ss_pred CCHHHHHHHHHHHHHHhhcccCceeccEEEEEeCC-CCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHH
Q psy8727 140 YTNSHMLQIHGMTYETLMEDEENQVRGFVHFNDGA-GVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKY 218 (300)
Q Consensus 140 ~~~~~~~r~~~~~le~~~~~~~~~~~g~v~IiD~~-g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~ 218 (300)
.+.+|+.++. -.++..+.. -..+-+++|++ ++.- .++.......++... ....++++-+|-.+.+...
T Consensus 11 ~t~ed~~~~~-~~~~~~~~~----~~~~~ll~d~~~~~~~-----~~~~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~ 79 (109)
T PF11964_consen 11 LTEEDYKELL-PALEELIAD----HGKIRLLVDLRRDFEG-----WSPEARWEDAKFGLK-HLKHFRRIAVVGDSEWIRM 79 (109)
T ss_dssp E-HHHHHHHH-HHHHHHHTT----SSSEEEEEEEC-CEEE-----EHHHHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHH
T ss_pred eCHHHHHHHH-HHHHHHHhc----CCceEEEEEecCccCC-----CCHHHHHHHHHhchh-hhcccCEEEEEECcHHHHH
Confidence 4677777733 344444432 24578888888 6621 234555555555554 8888999999999999999
Q ss_pred HHHHHhhh
Q psy8727 219 ALDFGLNL 226 (300)
Q Consensus 219 ~w~likpf 226 (300)
+-+++.+|
T Consensus 80 ~~~~~~~~ 87 (109)
T PF11964_consen 80 IANFFAAF 87 (109)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhc
Confidence 99999887
No 26
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=39.37 E-value=24 Score=31.25 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=23.5
Q ss_pred ceEEEEeCChHHHHHHHHHhhhcCHhh
Q psy8727 205 KEIHIINCHPSVKYALDFGLNLVSEKI 231 (300)
Q Consensus 205 ~~i~ivN~P~~f~~~w~likpfl~~~t 231 (300)
.+++|||+||-+.--...+-|+|...+
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~L 263 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTLL 263 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHHh
Confidence 589999999999999999989887654
No 27
>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]
Probab=34.98 E-value=1.4e+02 Score=30.67 Aligned_cols=31 Identities=10% Similarity=0.223 Sum_probs=20.4
Q ss_pred HHHHHHhhcCCCHHHHHHHHHHHHHHHhhcc
Q psy8727 61 FLLRFLRSKKFSVPMAEEALERYILLRNTYG 91 (300)
Q Consensus 61 ~llRFLra~~~dv~~A~~~l~~~~~~R~~~~ 91 (300)
....-|...+|-+++.++++.+|++-++..+
T Consensus 316 ~a~~iLd~dHYGLekVKeRIlEyLAV~~l~~ 346 (782)
T COG0466 316 KAEKILDKDHYGLEKVKERILEYLAVQKLTK 346 (782)
T ss_pred HHHHHhcccccCchhHHHHHHHHHHHHHHhc
Confidence 3455566666777777777777777766654
No 28
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=34.35 E-value=1.6e+02 Score=23.59 Aligned_cols=68 Identities=24% Similarity=0.227 Sum_probs=39.5
Q ss_pred cCCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHH
Q psy8727 13 ETSVSKQGLQIAKAELREDESTREDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERYI 84 (300)
Q Consensus 13 ~~~~~~~~~~~~~~el~e~~e~~~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~~ 84 (300)
...++++..+.+-+++.++. .+.+...+..........+ .....-+.+||..++|+.+.+...|...+
T Consensus 87 ~kGi~~~~I~~~l~~~~~d~--~e~a~~~~~k~~~~~~~~~--~~~k~Ki~~~L~rkGF~~~~I~~~l~~~~ 154 (157)
T PRK00117 87 QKGVDREIIEEALAELDIDW--EELARELARKKFRRPLPDD--AKEKAKLVRFLARRGFSMDVIQRVLRNAL 154 (157)
T ss_pred HcCCCHHHHHHHHHHcCccH--HHHHHHHHHHHcCCCCCCC--HHHHHHHHHHHHHCCCCHHHHHHHHHhhh
Confidence 34678888887777776222 2333333333222211110 01125699999999999998888877643
No 29
>PRK14136 recX recombination regulator RecX; Provisional
Probab=33.98 E-value=1.6e+02 Score=27.04 Aligned_cols=65 Identities=22% Similarity=0.189 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHH
Q psy8727 14 TSVSKQGLQIAKAELREDESTREDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERY 83 (300)
Q Consensus 14 ~~~~~~~~~~~~~el~e~~e~~~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~ 83 (300)
-.+++++.+.+-+++.+ +..+.+.+.++..+. .++.......-+.+||..+.|+.+...+.|..+
T Consensus 238 KGId~eLIEqALeeieE--DE~E~A~~L~eKK~~---~~~~d~kek~K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 238 HAVGDALVESVGAQLRE--TEFERAQAVWRKKFG---ALPQTPAERAKQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred cCCCHHHHHHHHHhccH--hHHHHHHHHHHHHhc---ccCcCHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 35677777777666622 122333333333332 222201123468999999999999888877643
No 30
>PHA02570 dexA exonuclease; Provisional
Probab=32.94 E-value=1.5e+02 Score=25.80 Aligned_cols=59 Identities=14% Similarity=0.313 Sum_probs=43.5
Q ss_pred HHHHcC--CChhHHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHh
Q psy8727 24 AKAELR--EDESTREDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERYILLRN 88 (300)
Q Consensus 24 ~~~el~--e~~e~~~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~~~~R~ 88 (300)
|++.+- .+.....+++.+|.+||.+++ .+...+.-|.++..||...-...++.++.-+.
