Query 029647
Match_columns 190
No_of_seqs 107 out of 1051
Neff 9.6
Searched_HMMs 46136
Date Fri Mar 29 16:16:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029647.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029647hhsearch_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 8.4E-50 1.8E-54 307.9 16.2 188 2-190 52-241 (324)
2 KOG1471 Phosphatidylinositol t 100.0 3.7E-37 8.1E-42 244.8 12.9 189 1-190 47-255 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 2E-36 4.3E-41 218.0 5.6 148 42-190 2-158 (159)
4 smart00516 SEC14 Domain in hom 100.0 1.5E-32 3.3E-37 197.5 12.4 137 53-190 14-155 (158)
5 cd00170 SEC14 Sec14p-like lipi 100.0 2E-30 4.4E-35 185.3 11.7 143 48-190 9-156 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.7 1.2E-17 2.6E-22 119.0 6.4 135 49-190 4-142 (149)
7 KOG4406 CDC42 Rho GTPase-activ 98.8 4.5E-08 9.8E-13 78.3 9.5 128 47-180 80-211 (467)
8 PF03765 CRAL_TRIO_N: CRAL/TRI 98.3 5.7E-07 1.2E-11 52.8 2.2 23 1-23 33-55 (55)
9 KOG1838 Alpha/beta hydrolase [ 86.8 9.1 0.0002 31.8 9.5 84 57-153 122-214 (409)
10 PF14555 UBA_4: UBA-like domai 84.8 0.99 2.1E-05 24.6 2.2 19 3-21 19-37 (43)
11 PF11964 SpoIIAA-like: SpoIIAA 77.9 12 0.00026 24.3 6.1 76 75-158 11-87 (109)
12 PF14213 DUF4325: Domain of un 70.4 18 0.00039 22.1 5.1 47 103-151 19-67 (74)
13 PF03474 DMA: DMRTA motif; In 68.2 5.3 0.00011 21.4 1.9 17 4-20 22-38 (39)
14 PF02845 CUE: CUE domain; Int 64.3 10 0.00022 20.3 2.7 21 2-22 20-40 (42)
15 PF00627 UBA: UBA/TS-N domain; 63.8 7.7 0.00017 20.2 2.1 16 4-19 21-36 (37)
16 KOG3824 Huntingtin interacting 59.2 17 0.00038 29.3 4.1 49 13-61 334-382 (472)
17 smart00546 CUE Domain that may 58.2 12 0.00025 20.2 2.2 20 2-21 21-40 (43)
18 PF04378 RsmJ: Ribosomal RNA s 56.9 6.5 0.00014 30.3 1.4 26 137-162 206-231 (245)
19 COG2961 ComJ Protein involved 56.1 8.7 0.00019 29.8 1.9 26 137-162 237-262 (279)
20 smart00804 TAP_C C-terminal do 55.9 15 0.00032 22.0 2.5 21 3-23 31-51 (63)
21 cd00194 UBA Ubiquitin Associat 55.3 14 0.0003 19.1 2.2 18 3-20 19-36 (38)
22 PF11385 DUF3189: Protein of u 54.1 57 0.0012 23.1 5.7 54 45-110 48-101 (148)
23 smart00165 UBA Ubiquitin assoc 52.1 17 0.00036 18.6 2.2 17 3-19 19-35 (37)
24 TIGR02364 dha_pts dihydroxyace 50.7 45 0.00097 22.8 4.6 63 89-160 49-111 (125)
25 PF11339 DUF3141: Protein of u 50.4 1.3E+02 0.0028 26.3 8.0 60 75-146 116-175 (581)
26 PF09949 DUF2183: Uncharacteri 49.2 74 0.0016 20.9 5.7 48 85-143 52-99 (100)
27 PRK14484 phosphotransferase ma 46.0 94 0.002 21.3 5.6 57 91-160 51-107 (124)
28 PF02954 HTH_8: Bacterial regu 45.4 18 0.00039 19.4 1.6 19 2-20 10-28 (42)
29 PF03943 TAP_C: TAP C-terminal 42.6 16 0.00036 20.7 1.3 19 3-21 19-37 (51)
30 PF06972 DUF1296: Protein of u 38.1 39 0.00085 19.9 2.3 20 3-22 25-44 (60)
31 PRK02399 hypothetical protein; 37.7 2.5E+02 0.0054 23.6 8.1 81 74-160 312-403 (406)
32 COG0401 Uncharacterized homolo 37.3 50 0.0011 19.1 2.6 26 117-142 28-53 (56)
33 PF13342 Toprim_Crpt: C-termin 29.2 59 0.0013 19.3 2.2 30 33-62 14-44 (62)
34 COG1219 ClpX ATP-dependent pro 28.5 31 0.00067 28.1 1.2 19 2-20 147-165 (408)
35 KOG1534 Putative transcription 26.9 1.8E+02 0.004 22.3 4.9 103 55-161 27-156 (273)
36 PF04256 DUF434: Protein of un 26.8 64 0.0014 18.9 2.0 27 3-29 10-36 (58)
37 PRK14741 spoVM stage V sporula 26.7 12 0.00026 17.7 -0.8 7 184-190 8-14 (26)
38 PRK00095 mutL DNA mismatch rep 26.5 1.4E+02 0.0031 26.4 5.0 48 19-66 557-605 (617)
39 PF04838 Baculo_LEF5: Baculovi 25.5 72 0.0016 22.7 2.4 41 120-161 16-58 (159)
40 PF08938 HBS1_N: HBS1 N-termin 24.5 42 0.00091 20.8 1.0 19 5-23 52-70 (79)
41 PF08828 DSX_dimer: Doublesex 24.2 93 0.002 18.4 2.3 19 6-24 31-49 (62)
42 PF01740 STAS: STAS domain; I 23.3 1.1E+02 0.0023 20.0 3.0 49 101-152 48-96 (117)
43 PF04548 AIG1: AIG1 family; I 22.8 2.7E+02 0.0058 20.6 5.3 76 56-142 45-122 (212)
44 cd07322 PriL_PriS_Eukaryotic E 22.4 2.6E+02 0.0055 23.4 5.5 22 2-23 249-270 (390)
45 KOG1533 Predicted GTPase [Gene 22.4 3.2E+02 0.0068 21.5 5.5 116 56-175 27-176 (290)
46 PF09740 DUF2043: Uncharacteri 21.9 46 0.00099 22.3 0.9 8 55-62 99-106 (110)
47 TIGR02613 mob_myst_B mobile my 20.7 1.4E+02 0.0031 21.8 3.4 17 45-61 116-132 (186)
48 PF03641 Lysine_decarbox: Poss 20.5 2.5E+02 0.0055 19.1 4.4 55 119-173 65-127 (133)
49 PF07872 DUF1659: Protein of u 20.3 1.7E+02 0.0037 16.1 3.6 23 49-72 11-34 (47)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=8.4e-50 Score=307.88 Aligned_cols=188 Identities=37% Similarity=0.685 Sum_probs=181.7
Q ss_pred hhhhHhhcCCCHHHHHHHHHHHHhHhhhcCCCC-cchhchHHHHhcCcceecCCCCCCCCcEEEEEccccCCCCCChhhh
Q 029647 2 ILWFLKDRKFSIEESLAKLTKAIKWRQEFRVSE-LNEDSVRGIAESGKAYVHDFLDINERPVLIVVASKHLPAVHDPVED 80 (190)
Q Consensus 2 l~RfL~~~~~d~~~a~~~l~~~~~~R~~~~~~~-~~~~~~~~~~~~~~~~~~g~~d~~G~pv~~~~~~~~~~~~~~~~~~ 80 (190)
++||||+++||+++|.+++.+++.||+++++.. +..+++..++++|++|++| .|++||||+|++++...+...+.+..
