Query 019727
Match_columns 336
No_of_seqs 242 out of 1373
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 04:03:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019727.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019727hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1470 Phosphatidylinositol t 100.0 2.4E-48 5.3E-53 352.5 21.8 237 18-260 24-263 (324)
2 KOG1471 Phosphatidylinositol t 100.0 3.5E-37 7.6E-42 288.9 20.6 228 10-243 14-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 4.2E-31 9.1E-36 222.8 7.8 149 88-239 4-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 1.1E-28 2.5E-33 207.7 14.5 140 99-241 15-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 1.6E-26 3.4E-31 193.1 13.7 144 92-239 9-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.7 3.5E-17 7.6E-22 136.7 3.4 143 93-246 3-148 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 98.9 1.2E-09 2.5E-14 75.3 4.4 48 20-67 1-55 (55)
8 KOG4406 CDC42 Rho GTPase-activ 98.7 1.2E-07 2.6E-12 88.7 10.0 130 91-231 80-214 (467)
9 PF02845 CUE: CUE domain; Int 83.7 4.3 9.2E-05 25.7 5.2 39 20-66 2-40 (42)
10 PF14555 UBA_4: UBA-like domai 83.5 4.2 9.1E-05 25.9 5.1 35 21-64 2-36 (43)
11 smart00546 CUE Domain that may 77.1 9.1 0.0002 24.2 5.1 37 21-65 4-40 (43)
12 PF08938 HBS1_N: HBS1 N-termin 73.9 1.3 2.9E-05 32.5 0.6 49 13-67 19-70 (79)
13 PF06972 DUF1296: Protein of u 66.1 23 0.00049 24.4 5.1 42 17-66 3-44 (60)
14 PF14213 DUF4325: Domain of un 61.5 28 0.00061 24.9 5.4 48 145-194 19-68 (74)
15 PF00627 UBA: UBA/TS-N domain; 53.3 23 0.0005 21.6 3.3 35 20-64 3-37 (37)
16 smart00165 UBA Ubiquitin assoc 51.4 25 0.00054 21.2 3.2 24 41-64 13-36 (37)
17 PF11964 SpoIIAA-like: SpoIIAA 51.3 63 0.0014 24.4 6.3 83 118-212 12-95 (109)
18 cd00194 UBA Ubiquitin Associat 51.1 26 0.00055 21.2 3.3 24 41-64 13-36 (38)
19 PF04838 Baculo_LEF5: Baculovi 49.1 18 0.00039 29.8 2.8 49 162-211 16-68 (159)
20 TIGR02364 dha_pts dihydroxyace 48.7 68 0.0015 25.7 6.2 62 131-201 49-110 (125)
21 PF03474 DMA: DMRTA motif; In 46.0 38 0.00083 21.2 3.3 23 42-64 16-38 (39)
22 smart00804 TAP_C C-terminal do 43.8 1.1E+02 0.0024 21.3 7.1 46 12-67 6-51 (63)
23 KOG1534 Putative transcription 41.5 72 0.0016 28.4 5.6 100 126-231 75-193 (273)
24 KOG1838 Alpha/beta hydrolase [ 41.0 2E+02 0.0044 28.0 9.1 83 101-194 122-213 (409)
25 COG2961 ComJ Protein involved 35.2 26 0.00056 31.7 1.9 26 179-204 237-262 (279)
26 PF04378 RsmJ: Ribosomal RNA s 34.5 23 0.0005 32.0 1.5 28 179-206 206-233 (245)
27 PF09932 DUF2164: Uncharacteri 32.7 46 0.001 24.2 2.6 40 13-52 2-41 (76)
28 PF03641 Lysine_decarbox: Poss 31.9 1.6E+02 0.0035 23.5 6.1 55 160-214 64-125 (133)
29 PF07308 DUF1456: Protein of u 28.6 90 0.0019 22.1 3.5 29 24-52 33-61 (68)
30 PRK02399 hypothetical protein; 27.7 4.4E+02 0.0095 25.7 9.0 78 119-202 315-403 (406)
31 PF04548 AIG1: AIG1 family; I 27.1 2.1E+02 0.0044 24.8 6.4 68 145-212 51-122 (212)
32 PF02954 HTH_8: Bacterial regu 26.0 94 0.002 19.4 2.9 22 43-64 7-28 (42)
33 COG2810 Predicted type IV rest 25.5 2.3E+02 0.0051 25.5 6.1 112 17-151 4-115 (284)
34 PF01740 STAS: STAS domain; I 25.4 93 0.002 23.8 3.5 50 144-196 49-98 (117)
35 PRK14484 phosphotransferase ma 24.9 3.6E+02 0.0078 21.5 6.8 56 132-200 50-105 (124)
36 cd07042 STAS_SulP_like_sulfate 24.8 2.4E+02 0.0051 20.7 5.6 50 144-196 42-91 (107)
37 PRK10363 cpxP periplasmic repr 24.8 3.8E+02 0.0082 22.7 7.0 61 12-74 49-109 (166)
38 TIGR02886 spore_II_AA anti-sig 23.3 2.8E+02 0.0062 20.6 5.9 50 144-197 40-90 (106)
39 PF05872 DUF853: Bacterial pro 22.8 6.5E+02 0.014 25.2 9.2 91 99-190 208-303 (502)
40 COG2994 HlyC ACP:hemolysin acy 22.4 85 0.0018 25.7 2.6 82 83-179 44-128 (148)
41 COG0052 RpsB Ribosomal protein 21.2 1.1E+02 0.0024 27.7 3.4 66 173-242 31-103 (252)
42 PF13466 STAS_2: STAS domain 20.6 3.1E+02 0.0067 19.2 5.6 51 144-197 27-77 (80)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=2.4e-48 Score=352.54 Aligned_cols=237 Identities=45% Similarity=0.793 Sum_probs=221.1
Q ss_pred HHHHHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHHHHHHhHHhCCCC-ccchhhHHHHhhCceEec
Q 019727 18 EQQAKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKMLVESVKWRLEYKPEK-IVWEDVAREAETGKLYRA 96 (336)
Q Consensus 18 ~~~~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~~~~~wR~~~~~~~-i~~~~~~~~l~~g~~~~~ 96 (336)
+..+++.+++..+++...+...+++|..++|||||++|||++|.+||.+++.||+.+++.. +.++++..++++|.+|++
T Consensus 24 ~~~~k~~~~~~~~~pl~~~~~~~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~ 103 (324)
T KOG1470|consen 24 ESLDKINSVKKLLGPLTEKESKWCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYIL 103 (324)
T ss_pred HHHHHHHHHHHhhcchhhhhHhcCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEe
Confidence 3336889999999888777778899999999999999999999999999999999999998 888899999999999999
Q ss_pred cccCCCCCcEEEEc--cCCCCCCCHHHHHHHHHHHHHHHHHhcCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhc
Q 019727 97 NFCDKLGRPVLIMR--PGFQNSSSTEGQIKYLVYCMENAIMNLNPDREQMVWLIDFQGWTMGSVSVKVTRETANVLQNHY 174 (336)
Q Consensus 97 g~~Dk~GrpV~i~~--~~~~d~~~~~~~~~~~~~~lE~~~~~~~~~~~~~vvI~D~~g~s~~~~~~~~~~~~~~~lq~~Y 174 (336)
| +|++||||+|++ ++.....+..++.++++|+||.++..++.++++++++||+.|+|++|++++..+.+++++|+||
T Consensus 104 G-~D~~gRPVl~~~~~~~~qn~~t~~~~~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs~sN~d~~~~k~~~~~lq~hY 182 (324)
T KOG1470|consen 104 G-HDKDGRPVLYLRPRPHRQNTKTQKELERLLVYTLENAILFLPPGQEQFVWLFDLTGFSMSNPDIKFLKELLHILQDHY 182 (324)
T ss_pred c-ccCCCCeEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCcceEEEEEecccCcccCCCcHHHHHHHHHHHHhC
Confidence 9 899999999995 4555667889999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceEEEEcCCcchHHHHHHhhhccCcchhccEEEecCCChhhHHHHHccCCcCCcchhcCCCCCCCCChHHHHhhhh
Q 019727 175 PERLGLAILYNPPKVFESFWTVVKPFLEPKTYKKVRFAYSNDPQSQKIMEALFDINKLDSSFGGRSRVGFDYEAFGQLMR 254 (336)
Q Consensus 175 Pe~l~~i~IvN~P~~~~~~~~~vkpfL~~~t~~KI~~~~~~~~~~~~~L~~~id~~~LP~~~GG~~~~~~~~~~~~~~~~ 254 (336)
|+||+..+|+|+||+|..+|+++||||++.|++||+|+.+. ..|.+|||+++||..|||+....|.++.+|..|.
