Query 012611
Match_columns 460
No_of_seqs 343 out of 1546
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 04:27:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012611.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012611hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1471 Phosphatidylinositol t 100.0 1E-45 2.2E-50 373.2 23.2 265 80-347 20-287 (317)
2 KOG1470 Phosphatidylinositol t 100.0 5.3E-39 1.1E-43 318.5 20.2 207 103-336 47-253 (324)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 6.6E-31 1.4E-35 237.6 9.9 157 153-319 2-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 3E-28 6.5E-33 220.0 15.3 154 154-321 5-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 2.8E-25 6.1E-30 197.9 15.1 146 161-319 12-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.5 1.5E-14 3.2E-19 130.4 2.6 140 161-322 5-146 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 98.8 1.3E-08 2.8E-13 76.7 5.3 47 83-130 1-55 (55)
8 KOG4406 CDC42 Rho GTPase-activ 98.3 4E-06 8.6E-11 86.0 10.0 126 165-311 89-214 (467)
9 PF14555 UBA_4: UBA-like domai 74.8 10 0.00022 26.8 5.3 36 84-128 2-37 (43)
10 PF02845 CUE: CUE domain; Int 65.0 21 0.00046 24.9 5.2 38 84-129 3-40 (42)
11 smart00546 CUE Domain that may 55.2 34 0.00074 23.9 4.9 38 84-129 4-41 (43)
12 KOG1838 Alpha/beta hydrolase [ 39.8 2.2E+02 0.0047 30.4 9.9 89 167-280 122-216 (409)
13 PRK00117 recX recombination re 39.0 38 0.00082 30.5 3.8 76 51-131 78-154 (157)
14 PRK14136 recX recombination re 38.9 21 0.00047 36.2 2.3 23 107-129 279-301 (309)
15 COG4479 Uncharacterized protei 36.0 99 0.0021 24.6 5.0 54 81-134 16-72 (74)
16 PF06972 DUF1296: Protein of u 34.3 1.4E+02 0.003 23.0 5.4 39 83-129 6-44 (60)
17 COG2137 OraA Uncharacterized p 28.3 1.2E+02 0.0025 28.4 5.2 32 99-130 133-164 (174)
18 PRK14137 recX recombination re 26.0 1.4E+02 0.003 28.4 5.4 27 107-133 156-182 (195)
19 PRK11613 folP dihydropteroate 25.7 7E+02 0.015 25.1 12.3 44 218-262 174-217 (282)
20 PRK09261 phospho-2-dehydro-3-d 23.4 4.9E+02 0.011 27.1 9.1 67 158-235 205-272 (349)
21 TIGR00034 aroFGH phospho-2-deh 23.4 1.6E+02 0.0034 30.7 5.5 68 157-235 199-266 (344)
22 COG1219 ClpX ATP-dependent pro 23.3 1.4E+02 0.003 31.1 4.9 18 107-124 145-162 (408)
23 PF04378 RsmJ: Ribosomal RNA s 22.1 54 0.0012 32.4 1.8 26 262-287 206-231 (245)
24 PF03641 Lysine_decarbox: Poss 21.9 1.9E+02 0.0041 25.4 5.2 43 263-307 86-133 (133)
25 PRK12822 phospho-2-dehydro-3-d 21.2 3.2E+02 0.0069 28.5 7.2 67 158-235 205-271 (356)
26 cd00194 UBA Ubiquitin Associat 21.0 1.3E+02 0.0029 20.0 3.1 21 107-127 16-36 (38)
27 cd07322 PriL_PriS_Eukaryotic E 20.7 5E+02 0.011 27.4 8.8 45 84-130 226-270 (390)
28 KOG1534 Putative transcription 20.7 2.6E+02 0.0056 27.5 5.9 105 199-311 76-193 (273)
29 COG2961 ComJ Protein involved 20.5 73 0.0016 31.7 2.3 26 262-287 237-262 (279)