T Consensus 52 llRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~G-~D~~gRPVl~~~~~~~~qn~~t~~~~ 130 (324)
T KOG1470|consen 52 LLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYILG-HDKDGRPVLYLRPRPHRQNTKTQKEL 130 (324)
T ss_pred HHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEec-ccCCCCeEEEEecCCCCCCCCCHHHH
Confidence 789999999999999999999999999999988 8888899999999999999 69999999999999888888999999
Q ss_pred hHHHHHHHHHHHhhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhccccccceEEEcCCcccHHHHHhhhhccc
Q 029647 81 EKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLK 160 (190)
Q Consensus 81 ~r~~~~~~E~~~~~~~~~~~~~~~i~D~~g~~~~~~~~~~~k~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~ik~fl~ 160 (190)
.|+++|+||.++..++.+++++++++|++|+|++|++.+..+.++.++|+||||||+..+++|+||+|..+|+++|||++
T Consensus 131 ~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs~sN~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~wkiikpflD 210 (324)
T KOG1470|consen 131 ERLLVYTLENAILFLPPGQEQFVWLFDLTGFSMSNPDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPFWKIIKPFLD 210 (324)
T ss_pred HHHHHHHHHHHHHhCCCCcceEEEEEecccCcccCCCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHHHHHhhhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccc-CeeEEccchhhhhhcCCCCCCCccccC
Q 029647 161 SYA-SLAKFCSVETVRKEYFTEATVPDNFRE 190 (190)
Q Consensus 161 ~~~-~Ki~~~~~~~~l~~~i~~~~lP~~~Gg 190 (190)
++| .||+|+.+.+.+.+|||++++|..|||
T Consensus 211 p~t~~Kv~F~~~~~~l~~~~d~~~l~s~~GG 241 (324)
T KOG1470|consen 211 PKTASKVKFVEPKDDLSEYFDESQLPSLFGG 241 (324)
T ss_pred hhhhceeEEecChhHHHhhCCccccchhhCC
Confidence 987 999999887766899999999999999
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=3.7e-37 Score=244.81 Aligned_cols=189 Identities=22% Similarity=0.384 Sum_probs=154.0
Q ss_pred ChhhhHhhcCCCHHHHHHHHHHHHhHhhhcCCCCcchh-ch-HHHHhcCcceecCCCCCCCCcEEEEEccccCCCC----
Q 029647 1 MILWFLKDRKFSIEESLAKLTKAIKWRQEFRVSELNED-SV-RGIAESGKAYVHDFLDINERPVLIVVASKHLPAV---- 74 (190)
Q Consensus 1 ~l~RfL~~~~~d~~~a~~~l~~~~~~R~~~~~~~~~~~-~~-~~~~~~~~~~~~g~~d~~G~pv~~~~~~~~~~~~---- 74 (190)
+|+||||+++||+++|.+++.+++.||++++++.+..+ +. ....+......+| .|++|+|+.+.+.|..++..
T Consensus 47 ~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~~~~~~~~~~~~~-~~~~g~~v~~~~~g~~~~~~l~~~ 125 (317)
T KOG1471|consen 47 NLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDDELLKYYPQGLHG-VDKEGRPVYIERLGKIDPKGLLKR 125 (317)
T ss_pred HHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccchhhhhhccccccc-cCCCCCEEEEeccCCCCcccceee
Confidence 48999999999999999999999999999998887654 22 2222234466778 69999999999999986432
Q ss_pred CChhhhhHHHHH--------HHHHHHhhCCCCcccEEEEEeCCCCCCCCC---CHHHHHHHHHHHHhhccccccceEEEc
Q 029647 75 HDPVEDEKLCVF--------FIEKALSKLPPGKEQILGIIDLRGFGTENA---DLKFLTFLFDVFYYYHPKRLGEVLFVE 143 (190)
Q Consensus 75 ~~~~~~~r~~~~--------~~E~~~~~~~~~~~~~~~i~D~~g~~~~~~---~~~~~k~~~~~~~~~yP~~l~~i~ivn 143 (190)
....+..++.+. .+|......+.+++|++.|+|++|++++++ .+..++.++..++++||++++++||||
T Consensus 126 ~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN 205 (317)
T KOG1471|consen 126 TGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKILQDNYPERLKRIHIIN 205 (317)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEc
Confidence 344555554443 444444444567999999999999999987 467899999999999999999999999
Q ss_pred CCcccHHHHHhhhhcccccc-CeeEEccc--hhhhhhcCCCCCCCccccC
Q 029647 144 APFVFKPFWQLTKPLLKSYA-SLAKFCSV--ETVRKEYFTEATVPDNFRE 190 (190)
Q Consensus 144 ~p~~~~~~~~~ik~fl~~~~-~Ki~~~~~--~~~l~~~i~~~~lP~~~Gg 190 (190)
+|++|+++|+++||||++++ +||++.+. .+.+.++|+++.||.+|||
T Consensus 206 ~P~~f~~~~~~ikpfL~~kt~~ki~~~~~~~~~~L~k~i~~~~LP~~yGG 255 (317)
T KOG1471|consen 206 APTIFSALWKVVKPFLDEKTRKKIHVLHSKDKESLLKYIPPEVLPEEYGG 255 (317)
T ss_pred CchhHHHHHHHHhccCCHHHHhhheecCCCchhhhhhhCCHhhCccccCC
Confidence 99999999999999999987 89994433 2445799999999999999
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=100.00 E-value=2e-36 Score=217.96 Aligned_cols=148 Identities=30% Similarity=0.569 Sum_probs=123.9
Q ss_pred HHHhcCcceecCCCCCCCCcEEEEEccccCCCCCChhhhhHHHHHHHHHHHhhCC--CCcccEEEEEeCCCCCCCCCC--
Q 029647 42 GIAESGKAYVHDFLDINERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSKLP--PGKEQILGIIDLRGFGTENAD-- 117 (190)
Q Consensus 42 ~~~~~~~~~~~g~~d~~G~pv~~~~~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~--~~~~~~~~i~D~~g~~~~~~~-- 117 (190)
++.+.+..+++| +|++||||++++++++++...+.+++.+++++++|.+++.++ .+.+|+++|+|++|+++++++
T Consensus 2 ~~~~~~~~~~~g-~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~ 80 (159)
T PF00650_consen 2 EILKSGPFYLHG-RDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFSLSNFDWW 80 (159)
T ss_dssp HHHTTSCEEEEE-E-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT--HHHHHCH
T ss_pred HHHCCeeEEECC-CCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCceEeccccc
Confidence 345778899999 699999999999999998888899999999999999986544 468999999999999999887
Q ss_pred -HHHHHHHHHHHHhhccccccceEEEcCCcccHHHHHhhhhcccccc-CeeEEccchh---hhhhcCCCCCCCccccC
Q 029647 118 -LKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLKSYA-SLAKFCSVET---VRKEYFTEATVPDNFRE 190 (190)
Q Consensus 118 -~~~~k~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~ik~fl~~~~-~Ki~~~~~~~---~l~~~i~~~~lP~~~Gg 190 (190)
.+.++.++++++++||+|++++|++|+|++++++|++++||+++++ +||+++++.+ .+.+++|+++||++|||
T Consensus 81 ~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~~GG 158 (159)
T PF00650_consen 81 PISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVEYGG 158 (159)
T ss_dssp HHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGGGTS
T ss_pred hhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchhcCC
Confidence 8999999999999999999999999999999999999999999987 9999996543 36799999999999999
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=100.00 E-value=1.5e-32 Score=197.49 Aligned_cols=137 Identities=28% Similarity=0.482 Sum_probs=128.5
Q ss_pred CCCCCCCCcEEEEEccccCCCCCChhhhhHHHHHHHHHHHhh--CCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHh
Q 029647 53 DFLDINERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSK--LPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYY 130 (190)
Q Consensus 53 g~~d~~G~pv~~~~~~~~~~~~~~~~~~~r~~~~~~E~~~~~--~~~~~~~~~~i~D~~g~~~~~~~~~~~k~~~~~~~~ 130 (190)
| .|++||||+++++++.++...+.+++.+++++.+|.+.+. .+.+++|+++|+|++|+++++++.+.+|.+++.+++
T Consensus 14 g-~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~lk~~~~~~~~ 92 (158)
T smart00516 14 G-YDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQREKKTGGIEGFTVIFDLKGLSMSNPDLSVLRKILKILQD 92 (158)
T ss_pred C-CCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHHHhcCCCeeeEEEEEECCCCCcccccHHHHHHHHHHHHH
Confidence 6 6999999999999999888899999999999999999876 567789999999999999999999999999999999
Q ss_pred hccccccceEEEcCCcccHHHHHhhhhcccccc-CeeEEccc--hhhhhhcCCCCCCCccccC
