Query 019670
Match_columns 337
No_of_seqs 237 out of 1321
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 03:36:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019670.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019670hhsearch_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 1E-49 2.2E-54 362.7 20.3 244 20-269 23-269 (324)
2 KOG1471 Phosphatidylinositol t 100.0 5.2E-38 1.1E-42 295.3 22.2 231 11-246 12-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 6.5E-31 1.4E-35 222.1 8.7 149 91-242 4-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 7.7E-29 1.7E-33 209.2 14.3 141 101-244 14-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 1.6E-26 3.5E-31 193.4 13.6 144 95-242 9-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.6 4E-16 8.6E-21 130.7 4.6 141 96-245 3-146 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 98.9 2.5E-09 5.4E-14 73.9 5.5 48 23-70 1-55 (55)
8 KOG4406 CDC42 Rho GTPase-activ 98.6 3.6E-07 7.7E-12 85.8 10.9 127 96-233 82-213 (467)
9 PF14555 UBA_4: UBA-like domai 87.8 1.8 3.8E-05 27.8 5.0 36 24-68 2-37 (43)
10 PF02845 CUE: CUE domain; Int 85.9 2.3 5E-05 27.1 4.7 38 24-69 3-40 (42)
11 PF06972 DUF1296: Protein of u 83.6 4.1 9E-05 28.1 5.2 42 20-69 3-44 (60)
12 smart00546 CUE Domain that may 80.4 5.1 0.00011 25.5 4.7 37 24-68 4-40 (43)
13 PF00627 UBA: UBA/TS-N domain; 71.3 16 0.00034 22.4 5.0 23 45-67 15-37 (37)
14 cd00194 UBA Ubiquitin Associat 51.2 24 0.00052 21.4 3.2 24 44-67 13-36 (38)
15 PF14213 DUF4325: Domain of un 50.3 51 0.0011 23.6 5.2 48 148-197 19-68 (74)
16 COG2810 Predicted type IV rest 50.0 47 0.001 29.9 5.8 96 20-138 4-99 (284)
17 smart00165 UBA Ubiquitin assoc 50.0 26 0.00056 21.2 3.2 24 44-67 13-36 (37)
18 KOG1838 Alpha/beta hydrolase [ 46.7 1.9E+02 0.0042 28.2 9.9 67 105-180 123-198 (409)
19 smart00804 TAP_C C-terminal do 41.9 1.2E+02 0.0026 21.2 6.8 42 20-70 10-51 (63)
20 PF08938 HBS1_N: HBS1 N-termin 39.9 11 0.00025 27.6 0.4 49 16-70 19-70 (79)
21 PF11964 SpoIIAA-like: SpoIIAA 36.9 1.1E+02 0.0024 23.1 5.7 75 121-203 12-87 (109)
22 PF07308 DUF1456: Protein of u 34.7 52 0.0011 23.4 3.1 29 27-55 33-61 (68)
23 COG2961 ComJ Protein involved 33.2 27 0.00059 31.7 1.7 27 182-208 237-263 (279)
24 PF04838 Baculo_LEF5: Baculovi 33.0 38 0.00083 28.0 2.4 48 166-214 17-68 (159)
25 KOG1534 Putative transcription 32.5 85 0.0018 28.0 4.6 100 129-234 75-193 (273)
26 PF03474 DMA: DMRTA motif; In 31.9 63 0.0014 20.4 2.7 23 45-67 16-38 (39)
27 PF11339 DUF3141: Protein of u 30.8 2.2E+02 0.0048 28.8 7.7 60 121-192 117-176 (581)
28 TIGR02364 dha_pts dihydroxyace 30.5 2E+02 0.0044 23.0 6.3 59 136-203 51-109 (125)
29 PF03641 Lysine_decarbox: Poss 29.2 2E+02 0.0044 23.0 6.2 55 163-217 64-125 (133)
30 COG0052 RpsB Ribosomal protein 28.9 41 0.00089 30.4 2.2 67 176-245 31-103 (252)
31 PF04378 RsmJ: Ribosomal RNA s 28.8 28 0.0006 31.6 1.1 28 182-209 206-233 (245)
32 TIGR02886 spore_II_AA anti-sig 27.3 1.9E+02 0.0041 21.7 5.5 51 147-201 40-91 (106)
33 KOG2267 Eukaryotic-type DNA pr 26.6 1.2E+02 0.0027 29.3 4.9 46 25-72 290-335 (475)
34 PF02954 HTH_8: Bacterial regu 24.3 1E+02 0.0022 19.3 2.8 22 46-67 7-28 (42)
35 PRK03592 haloalkane dehalogena 23.8 3.3E+02 0.0073 24.4 7.4 45 146-190 54-127 (295)
36 PF04552 Sigma54_DBD: Sigma-54 22.2 2.2E+02 0.0048 23.9 5.3 43 26-70 106-149 (160)
37 PRK05703 flhF flagellar biosyn 21.7 1.5E+02 0.0032 29.2 4.7 95 146-245 300-395 (424)
38 PF09932 DUF2164: Uncharacteri 20.7 1.3E+02 0.0029 21.9 3.2 39 16-54 2-40 (76)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=1e-49 Score=362.68 Aligned_cols=244 Identities=52% Similarity=0.843 Sum_probs=226.2
Q ss_pred HHHHHHHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHcCCCC-ccchhhHHHHhcCceEe
Q 019670 20 EEQQRKINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLKETLKWRAEYKPEE-IRWDEIANEAETGKIYR 98 (337)
Q Consensus 20 e~~~~~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~~~l~wR~~~~~d~-i~~~~v~~~~~~~~~~~ 98 (337)
++..+.+.+++..++++......+|+|.+++|||||++||+++|.+||.++|.||+.+++.. +.++++..++++|++|.