T Consensus 75 AR~~L~~s~~~~~l~~al~~F~~fi~~~~------~~~~~~~vWgnG~sFD~~IL~~a~r~~~~~~~ 135 (220)
T PHA02570 75 ARKNLKPSDEDVSTYEGHKKFFEYLEANG------VDPWKSQGWCRGNSFDFPILVDVIRDIHNTRD 135 (220)
T ss_pred HHHhccCCCccccHHHHHHHHHHHHHHcC------CCccceeEecCCCccCHHHHHHHHHHHhcccC
Confidence 566663 344577999999999999874 23344777899999999988888888764333
No 31
>TIGR02886 spore_II_AA anti-sigma F factor antagonist. The anti-sigma F factor antagonist, also called stage II sporulation protein AA, is a protein universal among endospore-forming bacteria, all of which belong to the Firmcutes
Probab=32.47 E-value=1.8e+02 Score=21.22 Aligned_cols=51 Identities=16% Similarity=0.065 Sum_probs=34.0
Q ss_pred EEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHHHHH
Q psy8727 167 FVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFG 223 (300)
Q Consensus 167 ~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~li 223 (300)
-.+|+||++++.-+ ......+..+.+-++ .+=++++++|++.-+.-++.+.
T Consensus 40 ~~vilDls~v~~iD--ssgi~~L~~~~~~~~----~~g~~l~l~~~~~~v~~~l~~~ 90 (106)
T TIGR02886 40 KHLILNLKNVTFMD--SSGLGVILGRYKKIK----NEGGEVIVCNVSPAVKRLFELS 90 (106)
T ss_pred CEEEEECCCCcEec--chHHHHHHHHHHHHH----HcCCEEEEEeCCHHHHHHHHHh
Confidence 47999999999733 223444444444444 3557899999988777776543
No 32
>cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta
Probab=32.12 E-value=1.4e+02 Score=26.59 Aligned_cols=58 Identities=9% Similarity=0.164 Sum_probs=47.3
Q ss_pred CChhHHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHhhcc
Q psy8727 30 EDESTREDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERYILLRNTYG 91 (300)
Q Consensus 30 e~~e~~~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~~~~R~~~~ 91 (300)
+.|+...+.+++.|+.|-+. +. ..||.++-+||-.-..+.+...+.|++...-+.-+|
T Consensus 187 ~ip~~~~~~~~~~r~~l~e~--va--e~dd~L~e~yl~~~~~~~~el~~~l~~~~~~~~~~P 244 (270)
T cd01886 187 EIPEDLLEEAEEAREELIET--LA--EFDDELMEKYLEGEEITEEEIKAAIRKGTIANKIVP 244 (270)
T ss_pred cCCHHHHHHHHHHHHHHHHH--Hh--cCCHHHHHHHhCCCCCCHHHHHHHHHHHHHcCcEEE
Confidence 45666677888888877543 33 479999999999999999999999999888777777
No 33
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=32.05 E-value=62 Score=25.48 Aligned_cols=38 Identities=13% Similarity=0.008 Sum_probs=31.5
Q ss_pred eEEEEeCChHHHHHHHHH-----hhhcCHhhhcceEEeccccc
Q psy8727 206 EIHIINCHPSVKYALDFG-----LNLVSEKIRKRIKVSVIVNA 243 (300)
Q Consensus 206 ~i~ivN~P~~f~~~w~li-----kpfl~~~t~~Ki~~~~~~~~ 243 (300)
-++++|...+++.+++.+ ..|+++...+.+.+..+.++
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~~~e 128 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDDPEE 128 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESSHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCCHHH
Confidence 589999998888988877 56889999998888866554
No 34
>TIGR02364 dha_pts dihydroxyacetone kinase, phosphotransfer subunit. In E. coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits. This protein, which resembles proteins of PTS transport systems, is found with its gene adjacent to
Probab=31.56 E-value=1.3e+02 Score=23.47 Aligned_cols=52 Identities=17% Similarity=0.088 Sum_probs=36.3
Q ss_pred ccEEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHHHHHhhhcC
Q psy8727 165 RGFVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFGLNLVS 228 (300)
Q Consensus 165 ~g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~likpfl~ 228 (300)
.|++++.|+ |=+..+ ...++.+++ ++..+.+..+|.|-+..++-..+..-..