Q 029647 131 YHPKRLGEVLFVEAPFVFKPFWQLTKPLLKSYA-SLAKFCSV--ETVRKEYFTEATVPDNFRE 190 (190)
Q Consensus 131 ~yP~~l~~i~ivn~p~~~~~~~~~ik~fl~~~~-~Ki~~~~~--~~~l~~~i~~~~lP~~~Gg 190 (190)
+||++++++||+|+|++++++|+++++|+++++ +||+++++ .+.+.+++|+++||++|||
T Consensus 93 ~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~L~~~i~~~~lP~~~GG 155 (158)
T smart00516 93 HYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGNDSKEELLEYIDPEQLPEELGG 155 (158)
T ss_pred HhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCCCHHHHHhhCCHhhCcHhhCC
Confidence 999999999999999999999999999999987 99999986 3446799999999999999
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=99.97 E-value=2e-30 Score=185.30 Aligned_cols=143 Identities=25% Similarity=0.390 Sum_probs=125.9
Q ss_pred cceecCCCCCCCCcEEEEEccccCCC-CCChhhhhHHHHHHHHHHHhhCCCCcccEEEEEeCCCCCCCCC--CHHHHHHH
Q 029647 48 KAYVHDFLDINERPVLIVVASKHLPA-VHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENA--DLKFLTFL 124 (190)
Q Consensus 48 ~~~~~g~~d~~G~pv~~~~~~~~~~~-~~~~~~~~r~~~~~~E~~~~~~~~~~~~~~~i~D~~g~~~~~~--~~~~~k~~ 124 (190)
.++..|.+|++||||++++++..++. ..+.++..++.++.+|..++.......|+++|+|++|.+++++ +.+.++.+
T Consensus 9 ~~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~~~k~~ 88 (157)
T cd00170 9 KVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQEDDEQVEGFVVIIDLKGLSLSHLLPDPSLLKKI 88 (157)
T ss_pred cccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhhhhhcccceEEEEECCCCChhccchhHHHHHHH
Confidence 34444447999999999999964433 3444889999999999998876665679999999999999988 78899999
Q ss_pred HHHHHhhccccccceEEEcCCcccHHHHHhhhhcccccc-CeeEEccc-hhhhhhcCCCCCCCccccC
Q 029647 125 FDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLKSYA-SLAKFCSV-ETVRKEYFTEATVPDNFRE 190 (190)
Q Consensus 125 ~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~ik~fl~~~~-~Ki~~~~~-~~~l~~~i~~~~lP~~~Gg 190 (190)
+.+++++||++++++|++|+|++++++|+++++|+++++ +||+++++ .+.+.+++|+++||.+|||
T Consensus 89 ~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~L~~~i~~~~Lp~~~GG 156 (157)
T cd00170 89 LKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSDKEELLKYIDKEQLPEEYGG 156 (157)
T ss_pred HHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCCHHHHHhhCChhhCcHhhCC
Confidence 999999999999999999999999999999999999987 99999987 4556899999999999999
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.72 E-value=1.2e-17 Score=118.98 Aligned_cols=135 Identities=20% Similarity=0.340 Sum_probs=94.4
Q ss_pred ceecCCCCCCCCcEEEEEccccCCCCCChhhhhHHHHHHHHHHHhhCCCCcccEEEEEeCCCCCCCCC-CHHHHHHHHHH
Q 029647 49 AYVHDFLDINERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENA-DLKFLTFLFDV 127 (190)
Q Consensus 49 ~~~~g~~d~~G~pv~~~~~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~~~~i~D~~g~~~~~~-~~~~~k~~~~~ 127 (190)
++..| +|++||||+++...+. +. .++..+++.|.+...... ....++++|+|+++.+..+- +.+.++.+.+.
T Consensus 4 ~~~gG-~d~~g~pV~~~~~~~~-~~---~~~~~~ll~yl~~~l~~~--~~~~~f~vVid~~~~~~~~~~~~~~l~~~~~~ 76 (149)
T PF13716_consen 4 FYPGG-RDREGRPVVVFIASRL-PS---SDDLERLLLYLLSTLSEE--VVDKPFSVVIDHTGFSRSSEPSLSWLKQLYKL 76 (149)
T ss_dssp -EEEE-EBTTS-EEEEEEGGG--C----TTHHHHHHHHHHHHH-TT--TTTS-EEEEEE-TT--GGG---HHHHHHTTTS
T ss_pred EEecc-cCCCcCEEEEEECCcC-cc---hhhHHHHHHHHHHhhhHH--hcCCCEEEEEEcCCCccccCCchHHHHHHHHH
Confidence 34556 7999999999998887 33 347777777777766333 22456999999999998654 78999999999
Q ss_pred HHhhccccccceEEEcCCcccHHHH-Hhhhhccccc--cCeeEEccchhhhhhcCCCCCCCccccC
Q 029647 128 FYYYHPKRLGEVLFVEAPFVFKPFW-QLTKPLLKSY--ASLAKFCSVETVRKEYFTEATVPDNFRE 190 (190)
Q Consensus 128 ~~~~yP~~l~~i~ivn~p~~~~~~~-~~ik~fl~~~--~~Ki~~~~~~~~l~~~i~~~~lP~~~Gg 190 (190)
+...|+..++++||+|++++++.+. .+.+++.+++ ..|++++++-+.+.++||+++||.++||
T Consensus 77 l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~sl~~L~~~i~~~qL~~~lp~ 142 (149)
T PF13716_consen 77 LPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSSLSELSKHIDPSQLPESLPG 142 (149)
T ss_dssp S-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESSTCGGGGTSGGGG------H
T ss_pred HHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECCHHHHHhhCCHHHhcccCCC
Confidence 9999999999999999999999999 6667777776 4889988777666899999999999986
No 7
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.80 E-value=4.5e-08 Score=78.28 Aligned_cols=128 Identities=18% Similarity=0.193 Sum_probs=100.8
Q ss_pred CcceecCC-CCCCCCcEEEEEccccCC-CCCChhhhhHHHHHHHHHHHhhCCCCcccEEEEEeCCCCCCCCCC-HHHHHH
Q 029647 47 GKAYVHDF-LDINERPVLIVVASKHLP-AVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENAD-LKFLTF 123 (190)
Q Consensus 47 ~~~~~~g~-~d~~G~pv~~~~~~~~~~-~~~~~~~~~r~~~~~~E~~~~~~~~~~~~~~~i~D~~g~~~~~~~-~~~~k~ 123 (190)
+...+.|. .|+.||+++++-+.+..+ +..+-...+++.++.++..++. ..+.++=-.|+...+.+ ..++..
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 EILQVIGDAKDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVEN------DYTLVYFHHGLPSDNKPYLQLLFD 153 (467)
T ss_pred heeeeccCcccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHhc------cceeeehhcCCcccccchHHHHHH
Confidence 55666664 599999999999988643 3344444888999999988765 26777777788777764 667777
Q ss_pred HHHHHHhhccccccceEEEcCCcccHHHHHhhhhccccc-cCeeEEccchhhhhhcCC
Q 029647 124 LFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLKSY-ASLAKFCSVETVRKEYFT 180 (190)
Q Consensus 124 ~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~ik~fl~~~-~~Ki~~~~~~~~l~~~i~ 180 (190)
...-+..+|--.++.+|+|++-|+.+++|+++|||++.| ++||+.++.-+.|.+++.
T Consensus 154 aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n~lseL~~~l~ 211 (467)
T KOG4406|consen 154 AYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFNSLSELFEALK 211 (467)
T ss_pred HHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEeehHHHHHHhhh
Confidence 777778889999999999999999999999999999998 699998876554445543
No 8
>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=98.26 E-value=5.7e-07 Score=52.83 Aligned_cols=23 Identities=39% Similarity=0.764 Sum_probs=20.2
Q ss_pred ChhhhHhhcCCCHHHHHHHHHHH
Q 029647 1 MILWFLKDRKFSIEESLAKLTKA 23 (190)
Q Consensus 1 ~l~RfL~~~~~d~~~a~~~l~~~ 23 (190)
+|+|||||++||+++|.++|.++
T Consensus 33 ~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 33 FLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp HHHHHHHHTTT-HHHHHHHHHHH
T ss_pred HHHHHHHHccCCHHHHHHHHHhC
Confidence 47999999999999999999875
No 9
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=86.82 E-value=9.1 Score=31.81 Aligned_cols=84 Identities=11% Similarity=0.027 Sum_probs=60.1
Q ss_pred CCCCcEEEEEccccCCCCCChhhhhHHHHHHHHHHHhhCCCCcccEEEEEeCCCCCCCCC---------CHHHHHHHHHH
Q 029647 57 INERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENA---------DLKFLTFLFDV 127 (190)
Q Consensus 57 ~~G~pv~~~~~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~~~~i~D~~g~~~~~~---------~~~~~k~~~~~ 127 (190)
.+..|++++-+|.-. .+.+.++|.++.... ++ + =-++|++-+|++-+.+ +.+-++.+.+.