T Consensus 23 ~~~~~k~~~~~~~~~pl~~~~~~~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi 102 (324)
T KOG1470|consen 23 EESLDKINSVKKLLGPLTEKESKWCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYI 102 (324)
T ss_pred HHHHHHHHHHHHhhcchhhhhHhcCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEE
Confidence 33336889999999888777778899999999999999999999999999999999999998 88888999999999999
Q ss_pred ccccCCCCCeEEEE--ccCCCCCCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHhhh
Q 019670 99 LNYVDKYGRAVLVM--RPSCQNTKSTKGQIRYLVYCMENAILNLPPHQEQMVWLIDFQGFNLSHISVKVTRETAHVLQDH 176 (337)
Q Consensus 99 ~~~~Dk~GrpV~i~--r~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~~v~IiDl~g~s~~~~~~~~~k~~~~~lq~~ 176 (337)
+| +|++||||+|+ ++++.+..+.+++.|+++|+||.++..++.+++++++|||++|+++++++++..+.++.++|+|
T Consensus 103 ~G-~D~~gRPVl~~~~~~~~qn~~t~~~~~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs~sN~d~~~~k~~~~~lq~h 181 (324)
T KOG1470|consen 103 LG-HDKDGRPVLYLRPRPHRQNTKTQKELERLLVYTLENAILFLPPGQEQFVWLFDLTGFSMSNPDIKFLKELLHILQDH 181 (324)
T ss_pred ec-ccCCCCeEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCcceEEEEEecccCcccCCCcHHHHHHHHHHHHh
Confidence 98 89999999999 6677788899999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccceEEEEcCCcchHHHHHHhcccCCHhhhcceEEEcCCCcchHHHHhccCCcccchhhcCCCCCCCCChHHHHHHh
Q 019670 177 YPERLGLAILYNPPKFFEPFWTVVKPFLELKTQNKVKFVYSDDINTRRIMEDLFDMDQLESAFGGNDRVGFNINKYAERM 256 (337)
Q Consensus 177 YPerl~~i~ivN~P~~~~~~~~lvkpfL~~kt~~KI~~~~~~~~~~~~~L~~~i~~~~LP~e~GG~~~~~~d~~~~~~~~ 256 (337)
|||||+..+++|+||+|..+|+++||||+++|+.||+|+.+. ..|.++||+++||..|||+....|.++++|..|
T Consensus 182 YPErLg~a~l~~~P~iF~~~wkiikpflDp~t~~Kv~F~~~~-----~~l~~~~d~~~l~s~~GG~~~~~y~~e~~~~~~ 256 (324)
T KOG1470|consen 182 YPERLGKALLVNAPWIFQPFWKIIKPFLDPKTASKVKFVEPK-----DDLSEYFDESQLPSLFGGKLLFEYTHEEYWPQM 256 (324)
T ss_pred ChHHhhhhhhcCChHHHHHHHHHhhhccChhhhceeEEecCh-----hHHHhhCCccccchhhCCCcccccCCcchhhhh
Confidence 999999999999999999999999999999999999999764 449999999999999999999999999999999
Q ss_pred hhcCCCccccccc
Q 019670 257 REDDKKMPSFWAM 269 (337)
Q Consensus 257 ~~~~~~~~~~~~~ 269 (337)
.+++...+..|..
T Consensus 257 ~~~~~~~~~~~~~ 269 (324)
T KOG1470|consen 257 KEDDSSLRLEYEA 269 (324)
T ss_pred hhhHHHHHHhHHH
Confidence 9987765444443
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=5.2e-38 Score=295.25 Aligned_cols=231 Identities=29% Similarity=0.418 Sum_probs=187.7
Q ss_pred CCCCCCCCcHHHHHHHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHcCCCCccch-hhHH
Q 019670 11 NGYEKPLPSEEQQRKINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLKETLKWRAEYKPEEIRWD-EIAN 89 (337)
Q Consensus 11 ~~~~~~lt~e~~~~~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~~~l~wR~~~~~d~i~~~-~v~~ 89 (337)
......++ +.+++.|+++| |+...+++.....+|.+|+||||||+||+++|+++|.+++.||..++.+.+... ....
T Consensus 12 ~~~~~~~~-~~~~~~i~~lr-~~~~~~~l~~~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~ 89 (317)
T KOG1471|consen 12 KEELNEIT-ESEEAVIAQLR-WLLQKPHLPNKYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDD 89 (317)
T ss_pred ccccCCCc-HHHHHHHHHHH-HHhhccCCCCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccch
Confidence 33455666 77889999999 888887776557899999999999999999999999999999999998887533 1112
Q ss_pred HHhcCceEeccccCCCCCeEEEEccCCCCCC------ChHHHHHH--------HHHHHHHHHHhCCCCcccEEEEEeCCC
Q 019670 90 EAETGKIYRLNYVDKYGRAVLVMRPSCQNTK------STKGQIRY--------LVYCMENAILNLPPHQEQMVWLIDFQG 155 (337)
Q Consensus 90 ~~~~~~~~~~~~~Dk~GrpV~i~r~~~~~~~------~~~~~~r~--------~~~~~E~~~~~~~~~~~~~v~IiDl~g 155 (337)
.+.........+.|+.|+|+++.+.|..+.. ...+..++ ....+|........+++|+++|+|++|
T Consensus 90 ~~~~~~~~~~~~~~~~g~~v~~~~~g~~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G 169 (317)
T KOG1471|consen 90 ELLKYYPQGLHGVDKEGRPVYIERLGKIDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKG 169 (317)
T ss_pred hhhhhccccccccCCCCCEEEEeccCCCCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCC
Confidence 2222111223468999999999999988643 23444444 444445444444567899999999999
Q ss_pred CCCCCCC---HHHHHHHHHHHhhhhhcccceEEEEcCCcchHHHHHHhcccCCHhhhcceEEEcCCCcchHHHHhccCCc
Q 019670 156 FNLSHIS---VKVTRETAHVLQDHYPERLGLAILYNPPKFFEPFWTVVKPFLELKTQNKVKFVYSDDINTRRIMEDLFDM 232 (337)
Q Consensus 156 ~s~~~~~---~~~~k~~~~~lq~~YPerl~~i~ivN~P~~~~~~~~lvkpfL~~kt~~KI~~~~~~~~~~~~~L~~~i~~ 232 (337)
++++|+. ++.++.++.++|++||++++++||||+|++|+++|+++||||+++|++||++++++ +.+.|.++|++
T Consensus 170 ~~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~~---~~~~L~k~i~~ 246 (317)
T KOG1471|consen 170 VSLSHLLKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHSK---DKESLLKYIPP 246 (317)
T ss_pred CcchhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCCC---chhhhhhhCCH
Confidence 9999985 88999999999999999999999999999999999999999999999999944443 48999999999
Q ss_pred ccchhhcCCCCCCC
Q 019670 233 DQLESAFGGNDRVG 246 (337)
Q Consensus 233 ~~LP~e~GG~~~~~ 246 (337)
++||.+|||++++.