T Consensus 183 PErLg~a~l~~~P~iF~~~wkiikpflDp~t~~Kv~F~~~~-----~~l~~~~d~~~l~s~~GG~~~~~y~~e~~~~~~~ 257 (324)
T KOG1470|consen 183 PERLGKALLVNAPWIFQPFWKIIKPFLDPKTASKVKFVEPK-----DDLSEYFDESQLPSLFGGKLLFEYTHEEYWPQMK 257 (324)
T ss_pred hHHhhhhhhcCChHHHHHHHHHhhhccChhhhceeEEecCh-----hHHHhhCCccccchhhCCCcccccCCcchhhhhh
Confidence 99999999999999999999999999999999999999763 4599999999999999999999999999999999
Q ss_pred hcchhh
Q 019727 255 ADDKKK 260 (336)
Q Consensus 255 ~~d~~~ 260 (336)
+++...
T Consensus 258 ~~~~~~ 263 (324)
T KOG1470|consen 258 EDDSSL 263 (324)
T ss_pred hhHHHH
Confidence 888633
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=3.5e-37 Score=288.95 Aligned_cols=228 Identities=26% Similarity=0.387 Sum_probs=184.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHHHHHHhHHhCCCCccch-hhHHHH
Q 019727 10 AEKSLSPEEQQAKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKMLVESVKWRLEYKPEKIVWE-DVAREA 88 (336)
Q Consensus 10 ~~~~lt~e~~~~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~~~~~wR~~~~~~~i~~~-~~~~~l 88 (336)
....++ +.+++.++++| |+...++......+|.+|+||||||+||+++|.++|.+++.||++++.+.|..+ .....+
T Consensus 14 ~~~~~~-~~~~~~i~~lr-~~~~~~~l~~~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~~~ 91 (317)
T KOG1471|consen 14 ELNEIT-ESEEAVIAQLR-WLLQKPHLPNKYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDDEL 91 (317)
T ss_pred ccCCCc-HHHHHHHHHHH-HHhhccCCCCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccchhh
Confidence 455667 68889999999 666665532357899999999999999999999999999999999999888643 222222
Q ss_pred hh-CceEeccccCCCCCcEEEEccCCCCCC------CHHHHHHHHH--------HHHHHHHHhcCCCcccEEEEEeCCCC
Q 019727 89 ET-GKLYRANFCDKLGRPVLIMRPGFQNSS------STEGQIKYLV--------YCMENAIMNLNPDREQMVWLIDFQGW 153 (336)
Q Consensus 89 ~~-g~~~~~g~~Dk~GrpV~i~~~~~~d~~------~~~~~~~~~~--------~~lE~~~~~~~~~~~~~vvI~D~~g~ 153 (336)
.. -..... +.|++|+||++.+.|..+.. ...+..++.+ ..+|........++.|+++|+|++|+
T Consensus 92 ~~~~~~~~~-~~~~~g~~v~~~~~g~~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~ 170 (317)
T KOG1471|consen 92 LKYYPQGLH-GVDKEGRPVYIERLGKIDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGV 170 (317)
T ss_pred hhhcccccc-ccCCCCCEEEEeccCCCCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCC
Confidence 22 112233 47999999999999998754 2344444444 44444444445678999999999999
Q ss_pred CCCCC---CHHHHHHHHHHHHhhcccccceEEEEcCCcchHHHHHHhhhccCcchhccEEEecCCChhhHHHHHccCCcC
Q 019727 154 TMGSV---SVKVTRETANVLQNHYPERLGLAILYNPPKVFESFWTVVKPFLEPKTYKKVRFAYSNDPQSQKIMEALFDIN 230 (336)
Q Consensus 154 s~~~~---~~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~vkpfL~~~t~~KI~~~~~~~~~~~~~L~~~id~~ 230 (336)
+++|+ .+..++.++.++|++||++++++||||+|++|+++|+++||||+++|++||++++++ +.+.|.++|+++
T Consensus 171 ~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~~---~~~~L~k~i~~~ 247 (317)
T KOG1471|consen 171 SLSHLLKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHSK---DKESLLKYIPPE 247 (317)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCCC---chhhhhhhCCHh
Confidence 99987 478999999999999999999999999999999999999999999999999955443 479999999999
Q ss_pred CcchhcCCCCCCC
Q 019727 231 KLDSSFGGRSRVG 243 (336)
Q Consensus 231 ~LP~~~GG~~~~~ 243 (336)
.||.+|||++++.
T Consensus 248 ~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 248 VLPEEYGGTCGDL 260 (317)
T ss_pred hCccccCCCcccc
Confidence 9999999999973
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=4.2e-31 Score=222.79 Aligned_cols=149 Identities=32% Similarity=0.630 Sum_probs=123.8
Q ss_pred HhhCceEeccccCCCCCcEEEEccCCCCCCC--HHHHHHHHHHHHHHHHHhcC--CCcccEEEEEeCCCCCCCCCC---H
Q 019727 88 AETGKLYRANFCDKLGRPVLIMRPGFQNSSS--TEGQIKYLVYCMENAIMNLN--PDREQMVWLIDFQGWTMGSVS---V 160 (336)
Q Consensus 88 l~~g~~~~~g~~Dk~GrpV~i~~~~~~d~~~--~~~~~~~~~~~lE~~~~~~~--~~~~~~vvI~D~~g~s~~~~~---~ 160 (336)
...+..+++| +|++||||++++++++++.. .+++.+++++.+|.+++.+. .+..|+++|+|++|+++++++ .
T Consensus 4 ~~~~~~~~~g-~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~~ 82 (159)
T PF00650_consen 4 LKSGPFYLHG-RDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFSLSNFDWWPI 82 (159)
T ss_dssp HTTSCEEEEE-E-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT--HHHHHCHHH
T ss_pred HCCeeEEECC-CCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCceEeccccchh
Confidence 4456677776 79999999999999988654 56899999999999997664 478999999999999999887 8
Q ss_pred HHHHHHHHHHHhhcccccceEEEEcCCcchHHHHHHhhhccCcchhccEEEecCCChhhHHHHHccCCcCCcchhcCCC
Q 019727 161 KVTRETANVLQNHYPERLGLAILYNPPKVFESFWTVVKPFLEPKTYKKVRFAYSNDPQSQKIMEALFDINKLDSSFGGR 239 (336)
Q Consensus 161 ~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~vkpfL~~~t~~KI~~~~~~~~~~~~~L~~~id~~~LP~~~GG~ 239 (336)
+.++.++++++.+||++++++||||+|++|+.+|+++++||+++|++||+|+++. ++.+.|.++||+++||.+|||+
T Consensus 83 ~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~--~~~~~l~~~i~~~~lP~~~GG~ 159 (159)
T PF00650_consen 83 SFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGS--DWKAKLKEYIDPEQLPVEYGGT 159 (159)
T ss_dssp HHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTT--CHCHHHCCCSTGGGSBGGGTSS
T ss_pred hhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCc--ccHHHHHhhCCHhHCchhcCCC
Confidence 9999999999999999999999999999999999999999999999999999653 3456899999999999999997
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=99.96 E-value=1.1e-28 Score=207.67 Aligned_cols=140 Identities=36% Similarity=0.661 Sum_probs=130.7
Q ss_pred cCCCCCcEEEEccCCCCC--CCHHHHHHHHHHHHHHHHHh--cCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhc
Q 019727 99 CDKLGRPVLIMRPGFQNS--SSTEGQIKYLVYCMENAIMN--LNPDREQMVWLIDFQGWTMGSVSVKVTRETANVLQNHY 174 (336)
Q Consensus 99 ~Dk~GrpV~i~~~~~~d~--~~~~~~~~~~~~~lE~~~~~--~~~~~~~~vvI~D~~g~s~~~~~~~~~~~~~~~lq~~Y 174 (336)
+|++||||++++++++++ .+.+++++++++.+|.++.. .+.++.|+++|+|++|+++++++++.++.++.+++.+|
T Consensus 15 ~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~lk~~~~~~~~~y 94 (158)
T smart00516 15 YDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQREKKTGGIEGFTVIFDLKGLSMSNPDLSVLRKILKILQDHY 94 (158)
T ss_pred CCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHHHhcCCCeeeEEEEEECCCCCcccccHHHHHHHHHHHHHHh
Confidence 799999999999999875 36789999999999999986 56678999999999999999999999999999999999
Q ss_pred ccccceEEEEcCCcchHHHHHHhhhccCcchhccEEEecCCChhhHHHHHccCCcCCcchhcCCCCC
Q 019727 175 PERLGLAILYNPPKVFESFWTVVKPFLEPKTYKKVRFAYSNDPQSQKIMEALFDINKLDSSFGGRSR 241 (336)
Q Consensus 175 Pe~l~~i~IvN~P~~~~~~~~~vkpfL~~~t~~KI~~~~~~~~~~~~~L~~~id~~~LP~~~GG~~~ 241 (336)
|++++++||||+|++++++|+++++|+++++++||++++++ +.+.|.++||+++||.+|||++.