T Consensus 122 ~~~~P~vvilpGltg---~S~~~YVr~lv~~a~---~~-G----~r~VVfN~RG~~g~~LtTpr~f~ag~t~Dl~~~v~~ 190 (409)
T KOG1838|consen 122 DGTDPIVVILPGLTG---GSHESYVRHLVHEAQ---RK-G----YRVVVFNHRGLGGSKLTTPRLFTAGWTEDLREVVNH 190 (409)
T ss_pred CCCCcEEEEecCCCC---CChhHHHHHHHHHHH---hC-C----cEEEEECCCCCCCCccCCCceeecCCHHHHHHHHHH
Confidence 456699999999854 345666665544332 22 1 3478999999775543 36789999999
Q ss_pred HHhhccccccceEEEcCCcccHHHHH
Q 029647 128 FYYYHPKRLGEVLFVEAPFVFKPFWQ 153 (190)
Q Consensus 128 ~~~~yP~~l~~i~ivn~p~~~~~~~~ 153 (190)
+.+.||++ .++.+=.+....+++|
T Consensus 191 i~~~~P~a--~l~avG~S~Gg~iL~n 214 (409)
T KOG1838|consen 191 IKKRYPQA--PLFAVGFSMGGNILTN 214 (409)
T ss_pred HHHhCCCC--ceEEEEecchHHHHHH
Confidence 99999998 8888888777766654
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=84.83 E-value=0.99 Score=24.63 Aligned_cols=19 Identities=11% Similarity=0.382 Sum_probs=15.2
Q ss_pred hhhHhhcCCCHHHHHHHHH
Q 029647 3 LWFLKDRKFSIEESLAKLT 21 (190)
Q Consensus 3 ~RfL~~~~~d~~~a~~~l~ 21 (190)
..||..++||++.|+..+-
T Consensus 19 ~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 19 IQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp HHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 4689999999999998763
No 11
>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=77.86 E-value=12 Score=24.29 Aligned_cols=76 Identities=13% Similarity=0.050 Sum_probs=53.3
Q ss_pred CChhhhhHHHHHHHHHHHhhCCCCcccEEEEEeCC-CCCCCCCCHHHHHHHHHHHHhhccccccceEEEcCCcccHHHHH
Q 029647 75 HDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLR-GFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQ 153 (190)
Q Consensus 75 ~~~~~~~r~~~~~~E~~~~~~~~~~~~~~~i~D~~-g~~~~~~~~~~~k~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~ 153 (190)
.+.+++.+ +.-.++..+. ....+.+++|++ ++ ..++++......+.... ....++++=+|-.+.+.+.+.+
T Consensus 11 ~t~ed~~~-~~~~~~~~~~----~~~~~~ll~d~~~~~--~~~~~~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~~~~ 82 (109)
T PF11964_consen 11 LTEEDYKE-LLPALEELIA----DHGKIRLLVDLRRDF--EGWSPEARWEDAKFGLK-HLKHFRRIAVVGDSEWIRMIAN 82 (109)
T ss_dssp E-HHHHHH-HHHHHHHHHT----TSSSEEEEEEEC-CE--EEEHHHHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHHHHH
T ss_pred eCHHHHHH-HHHHHHHHHh----cCCceEEEEEecCcc--CCCCHHHHHHHHHhchh-hhcccCEEEEEECcHHHHHHHH
Confidence 56777777 4455555544 245789999998 65 33455555555555444 7788899999999999999999
Q ss_pred hhhhc
Q 029647 154 LTKPL 158 (190)
Q Consensus 154 ~ik~f 158 (190)
++.+|
T Consensus 83 ~~~~~ 87 (109)
T PF11964_consen 83 FFAAF 87 (109)
T ss_dssp HHHHH
T ss_pred HHHhc
Confidence 99997
No 12
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=70.42 E-value=18 Score=22.07 Aligned_cols=47 Identities=19% Similarity=0.190 Sum_probs=33.7
Q ss_pred EEEEeCCCCCCCCCCHHHHHHHHHHHHhhcc--ccccceEEEcCCcccHHH
Q 029647 103 LGIIDLRGFGTENADLKFLTFLFDVFYYYHP--KRLGEVLFVEAPFVFKPF 151 (190)
Q Consensus 103 ~~i~D~~g~~~~~~~~~~~k~~~~~~~~~yP--~~l~~i~ivn~p~~~~~~ 151 (190)
.+++|++|+ ..++.+++-..+..+...|| +.-.++.+.|++.....+
T Consensus 19 ~V~lDF~gv--~~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~ 67 (74)
T PF14213_consen 19 KVVLDFEGV--ESITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEM 67 (74)
T ss_pred eEEEECCCc--ccccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHH
Confidence 388999998 44667777777776666676 445678888887665443
No 13
>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=68.16 E-value=5.3 Score=21.40 Aligned_cols=17 Identities=6% Similarity=0.192 Sum_probs=14.4
Q ss_pred hhHhhcCCCHHHHHHHH
Q 029647 4 WFLKDRKFSIEESLAKL 20 (190)
Q Consensus 4 RfL~~~~~d~~~a~~~l 20 (190)
.-|++|++|+-+|.+.+
T Consensus 22 ~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 22 LILQRCNGDVVQAIEQF 38 (39)
T ss_pred HHHHHcCCcHHHHHHHh
Confidence 45899999999998865
No 14
>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=64.29 E-value=10 Score=20.34 Aligned_cols=21 Identities=19% Similarity=0.210 Sum_probs=17.2
Q ss_pred hhhhHhhcCCCHHHHHHHHHH
Q 029647 2 ILWFLKDRKFSIEESLAKLTK 22 (190)
Q Consensus 2 l~RfL~~~~~d~~~a~~~l~~ 22 (190)
+.+-|..+++|++.|...|.+
T Consensus 20 I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 20 IEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHc
Confidence 456788999999999998854
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=63.79 E-value=7.7 Score=20.17 Aligned_cols=16 Identities=13% Similarity=0.009 Sum_probs=10.9
Q ss_pred hhHhhcCCCHHHHHHH
Q 029647 4 WFLKDRKFSIEESLAK 19 (190)
Q Consensus 4 RfL~~~~~d~~~a~~~ 19 (190)
+-|+.+++|+++|.+-
T Consensus 21 ~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 21 EALRACNGNVERAVDW 36 (37)
T ss_dssp HHHHHTTTSHHHHHHH
T ss_pred HHHHHcCCCHHHHHHh
Confidence 4567777777777654
No 16
>KOG3824 consensus Huntingtin interacting protein HYPE [General function prediction only]
Probab=59.19 E-value=17 Score=29.27 Aligned_cols=49 Identities=18% Similarity=0.279 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHhHhhhcCCCCcchhchHHHHhcCcceecCCCCCCCCc
Q 029647 13 IEESLAKLTKAIKWRQEFRVSELNEDSVRGIAESGKAYVHDFLDINERP 61 (190)
Q Consensus 13 ~~~a~~~l~~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~g~~d~~G~p 61 (190)
.+...++|+++..|-.+-....+.+-+..........++|++.|.+||.
T Consensus 334 P~dv~~qmq~fv~WLNsE~~~tlhPve~AAlAHYKLV~iHPF~DGNGRT 382 (472)
T KOG3824|consen 334 PEDVMEQMQDFVDWLNSESTLTLHPVERAALAHYKLVLIHPFTDGNGRT 382 (472)
T ss_pred hHHHHHHHHHHHHHhccccccccChHHHHHHhhheeEEEeccccCCchH
Confidence 4566788889999987765555666666555567778999999999985
No 17
>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=58.21 E-value=12 Score=20.20 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=16.6
Q ss_pred hhhhHhhcCCCHHHHHHHHH
Q 029647 2 ILWFLKDRKFSIEESLAKLT 21 (190)
Q Consensus 2 l~RfL~~~~~d~~~a~~~l~ 21 (190)
+.+.|+++++|++.|...+.