30 PRK14136 recX recombination re 20.4 2.8E+02 0.0061 28.4 6.5 58 40-115 161-221 (309)
No 1
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=1e-45 Score=373.16 Aligned_cols=265 Identities=47% Similarity=0.767 Sum_probs=239.8
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCcccccchhHHHHHHhhcc
Q 012611 80 VEELHAVDAFRRVLISEELLPARHDHYHMLLRFLKARKFDIAKATQMWADMIQWRKDFGTDTILEDFEFSEVNEVLQYYP 159 (460)
Q Consensus 80 ~~E~~~V~~lR~~L~~~~~LP~~~dD~~~LLRFLrArkfDvekA~k~L~~~l~WRk~~~~d~i~~d~~~~el~~vlk~~~ 159 (460)
+.+.+.++++| |+.++++++...+|..+||||||||+||+++|++||.+++.||+++..+.+..+ .....++.++++
T Consensus 20 ~~~~~~i~~lr-~~~~~~~l~~~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~--~~~~~~~~~~~~ 96 (317)
T KOG1471|consen 20 ESEEAVIAQLR-WLLQKPHLPNKYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFED--FEEDDELLKYYP 96 (317)
T ss_pred HHHHHHHHHHH-HHhhccCCCCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhc--cccchhhhhhcc
Confidence 45677788887 999999999744444699999999999999999999999999999999999876 234445666889
Q ss_pred cccccCCCCCCcEEEEecCccCCccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCCCccCCC
Q 012611 160 QGYHGMDKEGRPVYIERLGKVDPNKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGVGFKSLT 239 (460)
Q Consensus 160 ~~~~G~Dk~GRPVli~rlg~~d~~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~sl~~~~ 239 (460)
++++|.|++|+||++.+.|..+...++..+...+++++++..+|+.+..+++.|......+++|+++|+|++|+++.|+.
T Consensus 97 ~~~~~~~~~g~~v~~~~~g~~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~ 176 (317)
T KOG1471|consen 97 QGLHGVDKEGRPVYIERLGKIDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLL 176 (317)
T ss_pred ccccccCCCCCEEEEeccCCCCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHH
Confidence 99999999999999999999999999999999999999999999999999998887777899999999999999999999
Q ss_pred hHHHHHHHHHHHHhhhcCCcccceEEEEecChHHHHHHHHHhhccChhhhcceEEcCCcchHHHHhhcCCCCCccccCCC
Q 012611 240 KSARELIMQVQKIDSDNYPETLCRMFIINAGQGFKLLWNSVRRFLDPKTTSKIHVLGNKYQSKLLEIIDASELPEFLGGS 319 (460)
Q Consensus 240 ~~~~~~ik~i~~ilq~~YPerL~~i~IINaP~~f~~lw~ivKpFLd~kt~~KI~~l~~~~~~~L~e~Id~~~LP~eyGGt 319 (460)
...+..++.++.++|+|||++++++||||+|++|+++|++|||||+++|++||++++.++.++|.++|++++||++|||+
T Consensus 177 ~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~~~~~~L~k~i~~~~LP~~yGG~ 256 (317)
T KOG1471|consen 177 KPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHSKDKESLLKYIPPEVLPEEYGGT 256 (317)
T ss_pred HHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCCCchhhhhhhCCHhhCccccCCC
Confidence 99999999999999999999999999999999999999999999999999999977677789999999999999999999
Q ss_pred CCCCC---CCCCcCCCCCCCCChhHHHHhhh
Q 012611 320 CNCAD---QGGCMRSDKGPWKDPNILQIVLS 347 (460)
Q Consensus 320 ~~~~~---~ggc~~~~~~pw~dp~~~k~~~~ 347 (460)
|.+.+ .++|...+.++|.++.+.+....