T Consensus 95 p~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~---~~~~L~~~i~~~~lP~~~GG~~~ 158 (158)
T smart00516 95 PERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGND---SKEELLEYIDPEQLPEELGGTLD 158 (158)
T ss_pred HHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCC---CHHHHHhhCCHhhCcHhhCCCCC
Confidence 99999999999999999999999999999999999999873 36889999999999999999974
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=1.6e-26 Score=193.12 Aligned_cols=144 Identities=35% Similarity=0.612 Sum_probs=129.5
Q ss_pred ceEeccccCCCCCcEEEEccCCCCCC---CHHHHHHHHHHHHHHHHHhcCCCcccEEEEEeCCCCCCCCC--CHHHHHHH
Q 019727 92 KLYRANFCDKLGRPVLIMRPGFQNSS---STEGQIKYLVYCMENAIMNLNPDREQMVWLIDFQGWTMGSV--SVKVTRET 166 (336)
Q Consensus 92 ~~~~~g~~Dk~GrpV~i~~~~~~d~~---~~~~~~~~~~~~lE~~~~~~~~~~~~~vvI~D~~g~s~~~~--~~~~~~~~ 166 (336)
.+++.|++|++||||++++++..+.. ..++++++.++.+|..+........|+++|+|++|++++++ +.+.++.+
T Consensus 9 ~~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~~~k~~ 88 (157)
T cd00170 9 KVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQEDDEQVEGFVVIIDLKGLSLSHLLPDPSLLKKI 88 (157)
T ss_pred cccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhhhhhcccceEEEEECCCCChhccchhHHHHHHH
Confidence 44555568999999999999964433 24789999999999999887766689999999999999998 78899999
Q ss_pred HHHHHhhcccccceEEEEcCCcchHHHHHHhhhccCcchhccEEEecCCChhhHHHHHccCCcCCcchhcCCC
Q 019727 167 ANVLQNHYPERLGLAILYNPPKVFESFWTVVKPFLEPKTYKKVRFAYSNDPQSQKIMEALFDINKLDSSFGGR 239 (336)
Q Consensus 167 ~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~vkpfL~~~t~~KI~~~~~~~~~~~~~L~~~id~~~LP~~~GG~ 239 (336)
+.+++.+||++++++||||+|++++.+|+++++|+++++++||++++++ .+.|.++||+++||.+|||+
T Consensus 89 ~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~----~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 89 LKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD----KEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred HHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC----HHHHHhhCChhhCcHhhCCC
Confidence 9999999999999999999999999999999999999999999999763 57899999999999999996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.66 E-value=3.5e-17 Score=136.71 Aligned_cols=143 Identities=21% Similarity=0.341 Sum_probs=96.4
Q ss_pred eEeccccCCCCCcEEEEccCCCCCCCHHHHHHHHHHHHHHHHHhcCCCcccEEEEEeCCCCCCCC-CCHHHHHHHHHHHH
Q 019727 93 LYRANFCDKLGRPVLIMRPGFQNSSSTEGQIKYLVYCMENAIMNLNPDREQMVWLIDFQGWTMGS-VSVKVTRETANVLQ 171 (336)
Q Consensus 93 ~~~~g~~Dk~GrpV~i~~~~~~d~~~~~~~~~~~~~~lE~~~~~~~~~~~~~vvI~D~~g~s~~~-~~~~~~~~~~~~lq 171 (336)
+++.||+|++||||+++...+. + +..++.+++.|.+....... ...++++|+|+.+++..+ .++..++.+.+.+.
T Consensus 3 ~~~~gG~d~~g~pV~~~~~~~~-~-~~~~~~~ll~yl~~~l~~~~--~~~~f~vVid~~~~~~~~~~~~~~l~~~~~~l~ 78 (149)
T PF13716_consen 3 FFYPGGRDREGRPVVVFIASRL-P-SSDDLERLLLYLLSTLSEEV--VDKPFSVVIDHTGFSRSSEPSLSWLKQLYKLLP 78 (149)
T ss_dssp E-EEEEEBTTS-EEEEEEGGG--C--TTHHHHHHHHHHHHH-TTT--TTS-EEEEEE-TT--GGG---HHHHHHTTTSS-
T ss_pred EEEecccCCCcCEEEEEECCcC-c-chhhHHHHHHHHHHhhhHHh--cCCCEEEEEEcCCCccccCCchHHHHHHHHHHH
Confidence 4566789999999999997777 3 22355555555544442222 246799999999998755 47899999999999
Q ss_pred hhcccccceEEEEcCCcchHHHH-HHhhhccCcch-hccEEEecCCChhhHHHHHccCCcCCcchhcCCCCCCCCCh
Q 019727 172 NHYPERLGLAILYNPPKVFESFW-TVVKPFLEPKT-YKKVRFAYSNDPQSQKIMEALFDINKLDSSFGGRSRVGFDY 246 (336)
Q Consensus 172 ~~YPe~l~~i~IvN~P~~~~~~~-~~vkpfL~~~t-~~KI~~~~~~~~~~~~~L~~~id~~~LP~~~GG~~~~~~~~ 246 (336)
..|+.+|+++||||++++++.++ .+.+++.+.+. ..||.++.+ .++|.++||+++||.++||+.+ ||+
T Consensus 79 ~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s-----l~~L~~~i~~~qL~~~lp~~~~--~d~ 148 (149)
T PF13716_consen 79 RKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS-----LSELSKHIDPSQLPESLPGVLQ--YDH 148 (149)
T ss_dssp HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS-----TCGGGGTSGGGG------HHH------
T ss_pred HHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC-----HHHHHhhCCHHHhcccCCCEEe--cCc
Confidence 99999999999999999999999 66677888888 899999976 4789999999999999998876 554
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=1.2e-09 Score=75.32 Aligned_cols=48 Identities=29% Similarity=0.437 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhCCc-------cCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHHH
Q 019727 20 QAKINEVRKIIGPI-------ADKYPVLCSDESISRYLRARNWHTKKASKMLVES 67 (336)
Q Consensus 20 ~~~i~elr~~l~~~-------~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~~~ 67 (336)
++++++||++|... .+.....++|.+|+||||||+|||++|.+||.++
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 46799999999874 2335667899999999999999999999999875
No 8
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.67 E-value=1.2e-07 Score=88.66 Aligned_cols=130 Identities=18% Similarity=0.290 Sum_probs=106.0
Q ss_pred CceEeccc-cCCCCCcEEEEccCCCCCCC-HHH--HHHHHHHHHHHHHHhcCCCcccEEEEEeCCCCCCCCC-CHHHHHH
Q 019727 91 GKLYRANF-CDKLGRPVLIMRPGFQNSSS-TEG--QIKYLVYCMENAIMNLNPDREQMVWLIDFQGWTMGSV-SVKVTRE 165 (336)
Q Consensus 91 g~~~~~g~-~Dk~GrpV~i~~~~~~d~~~-~~~--~~~~~~~~lE~~~~~~~~~~~~~vvI~D~~g~s~~~~-~~~~~~~ 165 (336)
+.+.+.|+ .|+.||+|+++...++.+.+ +++ ++++.++.++..++ ..++.++=-.|+...+. ..+++..