T Consensus 21 I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 21 IKAVLEANNGNVEATINNLL 40 (43)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34678899999999998874
No 18
>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=56.90 E-value=6.5 Score=30.35 Aligned_cols=26 Identities=15% Similarity=0.310 Sum_probs=19.4
Q ss_pred cceEEEcCCcccHHHHHhhhhccccc
Q 029647 137 GEVLFVEAPFVFKPFWQLTKPLLKSY 162 (190)
Q Consensus 137 ~~i~ivn~p~~~~~~~~~ik~fl~~~ 162 (190)
+.++|||+||.+....+-+-|+|.+.
T Consensus 206 SGm~iiNPPw~l~~~l~~~l~~L~~~ 231 (245)
T PF04378_consen 206 SGMLIINPPWTLDEELEEILPWLAET 231 (245)
T ss_dssp EEEEEES--TTHHHHHHHHHHHHHHH
T ss_pred ceEEEEcCCccHHHHHHHHHHHHHHH
Confidence 45999999999988888777777663
No 19
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=56.10 E-value=8.7 Score=29.79 Aligned_cols=26 Identities=12% Similarity=0.394 Sum_probs=22.6
Q ss_pred cceEEEcCCcccHHHHHhhhhccccc
Q 029647 137 GEVLFVEAPFVFKPFWQLTKPLLKSY 162 (190)
Q Consensus 137 ~~i~ivn~p~~~~~~~~~ik~fl~~~ 162 (190)
+.++|||+||-+..-.+.+-|+|...
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~ 262 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTL 262 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHH
Confidence 46999999999999998888888764
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=55.88 E-value=15 Score=21.97 Aligned_cols=21 Identities=24% Similarity=0.398 Sum_probs=17.7
Q ss_pred hhhHhhcCCCHHHHHHHHHHH
Q 029647 3 LWFLKDRKFSIEESLAKLTKA 23 (190)
Q Consensus 3 ~RfL~~~~~d~~~a~~~l~~~ 23 (190)
.++|...+||.++|.+...+-
T Consensus 31 ~~cLe~~~Wd~~~Al~~F~~l 51 (63)
T smart00804 31 QMCLEDNNWDYERALKNFTEL 51 (63)
T ss_pred HHHHHHcCCCHHHHHHHHHHH
Confidence 478999999999999987653
No 21
>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=55.34 E-value=14 Score=19.06 Aligned_cols=18 Identities=17% Similarity=0.137 Sum_probs=13.3
Q ss_pred hhhHhhcCCCHHHHHHHH
Q 029647 3 LWFLKDRKFSIEESLAKL 20 (190)
Q Consensus 3 ~RfL~~~~~d~~~a~~~l 20 (190)
.+-|+.+++|+++|...|
T Consensus 19 ~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 19 RKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHHhCCCHHHHHHHH
Confidence 456778888888887655
No 22
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=54.06 E-value=57 Score=23.12 Aligned_cols=54 Identities=13% Similarity=0.062 Sum_probs=36.7
Q ss_pred hcCcceecCCCCCCCCcEEEEEccccCCCCCChhhhhHHHHHHHHHHHhhCCCCcccEEEEEeCCC
Q 029647 45 ESGKAYVHDFLDINERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRG 110 (190)
Q Consensus 45 ~~~~~~~~g~~d~~G~pv~~~~~~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~~~~i~D~~g 110 (190)
+.|..+..| +|..|..|+++-.+.. .+.+.+++.-+++.. .. .++=.+++|.+.
T Consensus 48 d~G~l~y~G-~De~gn~VY~lG~~~~------~~~~~~al~~l~~i~----~~-~~~~i~~vdt~~ 101 (148)
T PF11385_consen 48 DIGRLIYMG-TDEYGNEVYILGRKNN------GKIVERALKSLLEIL----GI-ENEEIILVDTSP 101 (148)
T ss_pred cCceEEEEE-EcCCCCEEEEEecCCh------HHHHHHHHHHHHHHh----CC-CCCcEEEEeccc
Confidence 457788999 7999999999988774 355666665555544 11 134566777653
No 23
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=52.05 E-value=17 Score=18.65 Aligned_cols=17 Identities=18% Similarity=0.108 Sum_probs=10.9
Q ss_pred hhhHhhcCCCHHHHHHH
Q 029647 3 LWFLKDRKFSIEESLAK 19 (190)
Q Consensus 3 ~RfL~~~~~d~~~a~~~ 19 (190)
.+-|+.+++|+++|..-
T Consensus 19 ~~aL~~~~~d~~~A~~~ 35 (37)
T smart00165 19 LKALRAANGNVERAAEY 35 (37)
T ss_pred HHHHHHhCCCHHHHHHH
Confidence 34566777777777654
No 24
>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=50.69 E-value=45 Score=22.83 Aligned_cols=63 Identities=22% Similarity=0.288 Sum_probs=39.5
Q ss_pred HHHHhhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhccccccceEEEcCCcccHHHHHhhhhccc
Q 029647 89 EKALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLK 160 (190)
Q Consensus 89 E~~~~~~~~~~~~~~~i~D~~g~~~~~~~~~~~k~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~ik~fl~ 160 (190)
+.++.+.....+++.++.|+ |-+..|.. . .+..+. ++..+.+..+|.|.+...+.+.+..-..
T Consensus 49 ~~ai~~~~~~~dgVlvl~DL-Ggs~~n~e--~---a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~~g 111 (125)
T TIGR02364 49 IEAIEKADNEADGVLIFYDL-GSAVMNAE--M---AVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQVG 111 (125)
T ss_pred HHHHHHhcCCCCCEEEEEcC-CCcHhHHH--H---HHHHhc---cccccEEEEechhHHHHHHHHHHHHcCC
Confidence 33344433336799999999 65532211 1 222222 3556889999999999888877765443
No 25
>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=50.43 E-value=1.3e+02 Score=26.29 Aligned_cols=60 Identities=15% Similarity=0.196 Sum_probs=41.6
Q ss_pred CChhhhhHHHHHHHHHHHhhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhccccccceEEEcCCc
Q 029647 75 HDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPF 146 (190)
Q Consensus 75 ~~~~~~~r~~~~~~E~~~~~~~~~~~~~~~i~D~~g~~~~~~~~~~~k~~~~~~~~~yP~~l~~i~ivn~p~ 146 (190)
.+.+++.++..-.+|......+... +.++|-+|.|- -.+.++...+|+..+-+.+-=+|-
T Consensus 116 QTl~DV~~ae~~Fv~~V~~~hp~~~-kp~liGnCQgG-----------Wa~~mlAA~~Pd~~gplvlaGaPl 175 (581)
T PF11339_consen 116 QTLEDVMRAEAAFVEEVAERHPDAP-KPNLIGNCQGG-----------WAAMMLAALRPDLVGPLVLAGAPL 175 (581)
T ss_pred CcHHHHHHHHHHHHHHHHHhCCCCC-CceEEeccHHH-----------HHHHHHHhcCcCccCceeecCCCc
Confidence 5678888888878887766655433 78888777651 234466778899888777766663
No 26
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=49.18 E-value=74 Score=20.86 Aligned_cols=48 Identities=19% Similarity=0.185 Sum_probs=34.6
Q ss_pred HHHHHHHHhhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhccccccceEEEc
Q 029647 85 VFFIEKALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVE 143 (190)
Q Consensus 85 ~~~~E~~~~~~~~~~~~~~~i~D~~g~~~~~~~~~~~k~~~~~~~~~yP~~l~~i~ivn 143 (190)
...++++++..| ..+++.|-|-+. -|++.... +...||+++.+|+|=+
T Consensus 52 ~~~i~~i~~~fP--~~kfiLIGDsgq-----~DpeiY~~----ia~~~P~~i~ai~IR~ 99 (100)
T PF09949_consen 52 RDNIERILRDFP--ERKFILIGDSGQ-----HDPEIYAE----IARRFPGRILAIYIRD 99 (100)
T ss_pred HHHHHHHHHHCC--CCcEEEEeeCCC-----cCHHHHHH----HHHHCCCCEEEEEEEe
Confidence 355677766655 458999999776 56666555 4566899999999854
No 27
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=46.00 E-value=94 Score=21.30 Aligned_cols=57 Identities=21% Similarity=0.284 Sum_probs=34.3
Q ss_pred HHhhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhccccccceEEEcCCcccHHHHHhhhhccc
Q 029647 91 ALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLK 160 (190)
Q Consensus 91 ~~~~~~~~~~~~~~i~D~~g~~~~~~~~~~~k~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~ik~fl~ 160 (190)
++.+... +|+.++.|+ |-+..|. ... ++. +.+- .++.++++|.+=..+-+.+.....