T Consensus 60 dgVlvl~DL-Ggs~~n--------~e~a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~~g 111 (125)
T TIGR02364 60 DGVLIFYDL-GSAVMN--------AEMAVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQVG 111 (125)
T ss_pred CCEEEEEcC-CCcHhH--------HHHHHHHhc---cccccEEEEechhHHHHHHHHHHHHcCC
Confidence 799999999 766532 112333333 3556789999999999999887765443
No 35
>PF04838 Baculo_LEF5: Baculoviridae late expression factor 5 ; InterPro: IPR006923 This is a family of Baculoviridae late expression factor 5, required for late and very late gene expression.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=30.36 E-value=34 Score=27.70 Aligned_cols=48 Identities=19% Similarity=0.160 Sum_probs=40.9
Q ss_pred HHHHHHHhhcccCceec--eEEEEeCChHHHHHHHHHhhhcCH--hhhcceEE
Q psy8727 189 AVRIVKNGERTLPMRHK--EIHIINCHPSVKYALDFGLNLVSE--KIRKRIKV 237 (300)
Q Consensus 189 ~k~~~~~lq~~yP~rl~--~i~ivN~P~~f~~~w~likpfl~~--~t~~Ki~~ 237 (300)
.+.++..+-.+||.-++ ..-++|+.-.|.++|+-+ |-++. +-|..|++
T Consensus 17 y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRL 68 (159)
T PF04838_consen 17 YKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRL 68 (159)
T ss_pred HHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhh
Confidence 46789999999999998 999999999999999877 77777 55666666
No 36
>PRK14137 recX recombination regulator RecX; Provisional
Probab=30.23 E-value=3.1e+02 Score=23.31 Aligned_cols=70 Identities=16% Similarity=0.096 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHh
Q psy8727 15 SVSKQGLQIAKAELREDESTREDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERYILLRN 88 (300)
Q Consensus 15 ~~~~~~~~~~~~el~e~~e~~~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~~~~R~ 88 (300)
.+++++.+.+-.++.+. +..+.+.+.+...+. .+........-+.+||..++|+.+.+...+........
T Consensus 115 GI~~~lI~~al~~~d~e-de~e~a~~l~~KK~~---~~~~~~~~k~K~~~~L~rRGFs~~~I~~al~~~~~~~~ 184 (195)
T PRK14137 115 GVEETLIEETLAARDPQ-EEQQEARNLLERRWS---SFARKRDPRASAYAFLARRGFSGAVIWPAIREVAALAG 184 (195)
T ss_pred CCCHHHHHHHHHhcCch-hHHHHHHHHHHHhcc---ccCcchhHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcC
Confidence 56666666666655322 222333333333322 12110122355899999999999999999988665443
No 37
>KOG2005|consensus
Probab=29.97 E-value=1.1e+02 Score=31.06 Aligned_cols=66 Identities=21% Similarity=0.288 Sum_probs=44.3
Q ss_pred ccCCCCHHHH------HHHHHHcCC-ChhHHHHHHHHHHHHHHhCC-CCCCCCCCHHHHHHHHhhcCCCHHHHHHHHH
Q psy8727 12 VETSVSKQGL------QIAKAELRE-DESTREDALIQLRQWITKNS-RIQTCRLDARFLLRFLRSKKFSVPMAEEALE 81 (300)
Q Consensus 12 ~~~~~~~~~~------~~~~~el~e-~~e~~~~~l~~Lr~~l~~~p-~l~~~~~dd~~llRFLra~~~dv~~A~~~l~ 81 (300)
.+.++|.|.+ +.+.+.+.+ +++.++.+|+.||+.+++.. .+ ++-.--++|||-.-+.+.+..+.+.