T Consensus 80 ei~qvi~~~~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~Ve------~DYt~vYfh~gl~s~nkp~l~~l~~ 153 (467)
T KOG4406|consen 80 EILQVIGDAKDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVE------NDYTLVYFHHGLPSDNKPYLQLLFD 153 (467)
T ss_pred heeeeccCcccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHh------ccceeeehhcCCcccccchHHHHHH
Confidence 44555554 69999999999998887653 444 78899999999886 33777777777777665 4678888
Q ss_pred HHHHHHhhcccccceEEEEcCCcchHHHHHHhhhccCcchhccEEEecCCChhhHHHHHccCCcCC
Q 019727 166 TANVLQNHYPERLGLAILYNPPKVFESFWTVVKPFLEPKTYKKVRFAYSNDPQSQKIMEALFDINK 231 (336)
Q Consensus 166 ~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~vkpfL~~~t~~KI~~~~~~~~~~~~~L~~~id~~~ 231 (336)
...-+..+|-..++.+|+|++-|+.+++|+++|||++.+..+||+.+.. ..+|.++|.-++
T Consensus 154 aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n~-----lseL~~~l~l~r 214 (467)
T KOG4406|consen 154 AYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFNS-----LSELFEALKLNR 214 (467)
T ss_pred HHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEeeh-----HHHHHHhhhhhh
Confidence 8888888999999999999999999999999999999999999998865 678888876443
No 9
>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=83.69 E-value=4.3 Score=25.71 Aligned_cols=39 Identities=21% Similarity=0.295 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHH
Q 019727 20 QAKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKMLVE 66 (336)
Q Consensus 20 ~~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~~ 66 (336)
.+.|..|++.+-. ++...+..-|.++++|++.|..+|-.
T Consensus 2 ~~~v~~L~~mFP~--------~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 2 EEMVQQLQEMFPD--------LDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHHSSS--------S-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHHCCC--------CCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 3567777777733 56789999999999999999998753
No 10
>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=83.53 E-value=4.2 Score=25.94 Aligned_cols=35 Identities=29% Similarity=0.529 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHH
Q 019727 21 AKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKML 64 (336)
Q Consensus 21 ~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l 64 (336)
++|.+|....+. ++.....||..++||++.|+..+
T Consensus 2 e~i~~F~~iTg~---------~~~~A~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 2 EKIAQFMSITGA---------DEDVAIQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp HHHHHHHHHH-S---------SHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHCc---------CHHHHHHHHHHcCCCHHHHHHHH
Confidence 567777766532 56889999999999999999875
No 11
>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=77.11 E-value=9.1 Score=24.25 Aligned_cols=37 Identities=16% Similarity=0.263 Sum_probs=29.5
Q ss_pred HHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHH
Q 019727 21 AKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKMLV 65 (336)
Q Consensus 21 ~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~ 65 (336)
+.++.|++.+- ..++..+.+.|+++++|++.|...|-
T Consensus 4 ~~v~~L~~mFP--------~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 4 EALHDLKDMFP--------NLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred HHHHHHHHHCC--------CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45777776662 25778999999999999999998874
No 12
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=73.92 E-value=1.3 Score=32.46 Aligned_cols=49 Identities=31% Similarity=0.506 Sum_probs=30.9
Q ss_pred CCCHHHHHH---HHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHHH
Q 019727 13 SLSPEEQQA---KINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKMLVES 67 (336)
Q Consensus 13 ~lt~e~~~~---~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~~~ 67 (336)
.|||+++.+ ++.++|+.|+... + ++..|..-|+.++|||++|+..|.+.
T Consensus 19 ~Ls~ed~~~L~~~l~~vr~~Lg~~~---~---~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 19 ELSPEDQAQLYSCLPQVREVLGDYV---P---PEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp H-TCHHHHHHCHHCCCHHHHCCCCC--------CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred cCCHHHHHHHHHHHHHHHHHHcccC---C---CHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 467544332 3445566565532 1 67788889999999999999988754
No 13
>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=66.10 E-value=23 Score=24.39 Aligned_cols=42 Identities=21% Similarity=0.388 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHH
Q 019727 17 EEQQAKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKMLVE 66 (336)
Q Consensus 17 e~~~~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~~ 66 (336)
..-+..|..+|+..+. .+|..+..-|+-|+.|..+|+++|-.
T Consensus 3 ~~~rk~VQ~iKEiv~~--------hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 3 AASRKTVQSIKEIVGC--------HSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred hHHHHHHHHHHHHhcC--------CCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 3445667777766644 46889999999999999999999854
No 14
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=61.54 E-value=28 Score=24.89 Aligned_cols=48 Identities=17% Similarity=0.197 Sum_probs=34.4
Q ss_pred EEEEeCCCCCCCCCCHHHHHHHHHHHHhhcc--cccceEEEEcCCcchHHHH
Q 019727 145 VWLIDFQGWTMGSVSVKVTRETANVLQNHYP--ERLGLAILYNPPKVFESFW 194 (336)
Q Consensus 145 vvI~D~~g~s~~~~~~~~~~~~~~~lq~~YP--e~l~~i~IvN~P~~~~~~~ 194 (336)
.+++|+.|+. .++.+++-.++..+...|| +.-.++.++|+......+.
T Consensus 19 ~V~lDF~gv~--~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I 68 (74)
T PF14213_consen 19 KVVLDFEGVE--SITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMI 68 (74)
T ss_pred eEEEECCCcc--cccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHH
Confidence 4889999983 4557788888888887777 5556777888765444443
No 15
>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=53.32 E-value=23 Score=21.55 Aligned_cols=35 Identities=26% Similarity=0.320 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHH
Q 019727 20 QAKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKML 64 (336)
Q Consensus 20 ~~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l 64 (336)
+++|++|++. . .+.....+-|+.+++|+++|+..|
T Consensus 3 ~~~v~~L~~m--G--------f~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 3 EEKVQQLMEM--G--------FSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHH--T--------S-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHc--C--------CCHHHHHHHHHHcCCCHHHHHHhC
Confidence 3556666655 1 345688899999999999998764
No 16
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=51.40 E-value=25 Score=21.16 Aligned_cols=24 Identities=33% Similarity=0.368 Sum_probs=20.3
Q ss_pred CCHHHHHHHhhhcCCCHHHHHHHH
Q 019727 41 CSDESISRYLRARNWHTKKASKML 64 (336)
Q Consensus 41 ~~D~~LlRfLra~~~dv~~A~~~l 64 (336)
.+.....+-|+.+++|+++|...|
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 456789999999999999998754
No 17
>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=51.30 E-value=63 Score=24.38 Aligned_cols=83 Identities=16% Similarity=0.180 Sum_probs=53.3
Q ss_pred CHHHHHHHHHHHHHHHHHhcCCCcccEEEEEeCC-CCCCCCCCHHHHHHHHHHHHhhcccccceEEEEcCCcchHHHHHH
Q 019727 118 STEGQIKYLVYCMENAIMNLNPDREQMVWLIDFQ-GWTMGSVSVKVTRETANVLQNHYPERLGLAILYNPPKVFESFWTV 196 (336)
Q Consensus 118 ~~~~~~~~~~~~lE~~~~~~~~~~~~~vvI~D~~-g~s~~~~~~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~ 196 (336)
+.+++.. ..-.++..+. ....+.+++|+. ++ ..+++.......+.... +...++++-||-.+.+...+.++
T Consensus 12 t~ed~~~-~~~~~~~~~~----~~~~~~ll~d~~~~~--~~~~~~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~~~~~ 83 (109)
T PF11964_consen 12 TEEDYKE-LLPALEELIA----DHGKIRLLVDLRRDF--EGWSPEARWEDAKFGLK-HLKHFRRIAVVGDSEWIRMIANF 83 (109)
T ss_dssp -HHHHHH-HHHHHHHHHT----TSSSEEEEEEEC-CE--EEEHHHHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHHHHHH
T ss_pred CHHHHHH-HHHHHHHHHh----cCCceEEEEEecCcc--CCCCHHHHHHHHHhchh-hhcccCEEEEEECcHHHHHHHHH
Confidence 3444444 3344444433 345688999988 64 34445666666655555 88889999999999999999999
Q ss_pred hhhccCcchhccEEEe
Q 019727 197 VKPFLEPKTYKKVRFA 212 (336)
Q Consensus 197 vkpfL~~~t~~KI~~~ 212 (336)
+.+| +..-+++.