T Consensus 257 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 (317)
T KOG1471|consen 257 CGDLDDPNGGGCDLSDEGPWKEPEIKKGKQE 287 (317)
T ss_pred ccccccccCCcCccccccccccccccccccc
Confidence 99963 47799999999988776654433
No 2
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=5.3e-39 Score=318.51 Aligned_cols=207 Identities=30% Similarity=0.524 Sum_probs=183.1
Q ss_pred CCcHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCcccccchhHHHHHHhhcccccccCCCCCCcEEEEecCccCC
Q 012611 103 HDHYHMLLRFLKARKFDIAKATQMWADMIQWRKDFGTDTILEDFEFSEVNEVLQYYPQGYHGMDKEGRPVYIERLGKVDP 182 (460)
Q Consensus 103 ~dD~~~LLRFLrArkfDvekA~k~L~~~l~WRk~~~~d~i~~d~~~~el~~vlk~~~~~~~G~Dk~GRPVli~rlg~~d~ 182 (460)
.+| .++|||||||+||+++|.+||.++|.||+.+++.... ...++..-+..+.+++.|.|++||||+|+++....+
T Consensus 47 ~~d-~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~---~~~Ev~~e~~tGK~yi~G~D~~gRPVl~~~~~~~~q 122 (324)
T KOG1470|consen 47 CSD-ACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVI---EADEVAAELETGKAYILGHDKDGRPVLYLRPRPHRQ 122 (324)
T ss_pred CcH-HHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCcccc---CHHHHHHHhhcCcEEEecccCCCCeEEEEecCCCCC
Confidence 356 5999999999999999999999999999999986622 345676677889999999999999999997665555
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCCCccCCChHHHHHHHHHHHHhhhcCCcccc
Q 012611 183 NKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGVGFKSLTKSARELIMQVQKIDSDNYPETLC 262 (460)
Q Consensus 183 ~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~sl~~~~~~~~~~ik~i~~ilq~~YPerL~ 262 (460)
+. .+.+++.+++|++||.++..+.+ .++++++++|++|++++|.+ +...+.+++++|+||||||+
T Consensus 123 n~----~t~~~~~r~~Vy~mE~Ai~~lp~--------~qe~~~~L~D~~~fs~sN~d---~~~~k~~~~~lq~hYPErLg 187 (324)
T KOG1470|consen 123 NT----KTQKELERLLVYTLENAILFLPP--------GQEQFVWLFDLTGFSMSNPD---IKFLKELLHILQDHYPERLG 187 (324)
T ss_pred CC----CCHHHHHHHHHHHHHHHHHhCCC--------CcceEEEEEecccCcccCCC---cHHHHHHHHHHHHhChHHhh
Confidence 44 47999999999999999987543 46889999999999999888 78999999999999999999
Q ss_pred eEEEEecChHHHHHHHHHhhccChhhhcceEEcCCcchHHHHhhcCCCCCccccCCCCCCCCCCCCcCCCCCCC
Q 012611 263 RMFIINAGQGFKLLWNSVRRFLDPKTTSKIHVLGNKYQSKLLEIIDASELPEFLGGSCNCADQGGCMRSDKGPW 336 (460)
Q Consensus 263 ~i~IINaP~~f~~lw~ivKpFLd~kt~~KI~~l~~~~~~~L~e~Id~~~LP~eyGGt~~~~~~ggc~~~~~~pw 336 (460)
..+|+|+||+|..+|++|||||||+|++||.|..+. ..|.+|||+++||..|||+..+.+ .+..+|
T Consensus 188 ~a~l~~~P~iF~~~wkiikpflDp~t~~Kv~F~~~~--~~l~~~~d~~~l~s~~GG~~~~~y------~~e~~~ 253 (324)
T KOG1470|consen 188 KALLVNAPWIFQPFWKIIKPFLDPKTASKVKFVEPK--DDLSEYFDESQLPSLFGGKLLFEY------THEEYW 253 (324)
T ss_pred hhhhcCChHHHHHHHHHhhhccChhhhceeEEecCh--hHHHhhCCccccchhhCCCccccc------CCcchh
Confidence 999999999999999999999999999999999773 559999999999999999888876 455577
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=6.6e-31 Score=237.60 Aligned_cols=157 Identities=33% Similarity=0.583 Sum_probs=130.9
Q ss_pred HHHhhcccccccCCCCCCcEEEEecCccCCccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCC
Q 012611 153 EVLQYYPQGYHGMDKEGRPVYIERLGKVDPNKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQG 232 (460)
Q Consensus 153 ~vlk~~~~~~~G~Dk~GRPVli~rlg~~d~~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G 232 (460)
++++.++.+++|+|++||||++++++++|+..+ +.+++++++++.+|.+++...+ ..+++++++|+|++|
T Consensus 2 ~~~~~~~~~~~g~D~~gr~v~~~~~~~~~~~~~----~~~~~~~~~~~~~E~~~~~~~~------~~~~~~~~~iiD~~g 71 (159)
T PF00650_consen 2 EILKSGPFYLHGRDKDGRPVIYIRLGRFDPKKF----SPEDVIRFFVYLLERMLKRMPE------GGQVEGIVVIIDLSG 71 (159)
T ss_dssp HHHTTSCEEEEEE-TTS-EEEEEEGTT--HHTS-----HHHHHHHHHHHHHHHHHTHHH------TSHHH-EEEEEE-TT
T ss_pred HHHCCeeEEECCCCCCcCEEEEEEcccCCCCcC----CHHHHHHHHHHHHHHHHhhhcc------cccceeEEEEEeCCC
Confidence 467889999999999999999999999999863 6889999999999999874321 357899999999999
Q ss_pred CCccCCChHHHHHHHHHHHHhhhcCCcccceEEEEecChHHHHHHHHHhhccChhhhcceEEcCC-cchHHHHhhcCCCC
Q 012611 233 VGFKSLTKSARELIMQVQKIDSDNYPETLCRMFIINAGQGFKLLWNSVRRFLDPKTTSKIHVLGN-KYQSKLLEIIDASE 311 (460)
Q Consensus 233 ~sl~~~~~~~~~~ik~i~~ilq~~YPerL~~i~IINaP~~f~~lw~ivKpFLd~kt~~KI~~l~~-~~~~~L~e~Id~~~ 311 (460)
++++++.....++++.+++++|++||++++++||||+|++|+++|+++++||+++|++||+++++ ++.+.|.++||+++
T Consensus 72 ~~~~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~ 151 (159)
T PF00650_consen 72 FSLSNFDWWPISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQ 151 (159)
T ss_dssp --HHHHHCHHHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGG
T ss_pred ceEeccccchhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhH
Confidence 99998875558999999999999999999999999999999999999999999999999999965 45578999999999
Q ss_pred CccccCCC
Q 012611 312 LPEFLGGS 319 (460)
Q Consensus 312 LP~eyGGt 319 (460)
||.+|||+
T Consensus 152 lP~~~GG~ 159 (159)
T PF00650_consen 152 LPVEYGGT 159 (159)
T ss_dssp SBGGGTSS
T ss_pred CchhcCCC
Confidence 99999997
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=3e-28 Score=219.96 Aligned_cols=154 Identities=38% Similarity=0.645 Sum_probs=138.6
Q ss_pred HHhhcccccccCCCCCCcEEEEecCccCCccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCC
Q 012611 154 VLQYYPQGYHGMDKEGRPVYIERLGKVDPNKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGV 233 (460)
Q Consensus 154 vlk~~~~~~~G~Dk~GRPVli~rlg~~d~~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~ 233 (460)
...+.+.++ |+|++||||++++++++++.. .+.+++++++++.+|.++... ....++.++++|+|++|+
T Consensus 5 ~~~~~~~~~-g~D~~GrpV~~~~~~~~~~~~----~~~~~~~~~~~~~~e~~~~~~------~~~~~~~~~~~i~D~~~~ 73 (158)
T smart00516 5 GKAYIPGGR-GYDKDGRPVLIFRAGRFDLKS----VTLEELLRYLVYVLEKILQRE------KKTGGIEGFTVIFDLKGL 73 (158)
T ss_pred HHHhcCCCC-CCCCCcCEEEEEeccccccCc----CCHHHHHHHHHHHHHHHHHHH------hcCCCeeeEEEEEECCCC
Confidence 344566666 999999999999999998765 489999999999999988641 135678999999999999
Q ss_pred CccCCChHHHHHHHHHHHHhhhcCCcccceEEEEecChHHHHHHHHHhhccChhhhcceEEcCCcchHHHHhhcCCCCCc
Q 012611 234 GFKSLTKSARELIMQVQKIDSDNYPETLCRMFIINAGQGFKLLWNSVRRFLDPKTTSKIHVLGNKYQSKLLEIIDASELP 313 (460)
Q Consensus 234 sl~~~~~~~~~~ik~i~~ilq~~YPerL~~i~IINaP~~f~~lw~ivKpFLd~kt~~KI~~l~~~~~~~L~e~Id~~~LP 313 (460)