T Consensus 35 k~e~lSEED~~lk~dLellVervqdpd~~Lq~~aLe~lr~~irsStSSm----tsvpkPlKFLrphy~~Lk~i~~~~~ 108 (878)
T KOG2005|consen 35 KEEDLSEEDLQLKGDLELLVERVQDPDPDLQKAALESLREEIRSSTSSM----TSVPKPLKFLRPHYGVLKEIYESMA 108 (878)
T ss_pred hhhhccHHHHHhhhhHHHHHHHhcCCChHHHHHHHHHHHHHHHhccccc----ccCCchhhhhccchhHHHHHHHhcc
Confidence 4556777644 345555555 88899999999999998752 12 2222258999988777766665544
No 38
>cd07042 STAS_SulP_like_sulfate_transporter Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Probab=27.48 E-value=1.6e+02 Score=21.14 Aligned_cols=50 Identities=22% Similarity=0.183 Sum_probs=31.2
Q ss_pred EEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHHHH
Q psy8727 167 FVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDF 222 (300)
Q Consensus 167 ~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~l 222 (300)
..+|+|+++++.- +.+.+..+..+.+ .+-.+=..+.+.|++.-+..++..
T Consensus 42 ~~lilD~~~v~~i-----Dss~~~~L~~~~~-~~~~~~~~~~l~~~~~~~~~~l~~ 91 (107)
T cd07042 42 KVVILDLSAVNFI-----DSTAAEALEELVK-DLRKRGVELYLAGLNPQVRELLER 91 (107)
T ss_pred eEEEEECCCCchh-----hHHHHHHHHHHHH-HHHHCCCEEEEecCCHHHHHHHHH
Confidence 5678999999863 3344444444433 222344778899999866655543
No 39
>KOG3923|consensus
Probab=26.81 E-value=27 Score=31.88 Aligned_cols=43 Identities=9% Similarity=0.132 Sum_probs=34.9
Q ss_pred ccEEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHH
Q psy8727 165 RGFVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYAL 220 (300)
Q Consensus 165 ~g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w 220 (300)
.++=+|++|+|++-+.+..- ++.||.| +.+.-|.|||+..+++
T Consensus 182 ~~~DVivNCtGL~a~~L~gD------------d~~yPiR-GqVl~V~ApWvkhf~~ 224 (342)
T KOG3923|consen 182 PEYDVIVNCTGLGAGKLAGD------------DDLYPIR-GQVLKVDAPWVKHFIY 224 (342)
T ss_pred CCCcEEEECCccccccccCC------------cceeecc-ceEEEeeCCceeEEEE
Confidence 67889999999998776433 4589999 7889999999976653
No 40
>KOG2267|consensus
Probab=26.15 E-value=1.4e+02 Score=28.31 Aligned_cols=48 Identities=19% Similarity=0.120 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHH
Q psy8727 36 EDALIQLRQWITKNSRIQTCRLDARFLLRFLRSKKFSVPMAEEALERYIL 85 (300)
Q Consensus 36 ~~~l~~Lr~~l~~~p~l~~~~~dd~~llRFLra~~~dv~~A~~~l~~~~~ 85 (300)
.-+.+.|.+.|+++-||. .-+...+--||.+.+-+++.|.+.++..++
T Consensus 288 ppCmk~lhe~LrkNhHLr--y~gR~qygLFLKgiGLS~deal~fwr~sFt 335 (475)
T KOG2267|consen 288 PPCMKQLHERLRKNHHLR--YGGRQQYGLFLKGIGLSVDEALAFWRGSFT 335 (475)
T ss_pred cHHHHHHHHHHhhccccc--ccchhhhhhhhhccCcCHHHHHHHHHHHHh
Confidence 457888889999988996 478889999999999999999998775444
No 41
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=26.01 E-value=2.4e+02 Score=19.82 Aligned_cols=66 Identities=15% Similarity=0.196 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHHhCCCCCC-----CCCCHHHHHHHHhhcCCCHHHHHHHHHHHH
Q psy8727 14 TSVSKQGLQIAKAELREDESTREDALIQLRQWITKNSRIQT-----CRLDARFLLRFLRSKKFSVPMAEEALERYI 84 (300)
Q Consensus 14 ~~~~~~~~~~~~~el~e~~e~~~~~l~~Lr~~l~~~p~l~~-----~~~dd~~llRFLra~~~dv~~A~~~l~~~~ 84 (300)
..+|+++.+.+ |....++.+.+..++++++.+. |.. ...-|..|..-+....+.+.+-.+.+..|+
T Consensus 5 ~~ls~~L~~~l----g~~~~tr~ev~~~lw~YIk~n~-L~d~~~k~~i~~D~~L~~l~~~~~v~~~~~~~ll~~Hl 75 (77)
T smart00151 5 VTLSPELAKVL----GAPEMTRTEIIKRLWEYIKEHN-LQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHL 75 (77)