T Consensus 84 ~~~~----~~~~~~~F 95 (109)
T PF11964_consen 84 FAAF----PPIEVRYF 95 (109)
T ss_dssp HHHH-----SSEEEEE
T ss_pred HHhc----CCCceEEE
Confidence 9987 23345555
No 18
>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=51.06 E-value=26 Score=21.23 Aligned_cols=24 Identities=33% Similarity=0.365 Sum_probs=20.8
Q ss_pred CCHHHHHHHhhhcCCCHHHHHHHH
Q 019727 41 CSDESISRYLRARNWHTKKASKML 64 (336)
Q Consensus 41 ~~D~~LlRfLra~~~dv~~A~~~l 64 (336)
.+.....+-|+.+++|+++|...|
T Consensus 13 f~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 13 FSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 457889999999999999998766
No 19
>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=49.15 E-value=18 Score=29.82 Aligned_cols=49 Identities=24% Similarity=0.419 Sum_probs=39.0
Q ss_pred HHHHHHHHHHhhcccccc--eEEEEcCCcchHHHHHHhhhccCc--chhccEEE
Q 019727 162 VTRETANVLQNHYPERLG--LAILYNPPKVFESFWTVVKPFLEP--KTYKKVRF 211 (336)
Q Consensus 162 ~~~~~~~~lq~~YPe~l~--~i~IvN~P~~~~~~~~~vkpfL~~--~t~~KI~~ 211 (336)
....++..+..+||..++ ..-++|..-.|.++|+-+ |-++. +-++.|+.
T Consensus 16 ~y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRL 68 (159)
T PF04838_consen 16 DYKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRL 68 (159)
T ss_pred CHHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhh
Confidence 356788999999999999 889999999999999877 55555 44444544
No 20
>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=48.69 E-value=68 Score=25.66 Aligned_cols=62 Identities=18% Similarity=0.233 Sum_probs=39.7
Q ss_pred HHHHHhcCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhcccccceEEEEcCCcchHHHHHHhhhcc
Q 019727 131 ENAIMNLNPDREQMVWLIDFQGWTMGSVSVKVTRETANVLQNHYPERLGLAILYNPPKVFESFWTVVKPFL 201 (336)
Q Consensus 131 E~~~~~~~~~~~~~vvI~D~~g~s~~~~~~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~vkpfL 201 (336)
+.++........+++++.|+ |-+..+ ....+..++ ++..+++.++|+|.+...+...+..-.
T Consensus 49 ~~ai~~~~~~~dgVlvl~DL-Ggs~~n-----~e~a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~~ 110 (125)
T TIGR02364 49 IEAIEKADNEADGVLIFYDL-GSAVMN-----AEMAVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQV 110 (125)
T ss_pred HHHHHHhcCCCCCEEEEEcC-CCcHhH-----HHHHHHHhc---cccccEEEEechhHHHHHHHHHHHHcC
Confidence 34444443335789999999 644322 111233332 356689999999999999888876543
No 21
>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=45.98 E-value=38 Score=21.25 Aligned_cols=23 Identities=13% Similarity=0.069 Sum_probs=19.8
Q ss_pred CHHHHHHHhhhcCCCHHHHHHHH
Q 019727 42 SDESISRYLRARNWHTKKASKML 64 (336)
Q Consensus 42 ~D~~LlRfLra~~~dv~~A~~~l 64 (336)
....|..-|+.|++||-+|.+.+
T Consensus 16 kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 16 KRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred ChHHHHHHHHHcCCcHHHHHHHh
Confidence 45788899999999999998865
No 22
>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=43.82 E-value=1.1e+02 Score=21.34 Aligned_cols=46 Identities=28% Similarity=0.355 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHHH
Q 019727 12 KSLSPEEQQAKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKMLVES 67 (336)
Q Consensus 12 ~~lt~e~~~~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~~~ 67 (336)
..++ +.+++.|.+|-..-+ .+-.|-.++|...+||.++|.+.+.+-
T Consensus 6 ~~~~-~~q~~~v~~~~~~Tg---------mn~~~s~~cLe~~~Wd~~~Al~~F~~l 51 (63)
T smart00804 6 PTLS-PEQQEMVQAFSAQTG---------MNAEYSQMCLEDNNWDYERALKNFTEL 51 (63)
T ss_pred CCCC-HHHHHHHHHHHHHHC---------CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4667 577788887765542 456799999999999999999998764
No 23
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=41.54 E-value=72 Score=28.35 Aligned_cols=100 Identities=18% Similarity=0.319 Sum_probs=61.1
Q ss_pred HHHHHHHHHHhcC------CCcccEEEEEeCCCC-C-CCCCCHHHHHHHHHHHHhhcccccceEEEEcCCcch------H
Q 019727 126 LVYCMENAIMNLN------PDREQMVWLIDFQGW-T-MGSVSVKVTRETANVLQNHYPERLGLAILYNPPKVF------E 191 (336)
Q Consensus 126 ~~~~lE~~~~~~~------~~~~~~vvI~D~~g~-s-~~~~~~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~------~ 191 (336)
.+|+||+.+..+. ...++-.+||||-|- - ..| ...+++++..++. .--++..+|++..+.++ +
T Consensus 75 Lv~cmEyl~~NldwL~~~~Gd~eddylifDcPGQIELytH--~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~KfiS 151 (273)
T KOG1534|consen 75 LVYCMEYLLENLDWLEEEIGDVEDDYLIFDCPGQIELYTH--LPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTKFIS 151 (273)
T ss_pred chhHHHHHHHHHHHHHhhccCccCCEEEEeCCCeeEEeec--ChhHHHHHHHHhc-ccCceeEEEEeccchhhhHHHHHH
Confidence 5788888877652 245677899999882 1 123 3577888888877 44577788888877654 3
Q ss_pred HHHHHhhhccCc-----chhccEEEecCCChhhHHHHHccCCcCC
Q 019727 192 SFWTVVKPFLEP-----KTYKKVRFAYSNDPQSQKIMEALFDINK 231 (336)
Q Consensus 192 ~~~~~vkpfL~~-----~t~~KI~~~~~~~~~~~~~L~~~id~~~ 231 (336)
.++..+...+.= .+.+|.-.++. +.++.|.+++.++.
T Consensus 152 G~lsAlsAMi~lE~P~INvlsKMDLlk~---~~k~~l~~Fl~~d~ 193 (273)
T KOG1534|consen 152 GCLSALSAMISLEVPHINVLSKMDLLKD---KNKKELERFLNPDE 193 (273)
T ss_pred HHHHHHHHHHHhcCcchhhhhHHHHhhh---hhHHHHHHhcCCch
Confidence 333333333221 24455555543 23567777776553
No 24
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=40.95 E-value=2e+02 Score=28.00 Aligned_cols=83 Identities=18% Similarity=0.209 Sum_probs=54.5
Q ss_pred CCCCcEEEEccCCCCCCCHHHHHHHHHHHHHHHHHhcCCCcccEEEEEeCCCCCCCCC---------CHHHHHHHHHHHH
Q 019727 101 KLGRPVLIMRPGFQNSSSTEGQIKYLVYCMENAIMNLNPDREQMVWLIDFQGWTMGSV---------SVKVTRETANVLQ 171 (336)
Q Consensus 101 k~GrpV~i~~~~~~d~~~~~~~~~~~~~~lE~~~~~~~~~~~~~vvI~D~~g~s~~~~---------~~~~~~~~~~~lq 171 (336)
....|++++-+|.... +.+.++|.++.. +.+ ..=-+||++-.|++-..+ +..-++.+++.+.
T Consensus 122 ~~~~P~vvilpGltg~-S~~~YVr~lv~~---a~~-----~G~r~VVfN~RG~~g~~LtTpr~f~ag~t~Dl~~~v~~i~ 192 (409)
T KOG1838|consen 122 DGTDPIVVILPGLTGG-SHESYVRHLVHE---AQR-----KGYRVVVFNHRGLGGSKLTTPRLFTAGWTEDLREVVNHIK 192 (409)
T ss_pred CCCCcEEEEecCCCCC-ChhHHHHHHHHH---HHh-----CCcEEEEECCCCCCCCccCCCceeecCCHHHHHHHHHHHH
Confidence 3556999998887643 344566665443 222 123478899999766554 3568999999999
Q ss_pred hhcccccceEEEEcCCcchHHHH
Q 019727 172 NHYPERLGLAILYNPPKVFESFW 194 (336)
Q Consensus 172 ~~YPe~l~~i~IvN~P~~~~~~~ 194 (336)
..||.+ +++.+--+.--.+++
T Consensus 193 ~~~P~a--~l~avG~S~Gg~iL~ 213 (409)
T KOG1838|consen 193 KRYPQA--PLFAVGFSMGGNILT 213 (409)
T ss_pred HhCCCC--ceEEEEecchHHHHH
Confidence 999998 666665443333333
No 25
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=35.15 E-value=26 Score=31.70 Aligned_cols=26 Identities=27% Similarity=0.378 Sum_probs=22.1
Q ss_pred ceEEEEcCCcchHHHHHHhhhccCcc
Q 019727 179 GLAILYNPPKVFESFWTVVKPFLEPK 204 (336)
Q Consensus 179 ~~i~IvN~P~~~~~~~~~vkpfL~~~ 204 (336)
..++|||+||-+..-...+-|+|...