T Consensus 247 ~~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 247 EVLPEEYGGTCGDL 260 (317)
T ss_pred hhCccccCCCcccc
Confidence 99999999999884
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=6.5e-31 Score=222.12 Aligned_cols=149 Identities=36% Similarity=0.662 Sum_probs=121.7
Q ss_pred HhcCceEeccccCCCCCeEEEEccCCCCCC--ChHHHHHHHHHHHHHHHHhCC--CCcccEEEEEeCCCCCCCCCC---H
Q 019670 91 AETGKIYRLNYVDKYGRAVLVMRPSCQNTK--STKGQIRYLVYCMENAILNLP--PHQEQMVWLIDFQGFNLSHIS---V 163 (337)
Q Consensus 91 ~~~~~~~~~~~~Dk~GrpV~i~r~~~~~~~--~~~~~~r~~~~~~E~~~~~~~--~~~~~~v~IiDl~g~s~~~~~---~ 163 (337)
...+..+.. |+|++||||++++++++++. +.++++++.++.+|.++..++ .+.+|+++|+|++|+++++++ +
T Consensus 4 ~~~~~~~~~-g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~~ 82 (159)
T PF00650_consen 4 LKSGPFYLH-GRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFSLSNFDWWPI 82 (159)
T ss_dssp HTTSCEEEE-EE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT--HHHHHCHHH
T ss_pred HCCeeEEEC-CCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCceEeccccchh
Confidence 345555555 57999999999999998754 467999999999999987654 467999999999999999888 9
Q ss_pred HHHHHHHHHHhhhhhcccceEEEEcCCcchHHHHHHhcccCCHhhhcceEEEcCCCcchHHHHhccCCcccchhhcCCC
Q 019670 164 KVTRETAHVLQDHYPERLGLAILYNPPKFFEPFWTVVKPFLELKTQNKVKFVYSDDINTRRIMEDLFDMDQLESAFGGN 242 (337)
Q Consensus 164 ~~~k~~~~~lq~~YPerl~~i~ivN~P~~~~~~~~lvkpfL~~kt~~KI~~~~~~~~~~~~~L~~~i~~~~LP~e~GG~ 242 (337)
+.++.+++++|++||+|++++||||+|++|+.+|+++++||+++|++||+|+++.+ +.+.|.++||+++||.+|||+
T Consensus 83 ~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~--~~~~l~~~i~~~~lP~~~GG~ 159 (159)
T PF00650_consen 83 SFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSD--WKAKLKEYIDPEQLPVEYGGT 159 (159)
T ss_dssp HHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTC--HCHHHCCCSTGGGSBGGGTSS
T ss_pred hhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcc--cHHHHHhhCCHhHCchhcCCC
Confidence 99999999999999999999999999999999999999999999999999995542 446899999999999999996
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=7.7e-29 Score=209.18 Aligned_cols=141 Identities=35% Similarity=0.656 Sum_probs=130.8
Q ss_pred ccCCCCCeEEEEccCCCCC--CChHHHHHHHHHHHHHHHHh--CCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHhhh
Q 019670 101 YVDKYGRAVLVMRPSCQNT--KSTKGQIRYLVYCMENAILN--LPPHQEQMVWLIDFQGFNLSHISVKVTRETAHVLQDH 176 (337)
Q Consensus 101 ~~Dk~GrpV~i~r~~~~~~--~~~~~~~r~~~~~~E~~~~~--~~~~~~~~v~IiDl~g~s~~~~~~~~~k~~~~~lq~~ 176 (337)
|+|++||||++++++.+++ .+.+++++++++.+|.++.. .+.+..|+++|+|++|+++++++++.++.++.++|.+
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~lk~~~~~~~~~ 93 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQREKKTGGIEGFTVIFDLKGLSMSNPDLSVLRKILKILQDH 93 (158)
T ss_pred CCCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHHHhcCCCeeeEEEEEECCCCCcccccHHHHHHHHHHHHHH
Confidence 4899999999999998764 47889999999999999876 5667799999999999999999999999999999999
Q ss_pred hhcccceEEEEcCCcchHHHHHHhcccCCHhhhcceEEEcCCCcchHHHHhccCCcccchhhcCCCCC
Q 019670 177 YPERLGLAILYNPPKFFEPFWTVVKPFLELKTQNKVKFVYSDDINTRRIMEDLFDMDQLESAFGGNDR 244 (337)
Q Consensus 177 YPerl~~i~ivN~P~~~~~~~~lvkpfL~~kt~~KI~~~~~~~~~~~~~L~~~i~~~~LP~e~GG~~~ 244 (337)
||++++++||||+|++++.+|+++++|+++++++||++++++ +.+.|.++||+++||.+|||++.
T Consensus 94 yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~---~~~~L~~~i~~~~lP~~~GG~~~ 158 (158)
T smart00516 94 YPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGND---SKEELLEYIDPEQLPEELGGTLD 158 (158)
T ss_pred hHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCC---CHHHHHhhCCHhhCcHhhCCCCC
Confidence 999999999999999999999999999999999999999763 46889999999999999999873
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=193.40 Aligned_cols=144 Identities=37% Similarity=0.661 Sum_probs=128.6
Q ss_pred ceEeccccCCCCCeEEEEccCCCCCC---ChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCC--CHHHHHHH
Q 019670 95 KIYRLNYVDKYGRAVLVMRPSCQNTK---STKGQIRYLVYCMENAILNLPPHQEQMVWLIDFQGFNLSHI--SVKVTRET 169 (337)
Q Consensus 95 ~~~~~~~~Dk~GrpV~i~r~~~~~~~---~~~~~~r~~~~~~E~~~~~~~~~~~~~v~IiDl~g~s~~~~--~~~~~k~~ 169 (337)
.++..++.|++||||++++++..+.. ..++.+++.++.+|..+........|+++|+|++|++++++ .++.++.+
T Consensus 9 ~~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~~~k~~ 88 (157)
T cd00170 9 KVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQEDDEQVEGFVVIIDLKGLSLSHLLPDPSLLKKI 88 (157)
T ss_pred cccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhhhhhcccceEEEEECCCCChhccchhHHHHHHH
Confidence 44455568999999999999954332 34889999999999998886666679999999999999998 68999999
Q ss_pred HHHHhhhhhcccceEEEEcCCcchHHHHHHhcccCCHhhhcceEEEcCCCcchHHHHhccCCcccchhhcCCC
Q 019670 170 AHVLQDHYPERLGLAILYNPPKFFEPFWTVVKPFLELKTQNKVKFVYSDDINTRRIMEDLFDMDQLESAFGGN 242 (337)
Q Consensus 170 ~~~lq~~YPerl~~i~ivN~P~~~~~~~~lvkpfL~~kt~~KI~~~~~~~~~~~~~L~~~i~~~~LP~e~GG~ 242 (337)
+.+++++||++++++||||+|++++.+|+++++|+++++++||+++.++ .+.|.++||+++||.+|||+
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 9999999999999999999999999999999999999999999999663 57899999999999999996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.61 E-value=4e-16 Score=130.65 Aligned_cols=141 Identities=23% Similarity=0.318 Sum_probs=96.3
Q ss_pred eEeccccCCCCCeEEEEccCCCCCCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCC-CHHHHHHHHHHHh
Q 019670 96 IYRLNYVDKYGRAVLVMRPSCQNTKSTKGQIRYLVYCMENAILNLPPHQEQMVWLIDFQGFNLSHI-SVKVTRETAHVLQ 174 (337)
Q Consensus 96 ~~~~~~~Dk~GrpV~i~r~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~~v~IiDl~g~s~~~~-~~~~~k~~~~~lq 174 (337)
++..+|+|++||||+++...+. .+..++.+.+.|.+...... ....++++|+|++|++..+. +...++.+...+.