T ss_pred ccCCHHHHHHh----CCCcCcHHHHHHHHHHHHHHhc-ccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHc
Confidence 45788877765 5567788999999999999763 221 112344444444444566666666665543
No 42
>KOG1838|consensus
Probab=25.44 E-value=6.1e+02 Score=24.32 Aligned_cols=85 Identities=11% Similarity=0.093 Sum_probs=57.1
Q ss_pred CCCCEEEEEecCCCCCCCCCHHHHHHHHHHHHHHhhcccCceecc-EEEEEeCCCCCcccccCC------CHHHHHHHHH
Q psy8727 122 KLGRRVIIARPGVFNPHKYTNSHMLQIHGMTYETLMEDEENQVRG-FVHFNDGAGVSFPHLTLF------TPKEAVRIVK 194 (300)
Q Consensus 122 k~GrpV~~~~~~~~~~~~~~~~~~~r~~~~~le~~~~~~~~~~~g-~v~IiD~~g~s~~~~~~~------~~~~~k~~~~ 194 (300)
....|++++-+|-.. -+.+.++|.++.... ..| -+||++-.|++-+.+... ...-++.+++
T Consensus 122 ~~~~P~vvilpGltg---~S~~~YVr~lv~~a~---------~~G~r~VVfN~RG~~g~~LtTpr~f~ag~t~Dl~~~v~ 189 (409)
T KOG1838|consen 122 DGTDPIVVILPGLTG---GSHESYVRHLVHEAQ---------RKGYRVVVFNHRGLGGSKLTTPRLFTAGWTEDLREVVN 189 (409)
T ss_pred CCCCcEEEEecCCCC---CChhHHHHHHHHHHH---------hCCcEEEEECCCCCCCCccCCCceeecCCHHHHHHHHH
Confidence 345699999988743 356788886655333 233 578999999776655422 3577999999
Q ss_pred HhhcccCceeceEEEEeCChHHHHHH
Q psy8727 195 NGERTLPMRHKEIHIINCHPSVKYAL 220 (300)
Q Consensus 195 ~lq~~yP~rl~~i~ivN~P~~f~~~w 220 (300)
.+..-||.+ .++.|-...--.+++
T Consensus 190 ~i~~~~P~a--~l~avG~S~Gg~iL~ 213 (409)
T KOG1838|consen 190 HIKKRYPQA--PLFAVGFSMGGNILT 213 (409)
T ss_pred HHHHhCCCC--ceEEEEecchHHHHH
Confidence 999999999 445554444444444
No 43
>PF11339 DUF3141: Protein of unknown function (DUF3141); InterPro: IPR024501 This family of proteins appears to be predominantly expressed in Proteobacteria. Their function is unknown.
Probab=24.41 E-value=3.5e+02 Score=26.91 Aligned_cols=79 Identities=9% Similarity=-0.094 Sum_probs=47.6
Q ss_pred CCEEEEEecCCCCCCCCCHHHHHHHHHHHHHHhh-cccCceeccEEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCc
Q psy8727 124 GRRVIIARPGVFNPHKYTNSHMLQIHGMTYETLM-EDEENQVRGFVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPM 202 (300)
Q Consensus 124 GrpV~~~~~~~~~~~~~~~~~~~r~~~~~le~~~-~~~~~~~~g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~ 202 (300)
|+||+++-.-.......+++|+.++..-.++... ..+.. ...++|=+|+| + -.+-++...+|+
T Consensus 100 GHPvYFV~F~p~P~pgQTl~DV~~ae~~Fv~~V~~~hp~~--~kp~liGnCQg-G-------------Wa~~mlAA~~Pd 163 (581)
T PF11339_consen 100 GHPVYFVGFFPEPEPGQTLEDVMRAEAAFVEEVAERHPDA--PKPNLIGNCQG-G-------------WAAMMLAALRPD 163 (581)
T ss_pred CCCeEEEEecCCCCCCCcHHHHHHHHHHHHHHHHHhCCCC--CCceEEeccHH-H-------------HHHHHHHhcCcC
Confidence 4444444432222223488888888777777665 44432 26677777764 1 233455778899
Q ss_pred eeceEEEEeCChHHHH
Q psy8727 203 RHKEIHIINCHPSVKY 218 (300)
Q Consensus 203 rl~~i~ivN~P~~f~~ 218 (300)
.++-+.+--+|--..+
T Consensus 164 ~~gplvlaGaPlsywa 179 (581)
T PF11339_consen 164 LVGPLVLAGAPLSYWA 179 (581)
T ss_pred ccCceeecCCCccccc
Confidence 8888888777755433
No 44
>PF13466 STAS_2: STAS domain
Probab=24.25 E-value=2.3e+02 Score=19.38 Aligned_cols=51 Identities=16% Similarity=0.206 Sum_probs=34.0
Q ss_pred EEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHHHHH
Q psy8727 167 FVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFG 223 (300)
Q Consensus 167 ~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~li 223 (300)
-.+++|+++++.-+ ...+.-++.. ....-.+=+.+.+.|+|.-+..++.+.