T Consensus 51 ai~~~~~--dGVlVltDL-Gssp~n~--~~a---~e~----~~~~-~~v~~~daPlVEGa~~Aav~~~~g 107 (124)
T PRK14484 51 AIEKNES--DGVLIFFDL-GSAEMNA--EMA---IEM----LDGE-KKIIIIDAPIVEGAFTAAVLLSAG 107 (124)
T ss_pred HHHhcCc--CCeEEEEeC-CChHHHH--HHH---HHh----cCCC-CcEEEECCcHHHHHHHHHHHHcCC
Confidence 3444433 899999999 6553221 111 222 2222 899999999876666666555443
No 28
>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=45.40 E-value=18 Score=19.38 Aligned_cols=19 Identities=16% Similarity=-0.001 Sum_probs=14.8
Q ss_pred hhhhHhhcCCCHHHHHHHH
Q 029647 2 ILWFLKDRKFSIEESLAKL 20 (190)
Q Consensus 2 l~RfL~~~~~d~~~a~~~l 20 (190)
+..-|..++||+.+|++.|
T Consensus 10 i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 10 IRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 4566888999999999876
No 29
>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=42.65 E-value=16 Score=20.68 Aligned_cols=19 Identities=16% Similarity=0.319 Sum_probs=15.0
Q ss_pred hhhHhhcCCCHHHHHHHHH
Q 029647 3 LWFLKDRKFSIEESLAKLT 21 (190)
Q Consensus 3 ~RfL~~~~~d~~~a~~~l~ 21 (190)
.++|..++||.++|.+...
T Consensus 19 ~~CL~~n~Wd~~~A~~~F~ 37 (51)
T PF03943_consen 19 QKCLEENNWDYERALQNFE 37 (51)
T ss_dssp HHHHHHTTT-CCHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 4689999999999988764
No 30
>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=38.07 E-value=39 Score=19.89 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=16.9
Q ss_pred hhhHhhcCCCHHHHHHHHHH
Q 029647 3 LWFLKDRKFSIEESLAKLTK 22 (190)
Q Consensus 3 ~RfL~~~~~d~~~a~~~l~~ 22 (190)
+.-|+-|+.|..+|+++|..
T Consensus 25 ya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 25 YAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred HHHHHHhCCCHHHHHHHHHh
Confidence 45688999999999999865
No 31
>PRK02399 hypothetical protein; Provisional
Probab=37.66 E-value=2.5e+02 Score=23.62 Aligned_cols=81 Identities=17% Similarity=0.185 Sum_probs=56.9
Q ss_pred CCChhhhhHHHHHHHHHHHhhCCCCcccEEEEEeCCCCCCCC------CCHHHHHHHHHHHHhhccccccceEE-----E
Q 029647 74 VHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTEN------ADLKFLTFLFDVFYYYHPKRLGEVLF-----V 142 (190)
Q Consensus 74 ~~~~~~~~r~~~~~~E~~~~~~~~~~~~~~~i~D~~g~~~~~------~~~~~~k~~~~~~~~~yP~~l~~i~i-----v 142 (190)
..++++..+.--++-|++ .....-+.+++-+.|+|.-. .+++.-..+++.++++.+..+. ++ |
T Consensus 312 RTt~eE~~~~g~~ia~kL----n~a~gpv~vllP~~G~S~~D~~G~~f~Dpead~alf~~l~~~l~~~~~--v~~~~~hI 385 (406)
T PRK02399 312 RTTPEENRQIGRWIAEKL----NRAKGPVAFLIPLGGVSALDRPGQPFHDPEADAAFFDALEETVTETRR--LIEVPAHI 385 (406)
T ss_pred ecCHHHHHHHHHHHHHHH----hcCCCCeEEEEeCCCCccccCCCCCccChhHHHHHHHHHHHhCCCCce--EEECCCCC
Confidence 345666666555556655 22244688999999999754 3688888889999999877654 55 7
Q ss_pred cCCcccHHHHHhhhhccc
Q 029647 143 EAPFVFKPFWQLTKPLLK 160 (190)
Q Consensus 143 n~p~~~~~~~~~ik~fl~ 160 (190)
|.|-+...+...+..++.
T Consensus 386 ND~~FA~a~~~~l~~~~~ 403 (406)
T PRK02399 386 NDPEFAEAAVEAFEELMA 403 (406)
T ss_pred CCHHHHHHHHHHHHHHHh
Confidence 999888877766655444
No 32
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=37.35 E-value=50 Score=19.12 Aligned_cols=26 Identities=15% Similarity=0.267 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHHHhhccccccceEEE
Q 029647 117 DLKFLTFLFDVFYYYHPKRLGEVLFV 142 (190)
Q Consensus 117 ~~~~~k~~~~~~~~~yP~~l~~i~iv 142 (190)
..+.+-.++-++-.++|+.++++|++
T Consensus 28 ~~df~iNiLLtlLg~~PGiiHA~yvi 53 (56)
T COG0401 28 GKDFLINILLTLLGYIPGIIHALYVI 53 (56)
T ss_pred cHHHHHHHHHHHHHhhhhhHhheEEE
Confidence 35666666667777999999999987
No 33
>PF13342 Toprim_Crpt: C-terminal repeat of topoisomerase
Probab=29.23 E-value=59 Score=19.27 Aligned_cols=30 Identities=23% Similarity=0.511 Sum_probs=23.6
Q ss_pred CCcchhchHHHHhcCcce-ecCCCCCCCCcE
Q 029647 33 SELNEDSVRGIAESGKAY-VHDFLDINERPV 62 (190)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~-~~g~~d~~G~pv 62 (190)
..+++.++...+..|..- +.|+.++.|++.
T Consensus 14 k~lt~~~~~~Ll~~gkT~~ikGF~SK~Gk~F 44 (62)
T PF13342_consen 14 KKLTDEEVKELLEKGKTGLIKGFKSKKGKPF 44 (62)
T ss_pred CCCCHHHHHHHHHcCCccCccCcccCCCCEE
Confidence 457888999999888765 668888999873
No 34
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=28.45 E-value=31 Score=28.07 Aligned_cols=19 Identities=16% Similarity=0.396 Sum_probs=16.8
Q ss_pred hhhhHhhcCCCHHHHHHHH
Q 029647 2 ILWFLKDRKFSIEESLAKL 20 (190)
Q Consensus 2 l~RfL~~~~~d~~~a~~~l 20 (190)
|+|-|.+++|||++|.+-+
T Consensus 147 llkLlqaadydV~rAerGI 165 (408)
T COG1219 147 LLKLLQAADYDVERAERGI 165 (408)
T ss_pred HHHHHHHcccCHHHHhCCe
Confidence 6899999999999998754
No 35
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=26.87 E-value=1.8e+02 Score=22.32 Aligned_cols=103 Identities=15% Similarity=0.091 Sum_probs=64.0
Q ss_pred CCCCCCcEEEEEcccc-----C------CCCCChhhhhH--------HHHHHHHHHHhhC------CCCcccEEEEEeCC
Q 029647 55 LDINERPVLIVVASKH-----L------PAVHDPVEDEK--------LCVFFIEKALSKL------PPGKEQILGIIDLR 109 (190)
Q Consensus 55 ~d~~G~pv~~~~~~~~-----~------~~~~~~~~~~r--------~~~~~~E~~~~~~------~~~~~~~~~i~D~~ 109 (190)
+-.-||.+-+++..-- . ++..+.++++. .++|++|....-. .+..++--.|+|+-
T Consensus 27 ~e~~gRs~~vVNLDPAae~f~y~~~iDiRdlIsvdDVmEdl~~GPNGgLv~cmEyl~~NldwL~~~~Gd~eddylifDcP 106 (273)
T KOG1534|consen 27 CETVGRSVHVVNLDPAAEHFNYPVTIDIRDLISVDDVMEDLDLGPNGGLVYCMEYLLENLDWLEEEIGDVEDDYLIFDCP 106 (273)
T ss_pred HHhhCceeEEeecCHHHHhhCCcccccHHHhccHHHHHHHhccCCCccchhHHHHHHHHHHHHHhhccCccCCEEEEeCC
Confidence 3556888888876431 1 23455555553 4678888876522 23467778899998
Q ss_pred CCC--CCCCCHHHHHHHHHHHHhhccccccceEEEcCCcccHHHHHhhhhcccc
Q 029647 110 GFG--TENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLKS 161 (190)
Q Consensus 110 g~~--~~~~~~~~~k~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~ik~fl~~ 161 (190)
|== +.| ...++.+.+-++. .-.++..+|++..+.++. ..+.++..+++
T Consensus 107 GQIELytH--~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD-~~KfiSG~lsA 156 (273)
T KOG1534|consen 107 GQIELYTH--LPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVD-STKFISGCLSA 156 (273)
T ss_pred CeeEEeec--ChhHHHHHHHHhc-ccCceeEEEEeccchhhh-HHHHHHHHHHH
Confidence 732 123 3456777777776 447888899888887765 23444544444
No 36
>PF04256 DUF434: Protein of unknown function (DUF434); InterPro: IPR007368 This is a family of uncharacterised proteins.