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~ 262 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTL 262 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHH
Confidence 36999999999999998888887654
No 26
>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=34.51 E-value=23 Score=31.98 Aligned_cols=28 Identities=18% Similarity=0.315 Sum_probs=20.4
Q ss_pred ceEEEEcCCcchHHHHHHhhhccCcchh
Q 019727 179 GLAILYNPPKVFESFWTVVKPFLEPKTY 206 (336)
Q Consensus 179 ~~i~IvN~P~~~~~~~~~vkpfL~~~t~ 206 (336)
..++|||+||-+.....-+-|+|.+...
T Consensus 206 SGm~iiNPPw~l~~~l~~~l~~L~~~L~ 233 (245)
T PF04378_consen 206 SGMLIINPPWTLDEELEEILPWLAETLA 233 (245)
T ss_dssp EEEEEES--TTHHHHHHHHHHHHHHHSS
T ss_pred ceEEEEcCCccHHHHHHHHHHHHHHHhC
Confidence 4699999999999888888777765443
No 27
>PF09932 DUF2164: Uncharacterized conserved protein (DUF2164); InterPro: IPR018680 This family of various hypothetical prokaryotic proteins has no known function.
Probab=32.70 E-value=46 Score=24.21 Aligned_cols=40 Identities=18% Similarity=0.181 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHHHhCCccCCCCCCCCHHHHHHHhhh
Q 019727 13 SLSPEEQQAKINEVRKIIGPIADKYPVLCSDESISRYLRA 52 (336)
Q Consensus 13 ~lt~e~~~~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra 52 (336)
.||+++++..+.+++..+....+..-....-.+|+.|...
T Consensus 2 ~l~ke~k~~li~~iq~yf~~E~d~eiG~~~Ae~LLDF~~~ 41 (76)
T PF09932_consen 2 KLSKEEKAELIDKIQRYFAEELDEEIGDFEAEFLLDFFIE 41 (76)
T ss_pred cCCHHHHHHHHHHHHHHHHHHhcCcHHHhHHHHHHHHHHH
Confidence 4788999999999999998775544445566788888754
No 28
>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=31.93 E-value=1.6e+02 Score=23.52 Aligned_cols=55 Identities=16% Similarity=0.210 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHhhcccc-cc-eEEEEcCCcchHHHHHHh-----hhccCcchhccEEEecC
Q 019727 160 VKVTRETANVLQNHYPER-LG-LAILYNPPKVFESFWTVV-----KPFLEPKTYKKVRFAYS 214 (336)
Q Consensus 160 ~~~~~~~~~~lq~~YPe~-l~-~i~IvN~P~~~~~~~~~v-----kpfL~~~t~~KI~~~~~ 214 (336)
...+-+++.++.-.+=.. -+ -++++|..-+.+.++..+ ..|+++.....+.++.+
T Consensus 64 ~GTl~El~~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~ 125 (133)
T PF03641_consen 64 IGTLDELFEALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDD 125 (133)
T ss_dssp HHHHHHHHHHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESS
T ss_pred CchHHHHHHHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCC
Confidence 456666666665333332 33 699999887888888876 47899999999999865
No 29
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=28.57 E-value=90 Score=22.15 Aligned_cols=29 Identities=21% Similarity=0.300 Sum_probs=20.9
Q ss_pred HHHHHHhCCccCCCCCCCCHHHHHHHhhh
Q 019727 24 NEVRKIIGPIADKYPVLCSDESISRYLRA 52 (336)
Q Consensus 24 ~elr~~l~~~~~~~~~~~~D~~LlRfLra 52 (336)
.|+..|+.+..+..-..++|..|..||.+
T Consensus 33 ~el~a~lrke~~~~y~~c~D~~L~~FL~G 61 (68)
T PF07308_consen 33 AELSAWLRKEDEKGYKECSDQLLRNFLNG 61 (68)
T ss_pred HHHHHHHCCCCCccccccChHHHHHHHHH
Confidence 45667777765444456899999999965
No 30
>PRK02399 hypothetical protein; Provisional
Probab=27.68 E-value=4.4e+02 Score=25.74 Aligned_cols=78 Identities=14% Similarity=0.175 Sum_probs=54.9
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCcccEEEEEeCCCCCCCC------CCHHHHHHHHHHHHhhcccccceEEE-----EcCC
Q 019727 119 TEGQIKYLVYCMENAIMNLNPDREQMVWLIDFQGWTMGS------VSVKVTRETANVLQNHYPERLGLAIL-----YNPP 187 (336)
Q Consensus 119 ~~~~~~~~~~~lE~~~~~~~~~~~~~vvI~D~~g~s~~~------~~~~~~~~~~~~lq~~YPe~l~~i~I-----vN~P 187 (336)
.++..+.--+.-|++ ......+.+++=++|+|.-. .++..-..++..++.+.+..+. ++ ||.|
T Consensus 315 ~eE~~~~g~~ia~kL----n~a~gpv~vllP~~G~S~~D~~G~~f~Dpead~alf~~l~~~l~~~~~--v~~~~~hIND~ 388 (406)
T PRK02399 315 PEENRQIGRWIAEKL----NRAKGPVAFLIPLGGVSALDRPGQPFHDPEADAAFFDALEETVTETRR--LIEVPAHINDP 388 (406)
T ss_pred HHHHHHHHHHHHHHH----hcCCCCeEEEEeCCCCccccCCCCCccChhHHHHHHHHHHHhCCCCce--EEECCCCCCCH
Confidence 445544444444443 33345688999999999866 3678888899999999977654 55 7999
Q ss_pred cchHHHHHHhhhccC
Q 019727 188 KVFESFWTVVKPFLE 202 (336)
Q Consensus 188 ~~~~~~~~~vkpfL~ 202 (336)
-|...+...+..++.
T Consensus 389 ~FA~a~~~~l~~~~~ 403 (406)
T PRK02399 389 EFAEAAVEAFEELMA 403 (406)
T ss_pred HHHHHHHHHHHHHHh
Confidence 888888776655543
No 31
>PF04548 AIG1: AIG1 family; InterPro: IPR006703 This entry represents a domain found in Arabidopsis protein AIG1 which appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 (avrRpt2-induced gene) exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2 []. The domain is also apparently found in a number of mammalian proteins, for example the rat immune-associated nucleotide 4 protein. ; GO: 0005525 GTP binding; PDB: 3LXX_A 3BB4_A 3DEF_A 3BB3_A 2J3E_A 3V70_B 3BB1_A 1H65_B 2XTP_A 3P1J_C ....