++++++ .+.++.++++++++||++++++||||+|++++++|+++++||++++++||+++++++.+.|.++||+++||
T Consensus 74 ~~~~~~---~~~lk~~~~~~~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~L~~~i~~~~lP 150 (158)
T smart00516 74 SMSNPD---LSVLRKILKILQDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGNDSKEELLEYIDPEQLP 150 (158)
T ss_pred Cccccc---HHHHHHHHHHHHHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCCCHHHHHhhCCHhhCc
Confidence 999865 78999999999999999999999999999999999999999999999999999986678999999999999
Q ss_pred cccCCCCC
Q 012611 314 EFLGGSCN 321 (460)
Q Consensus 314 ~eyGGt~~ 321 (460)
.+|||++.
T Consensus 151 ~~~GG~~~ 158 (158)
T smart00516 151 EELGGTLD 158 (158)
T ss_pred HhhCCCCC
Confidence 99999974
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=99.93 E-value=2.8e-25 Score=197.93 Aligned_cols=146 Identities=39% Similarity=0.605 Sum_probs=129.6
Q ss_pred ccccCCCCCCcEEEEecCccCCccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCCCccCCCh
Q 012611 161 GYHGMDKEGRPVYIERLGKVDPNKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGVGFKSLTK 240 (460)
Q Consensus 161 ~~~G~Dk~GRPVli~rlg~~d~~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~sl~~~~~ 240 (460)
+..|+|++||||+++++++.++.... ..+++++++++.+|.++.... ....++++|+|++|++++++.
T Consensus 12 ~~~~~D~~gr~V~~~~~~~~~~~~~~---~~~~~~~~~~~~~e~~~~~~~--------~~~~~~~~i~D~~~~~~~~~~- 79 (157)
T cd00170 12 YLGGRDKEGRPVLIIRAGNKDLSKSL---DSEELLRYLVYTLEKLLQEDD--------EQVEGFVVIIDLKGLSLSHLL- 79 (157)
T ss_pred ccCCCCCCcCEEEEEecCCcchhhcC---CHHHHHHHHHHHHHHHHhhhh--------hcccceEEEEECCCCChhccc-
Confidence 34457999999999999976665432 448999999999999887532 223799999999999999987
Q ss_pred HHHHHHHHHHHHhhhcCCcccceEEEEecChHHHHHHHHHhhccChhhhcceEEcCCcchHHHHhhcCCCCCccccCCC
Q 012611 241 SARELIMQVQKIDSDNYPETLCRMFIINAGQGFKLLWNSVRRFLDPKTTSKIHVLGNKYQSKLLEIIDASELPEFLGGS 319 (460)
Q Consensus 241 ~~~~~ik~i~~ilq~~YPerL~~i~IINaP~~f~~lw~ivKpFLd~kt~~KI~~l~~~~~~~L~e~Id~~~LP~eyGGt 319 (460)
...+.++.++++++++||++++++||||+|++|+.+|+++++|+++++++||++++++ .+.|.++||+++||.+|||+
T Consensus 80 ~~~~~~k~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~-~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 80 PDPSLLKKILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD-KEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred hhHHHHHHHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC-HHHHHhhCChhhCcHhhCCC
Confidence 6689999999999999999999999999999999999999999999999999999876 68999999999999999996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.47 E-value=1.5e-14 Score=130.36 Aligned_cols=140 Identities=24% Similarity=0.361 Sum_probs=96.0
Q ss_pred ccccCCCCCCcEEEEecCccCCccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCCCccCCCh
Q 012611 161 GYHGMDKEGRPVYIERLGKVDPNKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGVGFKSLTK 240 (460)
Q Consensus 161 ~~~G~Dk~GRPVli~rlg~~d~~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~sl~~~~~ 240 (460)
+..|+|++||||+++...++ ++. .+.+.++.|++..+.... ...++++|+|+.|.+..+-.