Probab=26.79 E-value=64 Score=18.90 Aligned_cols=27 Identities=15% Similarity=0.316 Sum_probs=23.7
Q ss_pred hhhHhhcCCCHHHHHHHHHHHHhHhhh
Q 029647 3 LWFLKDRKFSIEESLAKLTKAIKWRQE 29 (190)
Q Consensus 3 ~RfL~~~~~d~~~a~~~l~~~~~~R~~ 29 (190)
++||-.++|..+.|.+..-+++..-+.
T Consensus 10 l~yLLnRGY~~k~al~fVgnhy~Ls~r 36 (58)
T PF04256_consen 10 LRYLLNRGYPKKSALEFVGNHYRLSKR 36 (58)
T ss_pred HHHHHhCCCCchhHHHHHHHhccCCHH
Confidence 589999999999999999999877654
No 37
>PRK14741 spoVM stage V sporulation protein M; Provisional
Probab=26.72 E-value=12 Score=17.68 Aligned_cols=7 Identities=14% Similarity=0.335 Sum_probs=4.1
Q ss_pred CCccccC
Q 029647 184 VPDNFRE 190 (190)
Q Consensus 184 lP~~~Gg 190 (190)
||+.+||
T Consensus 8 lpkflgg 14 (26)
T PRK14741 8 LPKFLGG 14 (26)
T ss_pred ccHHHHH
Confidence 5666655
No 38
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=26.53 E-value=1.4e+02 Score=26.41 Aligned_cols=48 Identities=15% Similarity=0.142 Sum_probs=31.8
Q ss_pred HHHHHHhHhhhcCC-CCcchhchHHHHhcCcceecCCCCCCCCcEEEEE
Q 029647 19 KLTKAIKWRQEFRV-SELNEDSVRGIAESGKAYVHDFLDINERPVLIVV 66 (190)
Q Consensus 19 ~l~~~~~~R~~~~~-~~~~~~~~~~~~~~~~~~~~g~~d~~G~pv~~~~ 66 (190)
.+....+-|+.... +.++.++....++.-..+-.++..++|||+++--
T Consensus 557 ~~las~ACr~AIk~g~~Ls~~E~~~Ll~~L~~~~~P~~CPHGRPt~i~l 605 (617)
T PRK00095 557 ELLATMACHGAIRAGRRLTLEEMNALLRQLEATENPGTCPHGRPTYIEL 605 (617)
T ss_pred HHHHHHHHHHhhhccCCCCHHHHHHHHHHHHhcccccCCCCCCeeEEEC
Confidence 45555666665442 5577777777776554555556788999998753
No 39
>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=25.51 E-value=72 Score=22.66 Aligned_cols=41 Identities=17% Similarity=0.302 Sum_probs=34.1
Q ss_pred HHHHHHHHHHhhcccccc--ceEEEcCCcccHHHHHhhhhcccc
Q 029647 120 FLTFLFDVFYYYHPKRLG--EVLFVEAPFVFKPFWQLTKPLLKS 161 (190)
Q Consensus 120 ~~k~~~~~~~~~yP~~l~--~i~ivn~p~~~~~~~~~ik~fl~~ 161 (190)
-.+.+++.+..+||..++ ..-..|++-.|-++|+-+ |-++.
T Consensus 16 ~y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~ 58 (159)
T PF04838_consen 16 DYKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSN 58 (159)
T ss_pred CHHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCch
Confidence 356788999999999998 899999999999999865 44443
No 40
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=24.46 E-value=42 Score=20.84 Aligned_cols=19 Identities=26% Similarity=0.268 Sum_probs=14.2
Q ss_pred hHhhcCCCHHHHHHHHHHH
Q 029647 5 FLKDRKFSIEESLAKLTKA 23 (190)
Q Consensus 5 fL~~~~~d~~~a~~~l~~~ 23 (190)
-|..++||+++|+.-|.+.
T Consensus 52 al~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 52 ALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp HHHHTTT-CCHHHHHHHHC
T ss_pred HHHHHcCCHHHHHHHHHHh
Confidence 3677899999999888653
No 41
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=24.23 E-value=93 Score=18.40 Aligned_cols=19 Identities=26% Similarity=0.321 Sum_probs=13.7
Q ss_pred HhhcCCCHHHHHHHHHHHH
Q 029647 6 LKDRKFSIEESLAKLTKAI 24 (190)
Q Consensus 6 L~~~~~d~~~a~~~l~~~~ 24 (190)
|...+.|+++|-++|.+..
T Consensus 31 LK~A~~D~eeA~rrI~E~~ 49 (62)
T PF08828_consen 31 LKYADADVEEASRRIDEAK 49 (62)
T ss_dssp HHHTTT-HHHHHHHHHH--
T ss_pred HHhcCCCHHHHHHHHHHHH
Confidence 6677889999999998753
No 42
>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=23.33 E-value=1.1e+02 Score=20.00 Aligned_cols=49 Identities=16% Similarity=0.116 Sum_probs=32.6
Q ss_pred cEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhccccccceEEEcCCcccHHHH
Q 029647 101 QILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFW 152 (190)
Q Consensus 101 ~~~~i~D~~g~~~~~~~~~~~k~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~ 152 (190)
--.+|+|+++++ .++..-+..+.++.++.- .+=..++++|.+.-+.-.+
T Consensus 48 ~~~vIlD~s~v~--~iDssgi~~L~~~~~~~~-~~g~~~~l~~~~~~v~~~l 96 (117)
T PF01740_consen 48 IKNVILDMSGVS--FIDSSGIQALVDIIKELR-RRGVQLVLVGLNPDVRRIL 96 (117)
T ss_dssp SSEEEEEETTES--EESHHHHHHHHHHHHHHH-HTTCEEEEESHHHHHHHHH
T ss_pred ceEEEEEEEeCC--cCCHHHHHHHHHHHHHHH-HCCCEEEEEECCHHHHHHH
Confidence 358899999985 456655555555544444 4557888888876665443
No 43
>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=22.78 E-value=2.7e+02 Score=20.61 Aligned_cols=76 Identities=17% Similarity=0.132 Sum_probs=38.4
Q ss_pred CCCCCcEEEEEc-cccCCCCCChhhhhHHHHHHHHHHHhhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHHhhcc-
Q 029647 56 DINERPVLIVVA-SKHLPAVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHP- 133 (190)
Q Consensus 56 d~~G~pv~~~~~-~~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~~~~i~D~~g~~~~~~~~~~~k~~~~~~~~~yP- 133 (190)
..+|+.|.++.. |-.++.. +.+++.+-+.-+ +.....+.+-+++|+.++ .+..-+...++ .+++.|+
T Consensus 45 ~~~g~~v~VIDTPGl~d~~~-~~~~~~~~i~~~----l~~~~~g~ha~llVi~~~--r~t~~~~~~l~----~l~~~FG~ 113 (212)
T PF04548_consen 45 EVDGRQVTVIDTPGLFDSDG-SDEEIIREIKRC----LSLCSPGPHAFLLVIPLG--RFTEEDREVLE----LLQEIFGE 113 (212)
T ss_dssp EETTEEEEEEE--SSEETTE-EHHHHHHHHHHH----HHHTTT-ESEEEEEEETT--B-SHHHHHHHH----HHHHHHCG
T ss_pred eecceEEEEEeCCCCCCCcc-cHHHHHHHHHHH----HHhccCCCeEEEEEEecC--cchHHHHHHHH----HHHHHccH
Confidence 557888888865 5445442 334443333222 223345677788888877 32222333444 4444454
Q ss_pred ccccceEEE
Q 029647 134 KRLGEVLFV 142 (190)
Q Consensus 134 ~~l~~i~iv 142 (190)
+..+.+.|+
T Consensus 114 ~~~k~~ivv 122 (212)
T PF04548_consen 114 EIWKHTIVV 122 (212)
T ss_dssp GGGGGEEEE
T ss_pred HHHhHhhHH
Confidence 355666665
No 44
>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=22.41 E-value=2.6e+02 Score=23.35 Aligned_cols=22 Identities=32% Similarity=0.354 Sum_probs=18.8
Q ss_pred hhhhHhhcCCCHHHHHHHHHHH
Q 029647 2 ILWFLKDRKFSIEESLAKLTKA 23 (190)
Q Consensus 2 l~RfL~~~~~d~~~a~~~l~~~ 23 (190)
|.-||.+.+.++++|.+.++..