T Consensus 3 ~~~~gG~d~~g~pV~~~~~~~~--~~~~~~~~ll~yl~~~l~~~--~~~~~f~vVid~~~~~~~~~~~~~~l~~~~~~l~ 78 (149)
T PF13716_consen 3 FFYPGGRDREGRPVVVFIASRL--PSSDDLERLLLYLLSTLSEE--VVDKPFSVVIDHTGFSRSSEPSLSWLKQLYKLLP 78 (149)
T ss_dssp E-EEEEEBTTS-EEEEEEGGG---C-TTHHHHHHHHHHHHH-TT--TTTS-EEEEEE-TT--GGG---HHHHHHTTTSS-
T ss_pred EEEecccCCCcCEEEEEECCcC--cchhhHHHHHHHHHHhhhHH--hcCCCEEEEEEcCCCccccCCchHHHHHHHHHHH
Confidence 4456789999999999998777 32335555555555543222 23457999999999988665 4999999999999
Q ss_pred hhhhcccceEEEEcCCcchHHHH-HHhcccCCHhh-hcceEEEcCCCcchHHHHhccCCcccchhhcCCCCCC
Q 019670 175 DHYPERLGLAILYNPPKFFEPFW-TVVKPFLELKT-QNKVKFVYSDDINTRRIMEDLFDMDQLESAFGGNDRV 245 (337)
Q Consensus 175 ~~YPerl~~i~ivN~P~~~~~~~-~lvkpfL~~kt-~~KI~~~~~~~~~~~~~L~~~i~~~~LP~e~GG~~~~ 245 (337)
..|+.+++++||||++++++.++ .+.+++++.+. ..||.++.+ ..+|.++||+++||.++||..+.
T Consensus 79 ~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s-----l~~L~~~i~~~qL~~~lp~~~~~ 146 (149)
T PF13716_consen 79 RKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS-----LSELSKHIDPSQLPESLPGVLQY 146 (149)
T ss_dssp HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS-----TCGGGGTSGGGG------HHH--
T ss_pred HHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC-----HHHHHhhCCHHHhcccCCCEEec
Confidence 99999999999999999999999 66677889998 899988855 57799999999999999987653
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=98.91 E-value=2.5e-09 Score=73.86 Aligned_cols=48 Identities=35% Similarity=0.439 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHhcc-------cCCCCCCCCHHHHHHHhhccCCCHHHHHHHHHHH
Q 019670 23 QRKINEVRRLLGLL-------SGRLSIYCSDASIARHLRAQNWNVKKATKMLKET 70 (337)
Q Consensus 23 ~~~i~~lr~~l~~~-------~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~~~ 70 (337)
++++++||+.|... +......++|.+|+|||||++||+++|.+||+++
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 47899999999874 2334566899999999999999999999999875
No 8
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.60 E-value=3.6e-07 Score=85.83 Aligned_cols=127 Identities=18% Similarity=0.358 Sum_probs=104.4
Q ss_pred eEecc-ccCCCCCeEEEEccCCCCCCC-hHH--HHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCCC-HHHHHHHH
Q 019670 96 IYRLN-YVDKYGRAVLVMRPSCQNTKS-TKG--QIRYLVYCMENAILNLPPHQEQMVWLIDFQGFNLSHIS-VKVTRETA 170 (337)
Q Consensus 96 ~~~~~-~~Dk~GrpV~i~r~~~~~~~~-~~~--~~r~~~~~~E~~~~~~~~~~~~~v~IiDl~g~s~~~~~-~~~~k~~~ 170 (337)
+.+.+ +.|+.||.|+++-..++.+.+ +++ ++++.++.++..++. .++.+.=-.|+...+.+ ++++....
T Consensus 82 ~qvi~~~~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~Ve~------DYt~vYfh~gl~s~nkp~l~~l~~aY 155 (467)
T KOG4406|consen 82 LQVIGDAKDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVEN------DYTLVYFHHGLPSDNKPYLQLLFDAY 155 (467)
T ss_pred eeeccCcccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHhc------cceeeehhcCCcccccchHHHHHHHH
Confidence 33444 379999999999888876543 344 788999999988765 27777777888887776 88888888
Q ss_pred HHHhhhhhcccceEEEEcCCcchHHHHHHhcccCCHhhhcceEEEcCCCcchHHHHhccCCcc
Q 019670 171 HVLQDHYPERLGLAILYNPPKFFEPFWTVVKPFLELKTQNKVKFVYSDDINTRRIMEDLFDMD 233 (337)
Q Consensus 171 ~~lq~~YPerl~~i~ivN~P~~~~~~~~lvkpfL~~kt~~KI~~~~~~~~~~~~~L~~~i~~~ 233 (337)
.-+..+|--.++.+|+|++.|++.++|+++|||++.|+.+||.-+. ...+|.+++.-+
T Consensus 156 ke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n-----~lseL~~~l~l~ 213 (467)
T KOG4406|consen 156 KELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFN-----SLSELFEALKLN 213 (467)
T ss_pred HHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEee-----hHHHHHHhhhhh
Confidence 8888889999999999999999999999999999999999998773 477888887644
No 9
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=87.80 E-value=1.8 Score=27.81 Aligned_cols=36 Identities=22% Similarity=0.417 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHH
Q 019670 24 RKINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLK 68 (337)
Q Consensus 24 ~~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~ 68 (337)
+.|.++....+ +++.....||..++||++.|+..+-
T Consensus 2 e~i~~F~~iTg---------~~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 2 EKIAQFMSITG---------ADEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp HHHHHHHHHH----------SSHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHHHC---------cCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45666666654 3668999999999999999998753
No 10
>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=85.93 E-value=2.3 Score=27.08 Aligned_cols=38 Identities=21% Similarity=0.251 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHHH
Q 019670 24 RKINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLKE 69 (337)
Q Consensus 24 ~~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~~ 69 (337)
+.|..|++.+-. .+...|.+-|.++++|++.|..+|-.
T Consensus 3 ~~v~~L~~mFP~--------~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMFPD--------LDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHSSS--------S-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHCCC--------CCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 456677766633 57789999999999999999998753
No 11
>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=83.59 E-value=4.1 Score=28.05 Aligned_cols=42 Identities=17% Similarity=0.334 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHHH
Q 019670 20 EEQQRKINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLKE 69 (337)
Q Consensus 20 e~~~~~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~~ 69 (337)
..-++.|+.+|+.++. .+|.-++--|+-|+.|+..|.++|..
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 4556778888888765 37889999999999999999999865
No 12
>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=80.39 E-value=5.1 Score=25.52 Aligned_cols=37 Identities=19% Similarity=0.259 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHH
Q 019670 24 RKINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLK 68 (337)
Q Consensus 24 ~~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~ 68 (337)
+.++.|++.+-. .++..+.+-|+++++|++.|...|.