T Consensus 5 ~~gG~d~~g~pV~~~~~~~~-~~~----~~~~~ll~yl~~~l~~~~-------------~~~~f~vVid~~~~~~~~~~- 65 (149)
T PF13716_consen 5 YPGGRDREGRPVVVFIASRL-PSS----DDLERLLLYLLSTLSEEV-------------VDKPFSVVIDHTGFSRSSEP- 65 (149)
T ss_dssp EEEEEBTTS-EEEEEEGGG--C-T----THHHHHHHHHHHHH-TTT-------------TTS-EEEEEE-TT--GGG---
T ss_pred EecccCCCcCEEEEEECCcC-cch----hhHHHHHHHHHHhhhHHh-------------cCCCEEEEEEcCCCccccCC-
Confidence 34689999999999998887 432 257777777766652211 12569999999999875432
Q ss_pred HHHHHHHHHHHHhhhcCCcccceEEEEecChHHHHHH-HHHhhccChhh-hcceEEcCCcchHHHHhhcCCCCCccccCC
Q 012611 241 SARELIMQVQKIDSDNYPETLCRMFIINAGQGFKLLW-NSVRRFLDPKT-TSKIHVLGNKYQSKLLEIIDASELPEFLGG 318 (460)
Q Consensus 241 ~~~~~ik~i~~ilq~~YPerL~~i~IINaP~~f~~lw-~ivKpFLd~kt-~~KI~~l~~~~~~~L~e~Id~~~LP~eyGG 318 (460)
....++++.+.+...|+..|+++||||++++++.++ .+.+++++.+. ..||.++.+ .++|.++||+++||+.+||
T Consensus 66 -~~~~l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s--l~~L~~~i~~~qL~~~lp~ 142 (149)
T PF13716_consen 66 -SLSWLKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS--LSELSKHIDPSQLPESLPG 142 (149)
T ss_dssp --HHHHHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS--TCGGGGTSGGGG------H
T ss_pred -chHHHHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC--HHHHHhhCCHHHhcccCCC
Confidence 367899999999999999999999999999999999 66677778888 899999876 6899999999999999998
Q ss_pred CCCC
Q 012611 319 SCNC 322 (460)
Q Consensus 319 t~~~ 322 (460)
+...
T Consensus 143 ~~~~ 146 (149)
T PF13716_consen 143 VLQY 146 (149)
T ss_dssp HH--
T ss_pred EEec
Confidence 8765
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=98.76 E-value=1.3e-08 Score=76.70 Aligned_cols=47 Identities=36% Similarity=0.525 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHhC--------CCCCCCCCcHHHHHHHHHhcCCCHHHHHHHHHHH
Q 012611 83 LHAVDAFRRVLISE--------ELLPARHDHYHMLLRFLKARKFDIAKATQMWADM 130 (460)
Q Consensus 83 ~~~V~~lR~~L~~~--------~~LP~~~dD~~~LLRFLrArkfDvekA~k~L~~~ 130 (460)
+++|++|++.|... ......++| .+||||||||+||+++|.+||.++
T Consensus 1 k~~l~~l~~~l~~~~~~~~~~~~~~~~~~~d-~~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 1 KQKLKQLREHLSELDEKAPGLWDDEKEDHDD-NFLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp HHHHHHHHHHHHH--GGGTHHHTTHTSS-SH-HHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhccchhcccccccCCCCH-HHHHHHHHHccCCHHHHHHHHHhC
Confidence 47899999999863 344566777 599999999999999999999875
No 8
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.27 E-value=4e-06 Score=85.96 Aligned_cols=126 Identities=19% Similarity=0.270 Sum_probs=98.1
Q ss_pred CCCCCCcEEEEecCccCCccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCCCccCCChHHHH
Q 012611 165 MDKEGRPVYIERLGKVDPNKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGVGFKSLTKSARE 244 (460)
Q Consensus 165 ~Dk~GRPVli~rlg~~d~~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~sl~~~~~~~~~ 244 (460)
.|++||+|+++-..++.+..-. .-.++++|.++.++..++. .+++++=-.|+...+.. .+.