T Consensus 27 ~~v~lDls~v~~iD-----sagl~lL~~~-~~~~~~~g~~~~l~~~~~~~~~ll~~~ 77 (80)
T PF13466_consen 27 RPVVLDLSGVEFID-----SAGLQLLLAA-ARRARARGRQLRLTGPSPALRRLLELL 77 (80)
T ss_pred CeEEEECCCCCeec-----HHHHHHHHHH-HHHHHHCCCeEEEEcCCHHHHHHHHHh
Confidence 67899999999743 3333333333 333444667889999999888877654
No 45
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=23.72 E-value=4.4e+02 Score=22.23 Aligned_cols=108 Identities=15% Similarity=0.198 Sum_probs=62.4
Q ss_pred HHHHcCCC-hhHHHHHHHHHHHHHHhCCC-CC--C------CCC---CHHHHHHHHhhcCCCHHHHHHHHHHHHHHHhhc
Q psy8727 24 AKAELRED-ESTREDALIQLRQWITKNSR-IQ--T------CRL---DARFLLRFLRSKKFSVPMAEEALERYILLRNTY 90 (300)
Q Consensus 24 ~~~el~e~-~e~~~~~l~~Lr~~l~~~p~-l~--~------~~~---dd~~llRFLra~~~dv~~A~~~l~~~~~~R~~~ 90 (300)
+++-++.. ++..++.++.|++....+.+ +. . ..+ -..++.+|.....-.+.+|.-.-.+.++.++-.
T Consensus 23 La~il~~~~~~~~~~~l~~l~~~~~~~~~gl~l~~~~~~y~l~tk~e~~~~i~~~~~~~~~~LS~aaLEtLAIIAY~QPI 102 (186)
T TIGR00281 23 LVRILGKEKAEKLNAIMELLEDYLSRDTAGIEIIKFGQSYSLVTKPAFADYIHRFLPAKLKNLNSASLEVLAIIAYKQPI 102 (186)
T ss_pred HHHHhCCCchHHHHHHHHHHHHHHhcCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccccccCCHHHHHHHHHHHHcCCc
Confidence 33344554 45667788888888765432 21 0 001 123566665543222455666666677776643
Q ss_pred c-c---cccccCCCCCHHHHHHHHcCceeeCCCCCCCCCEEEEEecC
Q psy8727 91 G-D---LAFSKLDPKNPTMQELLKLGYLFATPKRDKLGRRVIIARPG 133 (300)
Q Consensus 91 ~-d---~~~~~~~~~~~~~~~~l~~g~~~~l~g~Dk~GrpV~~~~~~ 133 (300)
. . ++-+. + .+..++.+++.|++...+..|..|||++|.-..
T Consensus 103 Tr~eIe~IRGv-~-s~~~l~~L~ergLI~~~Gr~~~~Grp~ly~TT~ 147 (186)
T TIGR00281 103 TRARINEIRGV-K-SYQIVDDLVEKGLVVELGRKDTPGRSFIYETTP 147 (186)
T ss_pred CHHHHHHHcCC-C-HHHHHHHHHHCCCeEecCcCCCCCCCeeehhhH
Confidence 2 1 33221 1 245688999999998774467889999887543
No 46
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=23.42 E-value=1.2e+02 Score=19.73 Aligned_cols=26 Identities=12% Similarity=0.258 Sum_probs=20.5
Q ss_pred CCHHHHHHHHhhcCCCHHHHHHHHHH
Q psy8727 57 LDARFLLRFLRSKKFSVPMAEEALER 82 (300)
Q Consensus 57 ~dd~~llRFLra~~~dv~~A~~~l~~ 82 (300)
.+..+-.++|..++||.++|.+.+..
T Consensus 13 mn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 13 MNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp S-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34568999999999999999987764
No 47
>PF13950 Epimerase_Csub: UDP-glucose 4-epimerase C-term subunit; PDB: 1EK5_A 1I3K_B 1I3M_B 1HZJ_A 1EK6_A 1I3N_A 1I3L_A 2CNB_B 1GY8_D 1NAI_A ....