T Consensus 4 ~~v~~L~~mFP~--------l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 4 EALHDLKDMFPN--------LDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred HHHHHHHHHCCC--------CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 456666666532 5778999999999999999998874
No 13
>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=71.34 E-value=16 Score=22.37 Aligned_cols=23 Identities=39% Similarity=0.375 Sum_probs=18.9
Q ss_pred CHHHHHHHhhccCCCHHHHHHHH
Q 019670 45 SDASIARHLRAQNWNVKKATKML 67 (337)
Q Consensus 45 ~D~~LlRFLra~~~dvekA~~~l 67 (337)
+.....+-|+.+++|+++|...|
T Consensus 15 ~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 15 SREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp -HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHhC
Confidence 55688899999999999998754
No 14
>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=51.20 E-value=24 Score=21.42 Aligned_cols=24 Identities=38% Similarity=0.429 Sum_probs=20.7
Q ss_pred CCHHHHHHHhhccCCCHHHHHHHH
Q 019670 44 CSDASIARHLRAQNWNVKKATKML 67 (337)
Q Consensus 44 ~~D~~LlRFLra~~~dvekA~~~l 67 (337)
.+.....+-|+.+++|+++|...|
T Consensus 13 f~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 13 FSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 357889999999999999998765
No 15
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=50.33 E-value=51 Score=23.60 Aligned_cols=48 Identities=17% Similarity=0.173 Sum_probs=31.5
Q ss_pred EEEEeCCCCCCCCCCHHHHHHHHHHHhhhhh--cccceEEEEcCCcchHHHH
Q 019670 148 VWLIDFQGFNLSHISVKVTRETAHVLQDHYP--ERLGLAILYNPPKFFEPFW 197 (337)
Q Consensus 148 v~IiDl~g~s~~~~~~~~~k~~~~~lq~~YP--erl~~i~ivN~P~~~~~~~ 197 (337)
.+++|+.|+ ..+..+++-..+..+...|+ +.-.++.++|+......+.
T Consensus 19 ~V~lDF~gv--~~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I 68 (74)
T PF14213_consen 19 KVVLDFEGV--ESITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMI 68 (74)
T ss_pred eEEEECCCc--ccccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHH
Confidence 388999998 34456666666666666666 3445677777765554433
No 16
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=50.00 E-value=47 Score=29.85 Aligned_cols=96 Identities=16% Similarity=0.284 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHcCCCCccchhhHHHHhcCceEec
Q 019670 20 EEQQRKINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLKETLKWRAEYKPEEIRWDEIANEAETGKIYRL 99 (337)
Q Consensus 20 e~~~~~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~~~l~wR~~~~~d~i~~~~v~~~~~~~~~~~~ 99 (337)
+..+..++.++.|+.+.++... ..--.+++||++-+||+. +|++..++.-. +.|..-+.
T Consensus 4 ~~iq~~~~ni~~~y~~~~nEa~--vrq~lIlp~L~slGwdi~----------------nPkEV~PEe~t---~~GraDya 62 (284)
T COG2810 4 STIQKIKNNINKFYNKSRNEAA--VRQHLILPFLSSLGWDID----------------NPKEVRPEEKT---EEGRADYA 62 (284)
T ss_pred HHHHHHHHHHHHHhccCccHHH--HHHHHHHHHHHHcCCCCC----------------CccccCccccc---ccCccceE
Confidence 4567888888999877443221 223458999999999863 35555433221 22321111
Q ss_pred cccCCCCCeEEEEccCCCCCCChHHHHHHHHHHHHHHHH
Q 019670 100 NYVDKYGRAVLVMRPSCQNTKSTKGQIRYLVYCMENAIL 138 (337)
Q Consensus 100 ~~~Dk~GrpV~i~r~~~~~~~~~~~~~r~~~~~~E~~~~ 138 (337)
.=++|+.+.++..+........++.+..-|+.....+
T Consensus 63 --likd~kvfafieak~ls~~~akd~qq~~~Yav~~Gv~ 99 (284)
T COG2810 63 --LIKDGKVFAFIEAKNLSVNPAKDVQQLAKYAVDKGVE 99 (284)
T ss_pred --EEecCcEEEEEeccccCcCchHHHHHHHHHHHhcCcE
Confidence 3467777777777766666667888888888776544
No 17
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=49.97 E-value=26 Score=21.17 Aligned_cols=24 Identities=38% Similarity=0.432 Sum_probs=20.1
Q ss_pred CCHHHHHHHhhccCCCHHHHHHHH
Q 019670 44 CSDASIARHLRAQNWNVKKATKML 67 (337)
Q Consensus 44 ~~D~~LlRFLra~~~dvekA~~~l 67 (337)
.+.....+-|+.+++|+++|..-|
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 456689999999999999998654
No 18
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=46.65 E-value=1.9e+02 Score=28.23 Aligned_cols=67 Identities=19% Similarity=0.311 Sum_probs=47.8
Q ss_pred CCCeEEEEccCCCCCCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCCC---------HHHHHHHHHHHhh
Q 019670 105 YGRAVLVMRPSCQNTKSTKGQIRYLVYCMENAILNLPPHQEQMVWLIDFQGFNLSHIS---------VKVTRETAHVLQD 175 (337)
Q Consensus 105 ~GrpV~i~r~~~~~~~~~~~~~r~~~~~~E~~~~~~~~~~~~~v~IiDl~g~s~~~~~---------~~~~k~~~~~lq~ 175 (337)
...|++++-+|-.. .+.+.++|.++..... . .=-++|+.-+|+.-..+. ..-++.+++.+..
T Consensus 123 ~~~P~vvilpGltg-~S~~~YVr~lv~~a~~---~-----G~r~VVfN~RG~~g~~LtTpr~f~ag~t~Dl~~~v~~i~~ 193 (409)
T KOG1838|consen 123 GTDPIVVILPGLTG-GSHESYVRHLVHEAQR---K-----GYRVVVFNHRGLGGSKLTTPRLFTAGWTEDLREVVNHIKK 193 (409)
T ss_pred CCCcEEEEecCCCC-CChhHHHHHHHHHHHh---C-----CcEEEEECCCCCCCCccCCCceeecCCHHHHHHHHHHHHH
Confidence 45688888888643 3556788887663321 1 134688999996654442 7889999999999
Q ss_pred hhhcc
Q 019670 176 HYPER 180 (337)
Q Consensus 176 ~YPer 180 (337)
.||.+
T Consensus 194 ~~P~a 198 (409)
T KOG1838|consen 194 RYPQA 198 (409)
T ss_pred hCCCC
Confidence 99998
No 19
>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=41.94 E-value=1.2e+02 Score=21.23 Aligned_cols=42 Identities=24% Similarity=0.330 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHHHH
Q 019670 20 EEQQRKINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLKET 70 (337)
Q Consensus 20 e~~~~~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~~~ 70 (337)
+.+++.|.++-..-+ ++-.+-.++|...+||.+.|.+.+...