Probab=27.14 E-value=2.1e+02 Score=24.84 Aligned_cols=68 Identities=15% Similarity=0.166 Sum_probs=33.0
Q ss_pred EEEEeCCCCCCCCCC-HHHHHHHHHHHHhhcccccceEEEEcCCcch---HHHHHHhhhccCcchhccEEEe
Q 019727 145 VWLIDFQGWTMGSVS-VKVTRETANVLQNHYPERLGLAILYNPPKVF---ESFWTVVKPFLEPKTYKKVRFA 212 (336)
Q Consensus 145 vvI~D~~g~s~~~~~-~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~---~~~~~~vkpfL~~~t~~KI~~~ 212 (336)
+.|+|.-|+.=.... -..++.+...+..+.|+.-.-++|++...+- ..++..+...++++..+.+.|+
T Consensus 51 v~VIDTPGl~d~~~~~~~~~~~i~~~l~~~~~g~ha~llVi~~~r~t~~~~~~l~~l~~~FG~~~~k~~ivv 122 (212)
T PF04548_consen 51 VTVIDTPGLFDSDGSDEEIIREIKRCLSLCSPGPHAFLLVIPLGRFTEEDREVLELLQEIFGEEIWKHTIVV 122 (212)
T ss_dssp EEEEE--SSEETTEEHHHHHHHHHHHHHHTTT-ESEEEEEEETTB-SHHHHHHHHHHHHHHCGGGGGGEEEE
T ss_pred EEEEeCCCCCCCcccHHHHHHHHHHHHHhccCCCeEEEEEEecCcchHHHHHHHHHHHHHccHHHHhHhhHH
Confidence 456666665333222 2344555555555556555555555555442 3445555555566655555554
No 32
>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=26.01 E-value=94 Score=19.40 Aligned_cols=22 Identities=23% Similarity=0.285 Sum_probs=18.5
Q ss_pred HHHHHHHhhhcCCCHHHHHHHH
Q 019727 43 DESISRYLRARNWHTKKASKML 64 (336)
Q Consensus 43 D~~LlRfLra~~~dv~~A~~~l 64 (336)
..++..-|..++||+.+|++.|
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 3678889999999999999987
No 33
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=25.54 E-value=2.3e+02 Score=25.47 Aligned_cols=112 Identities=13% Similarity=0.162 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHHHHHHhHHhCCCCccchhhHHHHhhCceEec
Q 019727 17 EEQQAKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKMLVESVKWRLEYKPEKIVWEDVAREAETGKLYRA 96 (336)
Q Consensus 17 e~~~~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~~~~~wR~~~~~~~i~~~~~~~~l~~g~~~~~ 96 (336)
+..+.+++..++++.+.+. .....-..+++||++-+||+. +|++..+++- -..|..-+.
T Consensus 4 ~~iq~~~~ni~~~y~~~~n--Ea~vrq~lIlp~L~slGwdi~----------------nPkEV~PEe~---t~~GraDya 62 (284)
T COG2810 4 STIQKIKNNINKFYNKSRN--EAAVRQHLILPFLSSLGWDID----------------NPKEVRPEEK---TEEGRADYA 62 (284)
T ss_pred HHHHHHHHHHHHHhccCcc--HHHHHHHHHHHHHHHcCCCCC----------------CccccCcccc---cccCccceE
Confidence 4566788888888876432 122345689999999999874 3544443321 112221111
Q ss_pred cccCCCCCcEEEEccCCCCCCCHHHHHHHHHHHHHHHHHhcCCCcccEEEEEeCC
Q 019727 97 NFCDKLGRPVLIMRPGFQNSSSTEGQIKYLVYCMENAIMNLNPDREQMVWLIDFQ 151 (336)
Q Consensus 97 g~~Dk~GrpV~i~~~~~~d~~~~~~~~~~~~~~lE~~~~~~~~~~~~~vvI~D~~ 151 (336)
.=++|+.+..+-.+........++.++.-|++....+-.--....+-+|+|..
T Consensus 63 --likd~kvfafieak~ls~~~akd~qq~~~Yav~~Gv~~~iVtnGrvWiV~d~~ 115 (284)
T COG2810 63 --LIKDGKVFAFIEAKNLSVNPAKDVQQLAKYAVDKGVEVGIVTNGRVWIVVDAF 115 (284)
T ss_pred --EEecCcEEEEEeccccCcCchHHHHHHHHHHHhcCcEEEEEeCCeEEEEEecc
Confidence 23456666666565555556677788888887777654322223444566654
No 34
>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=25.38 E-value=93 Score=23.81 Aligned_cols=50 Identities=8% Similarity=0.051 Sum_probs=34.0
Q ss_pred EEEEEeCCCCCCCCCCHHHHHHHHHHHHhhcccccceEEEEcCCcchHHHHHH
Q 019727 144 MVWLIDFQGWTMGSVSVKVTRETANVLQNHYPERLGLAILYNPPKVFESFWTV 196 (336)
Q Consensus 144 ~vvI~D~~g~s~~~~~~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~ 196 (336)
-.+|+||++++ .++...+..+..+.+..- .+=..++++|++.-....+..
T Consensus 49 ~~vIlD~s~v~--~iDssgi~~L~~~~~~~~-~~g~~~~l~~~~~~v~~~l~~ 98 (117)
T PF01740_consen 49 KNVILDMSGVS--FIDSSGIQALVDIIKELR-RRGVQLVLVGLNPDVRRILER 98 (117)
T ss_dssp SEEEEEETTES--EESHHHHHHHHHHHHHHH-HTTCEEEEESHHHHHHHHHHH
T ss_pred eEEEEEEEeCC--cCCHHHHHHHHHHHHHHH-HCCCEEEEEECCHHHHHHHHH
Confidence 47899999975 556566665555555444 566789999987666555443
No 35
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=24.89 E-value=3.6e+02 Score=21.53 Aligned_cols=56 Identities=18% Similarity=0.185 Sum_probs=34.9
Q ss_pred HHHHhcCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhcccccceEEEEcCCcchHHHHHHhhhc
Q 019727 132 NAIMNLNPDREQMVWLIDFQGWTMGSVSVKVTRETANVLQNHYPERLGLAILYNPPKVFESFWTVVKPF 200 (336)
Q Consensus 132 ~~~~~~~~~~~~~vvI~D~~g~s~~~~~~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~vkpf 200 (336)
.++..... .|++++.|+ |-+..+. ...+..+ .+- .+++++++|..=..+-..+...
T Consensus 50 ~ai~~~~~--dGVlVltDL-Gssp~n~-----~~a~e~~----~~~-~~v~~~daPlVEGa~~Aav~~~ 105 (124)
T PRK14484 50 EAIEKNES--DGVLIFFDL-GSAEMNA-----EMAIEML----DGE-KKIIIIDAPIVEGAFTAAVLLS 105 (124)
T ss_pred HHHHhcCc--CCeEEEEeC-CChHHHH-----HHHHHhc----CCC-CcEEEECCcHHHHHHHHHHHHc
Confidence 34445543 899999999 6553221 1222333 322 8999999998776666666543
No 36
>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=24.81 E-value=2.4e+02 Score=20.71 Aligned_cols=50 Identities=8% Similarity=0.082 Sum_probs=31.3
Q ss_pred EEEEEeCCCCCCCCCCHHHHHHHHHHHHhhcccccceEEEEcCCcchHHHHHH
Q 019727 144 MVWLIDFQGWTMGSVSVKVTRETANVLQNHYPERLGLAILYNPPKVFESFWTV 196 (336)
Q Consensus 144 ~vvI~D~~g~s~~~~~~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~ 196 (336)
-.+|+||++++. ++...+..+..+.+. +-.+=..+++.|++.-+..++..
T Consensus 42 ~~lilD~~~v~~--iDss~~~~L~~~~~~-~~~~~~~~~l~~~~~~~~~~l~~ 91 (107)
T cd07042 42 KVVILDLSAVNF--IDSTAAEALEELVKD-LRKRGVELYLAGLNPQVRELLER 91 (107)
T ss_pred eEEEEECCCCch--hhHHHHHHHHHHHHH-HHHCCCEEEEecCCHHHHHHHHH
Confidence 468899999764 444455544444433 33345789999998755555543
No 37
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=24.79 E-value=3.8e+02 Score=22.68 Aligned_cols=61 Identities=13% Similarity=0.135 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHHHHHHHHhCCccCCCCCCCCHHHHHHHhhhcCCCHHHHHHHHHHHHHHhHHh
Q 019727 12 KSLSPEEQQAKINEVRKIIGPIADKYPVLCSDESISRYLRARNWHTKKASKMLVESVKWRLEY 74 (336)
Q Consensus 12 ~~lt~e~~~~~i~elr~~l~~~~~~~~~~~~D~~LlRfLra~~~dv~~A~~~l~~~~~wR~~~ 74 (336)
-+|| +++++.+.+|++.-..... ......-.-+...+.+-+||-.++...+.+..+-+.+.
T Consensus 49 LdLT-daQRqQmRdLm~~~r~~~~-~~~~~er~amh~LI~ad~FDEaavra~a~kma~~~~e~ 109 (166)
T PRK10363 49 ISLT-EHQRQQMRDLMQQARHEQP-PVNVSEMETMHRLVTAENFDENAVRAQAEKMAQEQVAR 109 (166)
T ss_pred CCCC-HHHHHHHHHHHHHHHhccc-ccCHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 4899 7999999999876654311 11111224567888999999888887776665555543
No 38
>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=23.35 E-value=2.8e+02 Score=20.60 Aligned_cols=50 Identities=10% Similarity=0.151 Sum_probs=32.1
Q ss_pred EEEEEeCCCCCCCCC-CHHHHHHHHHHHHhhcccccceEEEEcCCcchHHHHHHh
Q 019727 144 MVWLIDFQGWTMGSV-SVKVTRETANVLQNHYPERLGLAILYNPPKVFESFWTVV 197 (336)
Q Consensus 144 ~vvI~D~~g~s~~~~-~~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~v 197 (336)
-.+|+||+++..-.. -...+..+.+.++ ..=.+++++|++.-+.-++...