Probab=22.77 E-value=1.3e+02 Score=20.32 Aligned_cols=32 Identities=25% Similarity=0.363 Sum_probs=22.7
Q ss_pred HHHHHHHHcCCChh-HHHHHHHHHHHHHHhCCC
Q psy8727 20 GLQIAKAELREDES-TREDALIQLRQWITKNSR 51 (300)
Q Consensus 20 ~~~~~~~el~e~~e-~~~~~l~~Lr~~l~~~p~ 51 (300)
.-..|+++||=.|+ ..++.|....+|.+++|+
T Consensus 28 d~~kA~~~LgW~p~~~L~~~i~~~w~W~~~np~ 60 (62)
T PF13950_consen 28 DISKAREELGWKPKYSLEDMIRDAWNWQKKNPN 60 (62)
T ss_dssp --HHHHHHC----SSSHHHHHHHHHHHHHHSTT
T ss_pred CHHHHHHHhCCCcCCCHHHHHHHHHHHHHHCcC
Confidence 34589999999888 558999999999999985
No 48
>PF01740 STAS: STAS domain; InterPro: IPR002645 The STAS (Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. The establishment of differential gene expression in sporulating Bacillus subtilis involves four protein components one of which is SpoIIAA (P10727 from SWISSPROT). The four components regulate the sporulation sigma factor F. Early in sporulation, SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase SpoIIAB (P10728 from SWISSPROT). The site at which this protein is a conserved serine. SpoIIAB is an anti-sigma factor that in its free form inhibits F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases Sigma F activity []. The STAS domain is found in the anti-sigma factor antagonist SpoIIAA.; PDB: 3T6O_B 3LKL_B 1H4Z_A 1H4Y_B 1H4X_B 3NY7_A 3OIZ_A 1T6R_A 1VC1_B 1SBO_A ....
Probab=22.39 E-value=97 Score=23.17 Aligned_cols=49 Identities=20% Similarity=0.209 Sum_probs=32.0
Q ss_pred EEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHHH
Q psy8727 167 FVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALD 221 (300)
Q Consensus 167 ~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~ 221 (300)
-.+|+||++++.- +.+.+..+.++.+..- .+=..++++|.+.-....+.
T Consensus 49 ~~vIlD~s~v~~i-----Dssgi~~L~~~~~~~~-~~g~~~~l~~~~~~v~~~l~ 97 (117)
T PF01740_consen 49 KNVILDMSGVSFI-----DSSGIQALVDIIKELR-RRGVQLVLVGLNPDVRRILE 97 (117)
T ss_dssp SEEEEEETTESEE-----SHHHHHHHHHHHHHHH-HTTCEEEEESHHHHHHHHHH
T ss_pred eEEEEEEEeCCcC-----CHHHHHHHHHHHHHHH-HCCCEEEEEECCHHHHHHHH
Confidence 6899999999763 3344444444444333 56677899998887766643
No 49
>TIGR03824 FlgM_jcvi flagellar biosynthesis anti-sigma factor FlgM. FlgM interacts with and inhibits the alternative sigma factor sigma(28) FliA. The C-terminus of FlgM contains the sigma(28)-binding domain.
Probab=22.30 E-value=1.3e+02 Score=22.24 Aligned_cols=35 Identities=17% Similarity=0.265 Sum_probs=28.7
Q ss_pred CCCCHH--HHHHHHHHcCCChhHHHHHHHHHHHHHHh
Q psy8727 14 TSVSKQ--GLQIAKAELREDESTREDALIQLRQWITK 48 (300)
Q Consensus 14 ~~~~~~--~~~~~~~el~e~~e~~~~~l~~Lr~~l~~ 48 (300)
-.+|++ .++.+..++...|+...+.|++||+.+..