T Consensus 10 ~~q~~~v~~~~~~Tg---------mn~~~s~~cLe~~~Wd~~~Al~~F~~l 51 (63)
T smart00804 10 PEQQEMVQAFSAQTG---------MNAEYSQMCLEDNNWDYERALKNFTEL 51 (63)
T ss_pred HHHHHHHHHHHHHHC---------CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 556666666554332 456789999999999999999998764
No 20
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=39.95 E-value=11 Score=27.55 Aligned_cols=49 Identities=27% Similarity=0.368 Sum_probs=30.9
Q ss_pred CCCcHHHHH---HHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHHHH
Q 019670 16 PLPSEEQQR---KINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLKET 70 (337)
Q Consensus 16 ~lt~e~~~~---~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~~~ 70 (337)
.|+++++.+ ++.++|+.|+..- + ++..|..-|..++||+++|+..|.+.
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 466554322 3335566665521 1 67789999999999999999988764
No 21
>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=36.85 E-value=1.1e+02 Score=23.05 Aligned_cols=75 Identities=13% Similarity=0.171 Sum_probs=49.1
Q ss_pred ChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCC-CCCCCCCCHHHHHHHHHHHhhhhhcccceEEEEcCCcchHHHHHH
Q 019670 121 STKGQIRYLVYCMENAILNLPPHQEQMVWLIDFQ-GFNLSHISVKVTRETAHVLQDHYPERLGLAILYNPPKFFEPFWTV 199 (337)
Q Consensus 121 ~~~~~~r~~~~~~E~~~~~~~~~~~~~v~IiDl~-g~s~~~~~~~~~k~~~~~lq~~YPerl~~i~ivN~P~~~~~~~~l 199 (337)
+.+++.. ..-.++..+. ....+.+++|++ ++ ..+++........+... +...+.++=+|-.+.+...+.++
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 4455555 4444444433 334688899988 64 23345555555555555 88888999999999999999999
Q ss_pred hccc
Q 019670 200 VKPF 203 (337)
Q Consensus 200 vkpf 203 (337)
+.+|
T Consensus 84 ~~~~ 87 (109)
T PF11964_consen 84 FAAF 87 (109)
T ss_dssp HHHH
T ss_pred HHhc
Confidence 8887
No 22
>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=34.74 E-value=52 Score=23.43 Aligned_cols=29 Identities=21% Similarity=0.189 Sum_probs=21.6
Q ss_pred HHHHHHHhcccCCCCCCCCHHHHHHHhhc
Q 019670 27 NEVRRLLGLLSGRLSIYCSDASIARHLRA 55 (337)
Q Consensus 27 ~~lr~~l~~~~~~~~~~~~D~~LlRFLra 55 (337)
.+|..|+.+..+..-..|+|..|..||.+
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 46778888765544456899999999964
No 23
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=33.20 E-value=27 Score=31.68 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=22.3
Q ss_pred ceEEEEcCCcchHHHHHHhcccCCHhh
Q 019670 182 GLAILYNPPKFFEPFWTVVKPFLELKT 208 (337)
Q Consensus 182 ~~i~ivN~P~~~~~~~~lvkpfL~~kt 208 (337)
..++|||+||-+.--.+.+-|+|....
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~L 263 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTLL 263 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHHh
Confidence 479999999999998888888875543
No 24
>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=32.99 E-value=38 Score=28.03 Aligned_cols=48 Identities=19% Similarity=0.399 Sum_probs=39.5
Q ss_pred HHHHHHHHhhhhhcccc--eEEEEcCCcchHHHHHHhcccCCH--hhhcceEE
Q 019670 166 TRETAHVLQDHYPERLG--LAILYNPPKFFEPFWTVVKPFLEL--KTQNKVKF 214 (337)
Q Consensus 166 ~k~~~~~lq~~YPerl~--~i~ivN~P~~~~~~~~lvkpfL~~--kt~~KI~~ 214 (337)
.+.++..|-.+||..++ .+-+.|..-.|.++|+-+ |-++. +-|+-|++
T Consensus 17 y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRL 68 (159)
T PF04838_consen 17 YKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRL 68 (159)
T ss_pred HHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhh
Confidence 46788999999999998 899999999999999977 66666 55555554
No 25
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=32.51 E-value=85 Score=28.00 Aligned_cols=100 Identities=18% Similarity=0.337 Sum_probs=58.0
Q ss_pred HHHHHHHHHHhC------CCCcccEEEEEeCCCC-C-CCCCCHHHHHHHHHHHhhhhhcccceEEEEcCCcc------hH
Q 019670 129 LVYCMENAILNL------PPHQEQMVWLIDFQGF-N-LSHISVKVTRETAHVLQDHYPERLGLAILYNPPKF------FE 194 (337)
Q Consensus 129 ~~~~~E~~~~~~------~~~~~~~v~IiDl~g~-s-~~~~~~~~~k~~~~~lq~~YPerl~~i~ivN~P~~------~~ 194 (337)
++||||..+..+ .+..++-.+|+||-|- . +.| +.++++++.-++. .-.++..+|++..+.+ |+
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 678888777653 2334677799999882 1 123 5567777777776 4457778888877764 44
Q ss_pred HHHHHhcccC----CH-hhhcceEEEcCCCcchHHHHhccCCccc
Q 019670 195 PFWTVVKPFL----EL-KTQNKVKFVYSDDINTRRIMEDLFDMDQ 234 (337)
Q Consensus 195 ~~~~lvkpfL----~~-kt~~KI~~~~~~~~~~~~~L~~~i~~~~ 234 (337)
..+..+..++ |. ....|.-++.. ..++.|..+.+++.