T Consensus 40 ~~vilDls~v~~iDssgi~~L~~~~~~~~----~~g~~l~l~~~~~~v~~~l~~~ 90 (106)
T TIGR02886 40 KHLILNLKNVTFMDSSGLGVILGRYKKIK----NEGGEVIVCNVSPAVKRLFELS 90 (106)
T ss_pred CEEEEECCCCcEecchHHHHHHHHHHHHH----HcCCEEEEEeCCHHHHHHHHHh
Confidence 378999999875433 1333444444333 3557999999987777776544
No 39
>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold. This family is restricted to bacterial proteins, none of which have currently been characterised.
Probab=22.77 E-value=6.5e+02 Score=25.18 Aligned_cols=91 Identities=14% Similarity=0.217 Sum_probs=58.5
Q ss_pred cCCCCCcEEEE-ccCCCCCCCHHHHHHHHHHHHHHHHHhcCC----CcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhh
Q 019727 99 CDKLGRPVLIM-RPGFQNSSSTEGQIKYLVYCMENAIMNLNP----DREQMVWLIDFQGWTMGSVSVKVTRETANVLQNH 173 (336)
Q Consensus 99 ~Dk~GrpV~i~-~~~~~d~~~~~~~~~~~~~~lE~~~~~~~~----~~~~~vvI~D~~g~s~~~~~~~~~~~~~~~lq~~ 173 (336)
.|.+|+=++=+ .....- .+..-+--+++|++-.....+++ ....+|++||-.++=+.+.+..++.++-++..-.
T Consensus 208 ~~~~GrG~IniL~a~~l~-~~P~LysTFLLwLLsELfe~LPEvGD~dkPklVfFfDEAHLLF~da~kall~~ieqvvrLI 286 (502)
T PF05872_consen 208 TDADGRGVINILAADKLM-NSPKLYSTFLLWLLSELFEQLPEVGDLDKPKLVFFFDEAHLLFNDAPKALLDKIEQVVRLI 286 (502)
T ss_pred cCCCCCEEEEEEEhHhhh-hCcHHHHHHHHHHHHHHHHhCccCCCCCCceEEEEEechhhhhcCCCHHHHHHHHHHHHHh
Confidence 57788865544 332221 23333455666676666666644 4578999999998888888766666666666555
Q ss_pred cccccceEEEEcCCcch
Q 019727 174 YPERLGLAILYNPPKVF 190 (336)
Q Consensus 174 YPe~l~~i~IvN~P~~~ 190 (336)
=-.=++-.||-..|.=+
T Consensus 287 RSKGVGv~fvTQ~P~Di 303 (502)
T PF05872_consen 287 RSKGVGVYFVTQNPTDI 303 (502)
T ss_pred hccCceEEEEeCCCCCC
Confidence 55566677777777533
No 40
>COG2994 HlyC ACP:hemolysin acyltransferase (hemolysin-activating protein) [Posttranslational modification, protein turnover, chaperones]
Probab=22.42 E-value=85 Score=25.73 Aligned_cols=82 Identities=18% Similarity=0.373 Sum_probs=46.1
Q ss_pred hhHHHHhhCceEeccccCCCCCcEEEEccCCCCCCCHHHHHHHHHHHHHHHHHhc--CCCcccEEEEEeCCCCCCCCCCH
Q 019727 83 DVAREAETGKLYRANFCDKLGRPVLIMRPGFQNSSSTEGQIKYLVYCMENAIMNL--NPDREQMVWLIDFQGWTMGSVSV 160 (336)
Q Consensus 83 ~~~~~l~~g~~~~~g~~Dk~GrpV~i~~~~~~d~~~~~~~~~~~~~~lE~~~~~~--~~~~~~~vvI~D~~g~s~~~~~~ 160 (336)
.+.+.+..|-+.+ ++|++|+||.++.-+.++...-.+++. ...... +-....-++|+|+=- ++
T Consensus 44 ~iLPalk~~Qf~l--y~de~g~Piaf~~WA~vde~~e~~lL~-------~~~~l~p~dW~SG~~iwii~~iA------Pf 108 (148)
T COG2994 44 NILPALKLGQFAL--YFDEHGRPIAFCTWAFVDEQAEEELLE-------NDRNLSPEDWASGNNIWIIDWIA------PF 108 (148)
T ss_pred HHhHHHhcCceEE--EEcCCCCeeEEEEEeecCHHHHHHHHh-------CCCCCChhhccCCCeeEEEEEEc------cC
Confidence 3455666665544 469999999999988877543332221 111001 112344567777421 22
Q ss_pred HHHHHHH-HHHHhhcccccc
Q 019727 161 KVTRETA-NVLQNHYPERLG 179 (336)
Q Consensus 161 ~~~~~~~-~~lq~~YPe~l~ 179 (336)
.-.+.+. .+.+..||.+..
T Consensus 109 Gh~r~~~~dl~~~lFp~~~v 128 (148)
T COG2994 109 GHSRQMVKDLHRNLFPDRTV 128 (148)
T ss_pred CchHHHHHHHHHHhCchhhh
Confidence 3334444 778888998843
No 41
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=21.22 E-value=1.1e+02 Score=27.67 Aligned_cols=66 Identities=14% Similarity=0.155 Sum_probs=42.4
Q ss_pred hcccccceEEEEcCCc---chHHHHHHhhhccCcchhccEEEecCCChhhHH---HHHccCCcCCcchh-cCCCCCC
Q 019727 173 HYPERLGLAILYNPPK---VFESFWTVVKPFLEPKTYKKVRFAYSNDPQSQK---IMEALFDINKLDSS-FGGRSRV 242 (336)
Q Consensus 173 ~YPe~l~~i~IvN~P~---~~~~~~~~vkpfL~~~t~~KI~~~~~~~~~~~~---~L~~~id~~~LP~~-~GG~~~~ 242 (336)
.|.+| ..|||||.-. .+..++++++..-. --.+|-|+++.. ..++ +..+..+.-++... +||+++.
T Consensus 31 If~~R-ngihIIDL~kT~~~l~~A~~~v~~~~~--~~g~ILfVgTK~-~a~~~V~~~A~r~g~~yV~~RwLgG~LTN 103 (252)
T COG0052 31 IFGER-NGIHIIDLQKTLERLREAYKFLRRIAA--NGGKILFVGTKK-QAQEPVKEFAERTGAYYVNGRWLGGMLTN 103 (252)
T ss_pred ceeec-CCcEEEEHHHHHHHHHHHHHHHHHHHc--CCCEEEEEechH-HHHHHHHHHHHHhCCceecCcccCccccC
Confidence 58888 9999999654 33444555544432 146799998863 2233 33455777777775 5999986
No 42
>PF13466 STAS_2: STAS domain
Probab=20.64 E-value=3.1e+02 Score=19.17 Aligned_cols=51 Identities=10% Similarity=0.032 Sum_probs=33.2
Q ss_pred EEEEEeCCCCCCCCCCHHHHHHHHHHHHhhcccccceEEEEcCCcchHHHHHHh
Q 019727 144 MVWLIDFQGWTMGSVSVKVTRETANVLQNHYPERLGLAILYNPPKVFESFWTVV 197 (336)
Q Consensus 144 ~vvI~D~~g~s~~~~~~~~~~~~~~~lq~~YPe~l~~i~IvN~P~~~~~~~~~v 197 (336)
-.+++|++++..- +...+. ++-.+.......=+.+.+.|+|.-+..++.++
T Consensus 27 ~~v~lDls~v~~i--Dsagl~-lL~~~~~~~~~~g~~~~l~~~~~~~~~ll~~~ 77 (80)
T PF13466_consen 27 RPVVLDLSGVEFI--DSAGLQ-LLLAAARRARARGRQLRLTGPSPALRRLLELL 77 (80)
T ss_pred CeEEEECCCCCee--cHHHHH-HHHHHHHHHHHCCCeEEEEcCCHHHHHHHHHh
Confidence 5688999997753 333333 33333444445668899999998877776654
Done!