T Consensus 41 v~lS~~a~~l~~~~~~~~~~p~v~~~kV~~ik~aI~~ 77 (95)
T TIGR03824 41 VTLSSAAQQLQSLEAALASSPDVDAEKVAEIKAAIAN 77 (95)
T ss_pred EEECHHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHc
Confidence 346665 44567789999999999999999999975
No 50
>PF14053 DUF4248: Domain of unknown function (DUF4248)
Probab=21.61 E-value=95 Score=21.65 Aligned_cols=29 Identities=28% Similarity=0.555 Sum_probs=19.9
Q ss_pred HHHHHHcCCChhHHHHHHHHHHHHHHhCCCC
Q psy8727 22 QIAKAELREDESTREDALIQLRQWITKNSRI 52 (300)
Q Consensus 22 ~~~~~el~e~~e~~~~~l~~Lr~~l~~~p~l 52 (300)
|.|....... ..+.++..|+.|+..+|.|
T Consensus 10 ELA~lYfP~~--~~~sA~r~L~rwI~~~~~L 38 (69)
T PF14053_consen 10 ELAQLYFPDL--TPSSAVRKLRRWIRRNPEL 38 (69)
T ss_pred HHHHHHcCCC--CHHHHHHHHHHHHHHCHHH
Confidence 3344444433 5578999999999988755
No 51
>KOG4119|consensus
Probab=21.42 E-value=1.5e+02 Score=20.92 Aligned_cols=30 Identities=13% Similarity=0.130 Sum_probs=19.6
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHHHHhC
Q psy8727 20 GLQIAKAELREDESTREDALIQLRQWITKN 49 (300)
Q Consensus 20 ~~~~~~~el~e~~e~~~~~l~~Lr~~l~~~ 49 (300)
.++.++.|++..-....++-++|++|+.++
T Consensus 15 ~VeqLk~e~~~~R~~vS~a~~el~~y~E~~ 44 (71)
T KOG4119|consen 15 EVEQLKLEANIERIKVSKAAAELLEYCETH 44 (71)
T ss_pred HHHHHHHHHHhhHhhHHHHHHHHHHHHHhc
Confidence 455666666666555666677777777664
No 52
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=21.15 E-value=1.2e+02 Score=18.58 Aligned_cols=24 Identities=17% Similarity=0.124 Sum_probs=19.3
Q ss_pred CHHHHHHHHhhcCCCHHHHHHHHH
Q psy8727 58 DARFLLRFLRSKKFSVPMAEEALE 81 (300)
Q Consensus 58 dd~~llRFLra~~~dv~~A~~~l~ 81 (300)
+...+..-|..++||+.+|.+.|.
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHC
Confidence 456788899999999999998875
No 53
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=20.66 E-value=3.5e+02 Score=21.16 Aligned_cols=49 Identities=18% Similarity=-0.020 Sum_probs=33.9
Q ss_pred ccEEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHHHHHhhhc
Q psy8727 165 RGFVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFGLNLV 227 (300)
Q Consensus 165 ~g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~likpfl 227 (300)
+|++++.|+ |=+..+. ...+.++ .+- ++++++++|-+=.++-..+....
T Consensus 58 dGVlVltDL-Gssp~n~--------~~a~e~~----~~~-~~v~~~daPlVEGa~~Aav~~~~ 106 (124)
T PRK14484 58 DGVLIFFDL-GSAEMNA--------EMAIEML----DGE-KKIIIIDAPIVEGAFTAAVLLSA 106 (124)
T ss_pred CCeEEEEeC-CChHHHH--------HHHHHhc----CCC-CcEEEECCcHHHHHHHHHHHHcC
Confidence 899999999 6665331 2233333 322 88999999999888877765544
No 54
>TIGR00377 ant_ant_sig anti-anti-sigma factor. This superfamily includes small (105-125 residue) proteins related to SpoIIAA of Bacillus subtilis, an anti-anti-sigma factor. SpoIIAA can bind to and inhibit the anti-sigma F factor SpoIIAB. Also, it can be phosphorylated by SpoIIAB on a Ser residue at position 59 of the seed alignment. A similar arrangement is inferred for RsbV, an anti-anti-sigma factor for sigma B. This Ser is fairly well conserved within a motif resembling MXS[STA]G[VIL]X[VIL][VILF] among homologous known or predicted anti-anti-sigma factors. Regions similar to SpoIIAA and apparently homologous, but differing considerably near the phosphorlated Ser of SpoIIAA, appear in a single copy in several longer proteins.
Probab=20.28 E-value=3.5e+02 Score=19.60 Aligned_cols=53 Identities=15% Similarity=0.036 Sum_probs=35.2
Q ss_pred ccEEEEEeCCCCCcccccCCCHHHHHHHHHHhhcccCceeceEEEEeCChHHHHHHHHH
Q psy8727 165 RGFVHFNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFG 223 (300)
Q Consensus 165 ~g~v~IiD~~g~s~~~~~~~~~~~~k~~~~~lq~~yP~rl~~i~ivN~P~~f~~~w~li 223 (300)
..-.+++|+++++.- +......+..+...++. +=+.+.+++.+.-+..++.+.
T Consensus 42 ~~~~vvidls~v~~i--Dssgl~~L~~~~~~~~~----~~~~~~l~~~~~~~~~~l~~~ 94 (108)
T TIGR00377 42 GPRPIVLDLEDLEFM--DSSGLGVLLGRYKQVRR----VGGQLVLVSVSPRVARLLDIT 94 (108)
T ss_pred CCCeEEEECCCCeEE--ccccHHHHHHHHHHHHh----cCCEEEEEeCCHHHHHHHHHh
Confidence 344699999999863 33345556665555543 345789999888777776544
Done!