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 4444443332 21 13334444433 23566666666553
No 26
>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=31.89 E-value=63 Score=20.37 Aligned_cols=23 Identities=17% Similarity=0.147 Sum_probs=19.2
Q ss_pred CHHHHHHHhhccCCCHHHHHHHH
Q 019670 45 SDASIARHLRAQNWNVKKATKML 67 (337)
Q Consensus 45 ~D~~LlRFLra~~~dvekA~~~l 67 (337)
....|-.-|++|++|+-+|.+.+
T Consensus 16 kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 16 KRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred ChHHHHHHHHHcCCcHHHHHHHh
Confidence 34678889999999999998864
No 27
>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=30.82 E-value=2.2e+02 Score=28.84 Aligned_cols=60 Identities=18% Similarity=0.170 Sum_probs=44.7
Q ss_pred ChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHhhhhhcccceEEEEcCCcc
Q 019670 121 STKGQIRYLVYCMENAILNLPPHQEQMVWLIDFQGFNLSHISVKVTRETAHVLQDHYPERLGLAILYNPPKF 192 (337)
Q Consensus 121 ~~~~~~r~~~~~~E~~~~~~~~~~~~~v~IiDl~g~s~~~~~~~~~k~~~~~lq~~YPerl~~i~ivN~P~~ 192 (337)
++++.++.....+|.....-+.. ...++|=+|+| -.++.++...+|+.++.+.+--+|--
T Consensus 117 Tl~DV~~ae~~Fv~~V~~~hp~~-~kp~liGnCQg-----------GWa~~mlAA~~Pd~~gplvlaGaPls 176 (581)
T PF11339_consen 117 TLEDVMRAEAAFVEEVAERHPDA-PKPNLIGNCQG-----------GWAAMMLAALRPDLVGPLVLAGAPLS 176 (581)
T ss_pred cHHHHHHHHHHHHHHHHHhCCCC-CCceEEeccHH-----------HHHHHHHHhcCcCccCceeecCCCcc
Confidence 67888888888888766654333 37788888876 34566778889999999988888853
No 28
>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=30.49 E-value=2e+02 Score=23.01 Aligned_cols=59 Identities=17% Similarity=0.192 Sum_probs=37.4
Q ss_pred HHHhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHhhhhhcccceEEEEcCCcchHHHHHHhccc
Q 019670 136 AILNLPPHQEQMVWLIDFQGFNLSHISVKVTRETAHVLQDHYPERLGLAILYNPPKFFEPFWTVVKPF 203 (337)
Q Consensus 136 ~~~~~~~~~~~~v~IiDl~g~s~~~~~~~~~k~~~~~lq~~YPerl~~i~ivN~P~~~~~~~~lvkpf 203 (337)
++.+......+++++.|+ |=+..+. ..++.+++ ++..+.+..+|+|.+...+...+..-
T Consensus 51 ai~~~~~~~dgVlvl~DL-Ggs~~n~-----e~a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~ 109 (125)
T TIGR02364 51 AIEKADNEADGVLIFYDL-GSAVMNA-----EMAVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQ 109 (125)
T ss_pred HHHHhcCCCCCEEEEEcC-CCcHhHH-----HHHHHHhc---cccccEEEEechhHHHHHHHHHHHHc
Confidence 444443334799999999 6443221 11222222 45668899999999988888777543
No 29
>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=29.16 E-value=2e+02 Score=23.03 Aligned_cols=55 Identities=20% Similarity=0.247 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHhhhhhcc-cc-eEEEEcCCcchHHHHHHh-----cccCCHhhhcceEEEcC
Q 019670 163 VKVTRETAHVLQDHYPER-LG-LAILYNPPKFFEPFWTVV-----KPFLELKTQNKVKFVYS 217 (337)
Q Consensus 163 ~~~~k~~~~~lq~~YPer-l~-~i~ivN~P~~~~~~~~lv-----kpfL~~kt~~KI~~~~~ 217 (337)
...+-+++.++.-.+=.. -+ .++++|..-+++.++..+ .-|+++...+.+.|+.+
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 556666666665333332 33 699999988888888876 46999999999988844
No 30
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=28.90 E-value=41 Score=30.40 Aligned_cols=67 Identities=12% Similarity=0.143 Sum_probs=43.4
Q ss_pred hhhcccceEEEEcCCcch---HHHHHHhcccCCHhhhcceEEEcCCCc--chHHHHhccCCcccchhhc-CCCCCC
Q 019670 176 HYPERLGLAILYNPPKFF---EPFWTVVKPFLELKTQNKVKFVYSDDI--NTRRIMEDLFDMDQLESAF-GGNDRV 245 (337)
Q Consensus 176 ~YPerl~~i~ivN~P~~~---~~~~~lvkpfL~~kt~~KI~~~~~~~~--~~~~~L~~~i~~~~LP~e~-GG~~~~ 245 (337)
-|.+| ..+||||.-.-. ...+++++.... --.+|-|+++... .......+..+.-.+...| ||+++.
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--NGGKILFVGTKKQAQEPVKEFAERTGAYYVNGRWLGGMLTN 103 (252)
T ss_pred ceeec-CCcEEEEHHHHHHHHHHHHHHHHHHHc--CCCEEEEEechHHHHHHHHHHHHHhCCceecCcccCccccC
Confidence 48889 999999987644 334444443321 1457889987632 2334455667777788775 999987
No 31
>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=28.78 E-value=28 Score=31.55 Aligned_cols=28 Identities=18% Similarity=0.277 Sum_probs=19.4
Q ss_pred ceEEEEcCCcchHHHHHHhcccCCHhhh
Q 019670 182 GLAILYNPPKFFEPFWTVVKPFLELKTQ 209 (337)
Q Consensus 182 ~~i~ivN~P~~~~~~~~lvkpfL~~kt~ 209 (337)
..++|||+||-+.--.+-+-|+|.+...
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 4699999999998877777776655443
No 32
>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=27.29 E-value=1.9e+02 Score=21.66 Aligned_cols=51 Identities=10% Similarity=0.155 Sum_probs=35.4
Q ss_pred EEEEEeCCCCCCCCCC-HHHHHHHHHHHhhhhhcccceEEEEcCCcchHHHHHHhc
Q 019670 147 MVWLIDFQGFNLSHIS-VKVTRETAHVLQDHYPERLGLAILYNPPKFFEPFWTVVK 201 (337)
Q Consensus 147 ~v~IiDl~g~s~~~~~-~~~~k~~~~~lq~~YPerl~~i~ivN~P~~~~~~~~lvk 201 (337)
-.+|+||++++.=..+ +..+..+...++. +=..++++|++.-+.-++.+..