T Consensus 249 l~lFLk~iGl~~~e~l~~~~~~ 270 (390)
T cd07322 249 LGLFLKGIGLSLEEALKFWRSE 270 (390)
T ss_pred HHHHHHhCCCCHHHHHHHHHHh
Confidence 4569999999999999988765
No 45
>KOG1533 consensus Predicted GTPase [General function prediction only]
Probab=22.38 E-value=3.2e+02 Score=21.45 Aligned_cols=116 Identities=14% Similarity=0.050 Sum_probs=59.3
Q ss_pred CCCCCcEEEEEcccc---C--CCC------CChhhhhH--------HHHHHHHHHHh-------hCCCCcccEEEEEeCC
Q 029647 56 DINERPVLIVVASKH---L--PAV------HDPVEDEK--------LCVFFIEKALS-------KLPPGKEQILGIIDLR 109 (190)
Q Consensus 56 d~~G~pv~~~~~~~~---~--~~~------~~~~~~~r--------~~~~~~E~~~~-------~~~~~~~~~~~i~D~~ 109 (190)
..-||++.+++..-- . +.. .+.++++. ...|++|.+-. .... -.+--+++|+-
T Consensus 27 s~~gr~~~vVNLDPaNd~~~Y~~~v~I~elit~edvm~~~~LGPNg~l~yc~E~l~~~idwl~~~l~~-~~~~Y~lFDcP 105 (290)
T KOG1533|consen 27 SAIGRPVAVVNLDPANDNLPYECAVDIRELITVEDVMEELGLGPNGALKYCMEYLEANIDWLLEKLKP-LTDHYVLFDCP 105 (290)
T ss_pred HHhCCceEEEecCCcccCCCCCCcccHHHHccHHHHHHHhCCCCchhHHHHHHHHHhhhHHHHHHhhh-ccCcEEEEeCC
Confidence 557899999876431 1 222 33344432 35566665532 2222 35667899998
Q ss_pred CCC---CCC-CCHHHHHHHHHHHHhhcc----ccccceEEEcCCcccHHHHHhhhhccccccCeeEEccchhhh
Q 029647 110 GFG---TEN-ADLKFLTFLFDVFYYYHP----KRLGEVLFVEAPFVFKPFWQLTKPLLKSYASLAKFCSVETVR 175 (190)
Q Consensus 110 g~~---~~~-~~~~~~k~~~~~~~~~yP----~~l~~i~ivn~p~~~~~~~~~ik~fl~~~~~Ki~~~~~~~~l 175 (190)
|=- .+| ...++++.+.+ ..|. ..+...|.-|+..+++.+..-.+.++-=...-|.++++-+++
T Consensus 106 GQVELft~h~~l~~I~~~Lek---~~~rl~~V~LiDs~ycs~p~~~iS~lL~sl~tMl~melphVNvlSK~Dl~ 176 (290)
T KOG1533|consen 106 GQVELFTHHDSLNKIFRKLEK---LDYRLVAVNLIDSHYCSDPSKFISSLLVSLATMLHMELPHVNVLSKADLL 176 (290)
T ss_pred CcEEEEeccchHHHHHHHHHH---cCceEEEEEeeeceeeCChHHHHHHHHHHHHHHHhhcccchhhhhHhHHH
Confidence 732 111 22344444443 2221 112445666788888777765555544322334444444443
No 46
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=21.94 E-value=46 Score=22.32 Aligned_cols=8 Identities=25% Similarity=0.410 Sum_probs=5.6
Q ss_pred CCCCCCcE
Q 029647 55 LDINERPV 62 (190)
Q Consensus 55 ~d~~G~pv 62 (190)
+|..|.|+
T Consensus 99 RD~~G~Pi 106 (110)
T PF09740_consen 99 RDDEGNPI 106 (110)
T ss_pred CCCCCCCC
Confidence 67777775
No 47
>TIGR02613 mob_myst_B mobile mystery protein B. Members of this protein family, which we designate mobile mystery protein B, are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein A (TIGR02612), a member of the family of helix-turn-helix DNA binding proteins (pfam01381). This protein is encoded by the downstream member of the gene pair and belongs to the Fic protein family (pfam02661), where Fic (filamentation induced by cAMP) is a regulator of cell division. The characteristics of having a two-gene operon in a varied context and often on plasmids, with one member affecting cell division and the other able to bind DNA, suggests similarity to addiction modules.
Probab=20.69 E-value=1.4e+02 Score=21.79 Aligned_cols=17 Identities=24% Similarity=0.245 Sum_probs=13.2
Q ss_pred hcCcceecCCCCCCCCc
Q 029647 45 ESGKAYVHDFLDINERP 61 (190)
Q Consensus 45 ~~~~~~~~g~~d~~G~p 61 (190)
.....++|++.|-+||.
T Consensus 116 H~~f~~IHPF~DGNGRt 132 (186)
T TIGR02613 116 HHRLVAIHPFPNGNGRH 132 (186)
T ss_pred HHHHheecCcCCCCcHH
Confidence 33457899999999986
No 48
>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=20.49 E-value=2.5e+02 Score=19.13 Aligned_cols=55 Identities=13% Similarity=0.225 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHhhcccc-cc-ceEEEcCCcccHHHHHhhh-----hcccccc-CeeEEccchh
Q 029647 119 KFLTFLFDVFYYYHPKR-LG-EVLFVEAPFVFKPFWQLTK-----PLLKSYA-SLAKFCSVET 173 (190)
Q Consensus 119 ~~~k~~~~~~~~~yP~~-l~-~i~ivn~p~~~~~~~~~ik-----~fl~~~~-~Ki~~~~~~~ 173 (190)
..+-.++..++-.+=.. -+ -++++|..-+.+.+++.++ .|+++.. +.+.+++..+
T Consensus 65 GTl~El~~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~~~ 127 (133)
T PF03641_consen 65 GTLDELFEALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDDPE 127 (133)
T ss_dssp HHHHHHHHHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESSHH
T ss_pred chHHHHHHHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCCHH
Confidence 35555555554222222 23 5999998878888888774 4555533 6777776544
No 49
>PF07872 DUF1659: Protein of unknown function (DUF1659); InterPro: IPR012454 This family consists of hypothetical bacterial proteins of unknown function
Probab=20.35 E-value=1.7e+02 Score=16.10 Aligned_cols=23 Identities=22% Similarity=0.388 Sum_probs=16.1
Q ss_pred ceecCCCCCCCCcEEEEEcc-ccCC
Q 029647 49 AYVHDFLDINERPVLIVVAS-KHLP 72 (190)
Q Consensus 49 ~~~~g~~d~~G~pv~~~~~~-~~~~ 72 (190)
-+..| .|.+|.|++--+.= ...+
T Consensus 11 ~~~~G-~d~~Gkpi~k~ks~~nvk~ 34 (47)
T PF07872_consen 11 KYQTG-VDENGKPIFKTKSFSNVKP 34 (47)
T ss_pred EEEcc-cCCCCCEEEEeeehhhcCC
Confidence 35568 69999999987553 3443
Done!