T Consensus 40 ~~vilDls~v~~iDssgi~~L~~~~~~~~~----~g~~l~l~~~~~~v~~~l~~~g 91 (106)
T TIGR02886 40 KHLILNLKNVTFMDSSGLGVILGRYKKIKN----EGGEVIVCNVSPAVKRLFELSG 91 (106)
T ss_pred CEEEEECCCCcEecchHHHHHHHHHHHHHH----cCCEEEEEeCCHHHHHHHHHhC
Confidence 4699999998875554 5555555555542 4478999999887776666543
No 33
>KOG2267 consensus Eukaryotic-type DNA primase, large subunit [Replication, recombination and repair]
Probab=26.63 E-value=1.2e+02 Score=29.30 Aligned_cols=46 Identities=11% Similarity=0.118 Sum_probs=35.5
Q ss_pred HHHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHHHHHHHHHHHH
Q 019670 25 KINEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKKATKMLKETLK 72 (337)
Q Consensus 25 ~i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvekA~~~l~~~l~ 72 (337)
+..+|-+.|+...|+ .+.....+--||.+++-.+++|++.++..++
T Consensus 290 Cmk~lhe~LrkNhHL--ry~gR~qygLFLKgiGLS~deal~fwr~sFt 335 (475)
T KOG2267|consen 290 CMKQLHERLRKNHHL--RYGGRQQYGLFLKGIGLSVDEALAFWRGSFT 335 (475)
T ss_pred HHHHHHHHHhhcccc--cccchhhhhhhhhccCcCHHHHHHHHHHHHh
Confidence 456777777776554 4577888999999999999999998555443
No 34
>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=24.31 E-value=1e+02 Score=19.33 Aligned_cols=22 Identities=32% Similarity=0.351 Sum_probs=18.5
Q ss_pred HHHHHHHhhccCCCHHHHHHHH
Q 019670 46 DASIARHLRAQNWNVKKATKML 67 (337)
Q Consensus 46 D~~LlRFLra~~~dvekA~~~l 67 (337)
...|..-|..++||+.+|++.|
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 3578889999999999999988
No 35
>PRK03592 haloalkane dehalogenase; Provisional
Probab=23.76 E-value=3.3e+02 Score=24.39 Aligned_cols=45 Identities=11% Similarity=0.057 Sum_probs=29.6
Q ss_pred cEEEEEeCCCCCCCCCC-----H----HHHHHH--------------------HHHHhhhhhcccceEEEEcCC
Q 019670 146 QMVWLIDFQGFNLSHIS-----V----KVTRET--------------------AHVLQDHYPERLGLAILYNPP 190 (337)
Q Consensus 146 ~~v~IiDl~g~s~~~~~-----~----~~~k~~--------------------~~~lq~~YPerl~~i~ivN~P 190 (337)
+-|+.+|+.|++.+..+ + ..+..+ +..+...||++++++.++|++
T Consensus 54 ~~via~D~~G~G~S~~~~~~~~~~~~a~dl~~ll~~l~~~~~~lvGhS~Gg~ia~~~a~~~p~~v~~lil~~~~ 127 (295)
T PRK03592 54 GRCLAPDLIGMGASDKPDIDYTFADHARYLDAWFDALGLDDVVLVGHDWGSALGFDWAARHPDRVRGIAFMEAI 127 (295)
T ss_pred CEEEEEcCCCCCCCCCCCCCCCHHHHHHHHHHHHHHhCCCCeEEEEECHHHHHHHHHHHhChhheeEEEEECCC
Confidence 46899999999877431 1 112222 222346789999999999973
No 36
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=22.20 E-value=2.2e+02 Score=23.92 Aligned_cols=43 Identities=16% Similarity=0.265 Sum_probs=25.7
Q ss_pred HHHHHHHHhcccCCCCCCCCHHHHHHHhhccCCCHHH-HHHHHHHH
Q 019670 26 INEVRRLLGLLSGRLSIYCSDASIARHLRAQNWNVKK-ATKMLKET 70 (337)
Q Consensus 26 i~~lr~~l~~~~~~~~~~~~D~~LlRFLra~~~dvek-A~~~l~~~ 70 (337)
-..++++|.......| ++|.-|..-|...+..+.+ ++.++++.
T Consensus 106 k~~i~~lI~~Ed~~~P--lSD~~i~~~L~~~gi~isRRTVaKYR~~ 149 (160)
T PF04552_consen 106 KARIKELIEEEDKKKP--LSDQEIAELLKEEGIKISRRTVAKYREE 149 (160)
T ss_dssp -HHHHHHHTTS-TTS-----HHHHHHHHTTTTS---HHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCC--CCHHHHHHHHHHcCCCccHHHHHHHHHH
Confidence 3578888887643333 8999999999999987765 55554443
No 37
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=21.67 E-value=1.5e+02 Score=29.22 Aligned_cols=95 Identities=17% Similarity=0.204 Sum_probs=58.4
Q ss_pred cEEEEEeCCCCCCCCCCHHHHHHHHHHHh-hhhhcccceEEEEcCCcchHHHHHHhcccCCHhhhcceEEEcCCCcchHH
Q 019670 146 QMVWLIDFQGFNLSHISVKVTRETAHVLQ-DHYPERLGLAILYNPPKFFEPFWTVVKPFLELKTQNKVKFVYSDDINTRR 224 (337)
Q Consensus 146 ~~v~IiDl~g~s~~~~~~~~~k~~~~~lq-~~YPerl~~i~ivN~P~~~~~~~~lvkpfL~~kt~~KI~~~~~~~~~~~~ 224 (337)
.-++|||..|.+. .+...+..+..++. ..+| +...+|+++..--..+..+++.|=.-. ...+.|..-+......
T Consensus 300 ~DlVlIDt~G~~~--~d~~~~~~L~~ll~~~~~~--~~~~LVl~a~~~~~~l~~~~~~f~~~~-~~~vI~TKlDet~~~G 374 (424)
T PRK05703 300 CDVILIDTAGRSQ--RDKRLIEELKALIEFSGEP--IDVYLVLSATTKYEDLKDIYKHFSRLP-LDGLIFTKLDETSSLG 374 (424)
T ss_pred CCEEEEeCCCCCC--CCHHHHHHHHHHHhccCCC--CeEEEEEECCCCHHHHHHHHHHhCCCC-CCEEEEeccccccccc
Confidence 3568999988654 34343444444444 3344 677888999877666666665553222 2456555433333445
Q ss_pred HHhccCCcccchhhcCCCCCC
Q 019670 225 IMEDLFDMDQLESAFGGNDRV 245 (337)
Q Consensus 225 ~L~~~i~~~~LP~e~GG~~~~ 245 (337)
.+...+-...+|..|=|+.+.
T Consensus 375 ~i~~~~~~~~lPv~yit~Gq~ 395 (424)
T PRK05703 375 SILSLLIESGLPISYLTNGQR 395 (424)
T ss_pred HHHHHHHHHCCCEEEEeCCCC
Confidence 666777778899998777765
No 38
>PF09932 DUF2164: Uncharacterized conserved protein (DUF2164); InterPro: IPR018680 This family of various hypothetical prokaryotic proteins has no known function.
Probab=20.68 E-value=1.3e+02 Score=21.85 Aligned_cols=39 Identities=13% Similarity=0.070 Sum_probs=28.8
Q ss_pred CCCcHHHHHHHHHHHHHHhcccCCCCCCCCHHHHHHHhh
Q 019670 16 PLPSEEQQRKINEVRRLLGLLSGRLSIYCSDASIARHLR 54 (337)
Q Consensus 16 ~lt~e~~~~~i~~lr~~l~~~~~~~~~~~~D~~LlRFLr 54 (337)
.|++++++..+.+|+..+...-+..-+...-.+||.|+.
T Consensus 2 ~l~ke~k~~li~~iq~yf~~E~d~eiG~~~Ae~LLDF~~ 40 (76)
T PF09932_consen 2 KLSKEEKAELIDKIQRYFAEELDEEIGDFEAEFLLDFFI 40 (76)
T ss_pred cCCHHHHHHHHHHHHHHHHHHhcCcHHHhHHHHHHHHHH
Confidence 367889999999999999886554434445567777764
Done!