T Consensus 89 ~D~~gr~iivv~a~rlp~~~el---d~~~li~~~v~~id~~Ve~--------------DYt~vYfh~gl~s~nkp--~l~ 149 (467)
T KOG4406|consen 89 KDKQGRKIIVVYACRLPSSSEL---DDIRLISYLVYTIDKYVEN--------------DYTLVYFHHGLPSDNKP--YLQ 149 (467)
T ss_pred ccccCCeeEEEEEecCCchhhh---hhHHHHHHHHHHHHHHHhc--------------cceeeehhcCCcccccc--hHH
Confidence 6999999999999888776421 2334899999999998873 26666656666665544 355
Q ss_pred HHHHHHHHhhhcCCcccceEEEEecChHHHHHHHHHhhccChhhhcceEEcCCcchHHHHhhcCCCC
Q 012611 245 LIMQVQKIDSDNYPETLCRMFIINAGQGFKLLWNSVRRFLDPKTTSKIHVLGNKYQSKLLEIIDASE 311 (460)
Q Consensus 245 ~ik~i~~ilq~~YPerL~~i~IINaP~~f~~lw~ivKpFLd~kt~~KI~~l~~~~~~~L~e~Id~~~ 311 (460)
++....+-+-.+|---++.+|+|.+-|+.+++|+++|||++.|...||+-+. +.++|.++|.-++
T Consensus 150 ~l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n--~lseL~~~l~l~r 214 (467)
T KOG4406|consen 150 LLFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFN--SLSELFEALKLNR 214 (467)
T ss_pred HHHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEee--hHHHHHHhhhhhh
Confidence 5555555555678899999999999999999999999999999999999884 4788888876443
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=74.81 E-value=10 Score=26.77 Aligned_cols=36 Identities=17% Similarity=0.418 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHhcCCCHHHHHHHHH
Q 012611 84 HAVDAFRRVLISEELLPARHDHYHMLLRFLKARKFDIAKATQMWA 128 (460)
Q Consensus 84 ~~V~~lR~~L~~~~~LP~~~dD~~~LLRFLrArkfDvekA~k~L~ 128 (460)
+.|.+|.+..-. ++ .....||.+++||++.|...+-
T Consensus 2 e~i~~F~~iTg~--------~~-~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 2 EKIAQFMSITGA--------DE-DVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp HHHHHHHHHH-S--------SH-HHHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHHHCc--------CH-HHHHHHHHHcCCCHHHHHHHHH
Confidence 578888877621 33 4689999999999999988764
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=65.00 E-value=21 Score=24.89 Aligned_cols=38 Identities=18% Similarity=0.330 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHhcCCCHHHHHHHHHH
Q 012611 84 HAVDAFRRVLISEELLPARHDHYHMLLRFLKARKFDIAKATQMWAD 129 (460)
Q Consensus 84 ~~V~~lR~~L~~~~~LP~~~dD~~~LLRFLrArkfDvekA~k~L~~ 129 (460)
+.|++|++.. |. .+. ..+..-|.++++|++.|..+|-+
T Consensus 3 ~~v~~L~~mF------P~-~~~-~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMF------PD-LDR-EVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHS------SS-S-H-HHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHC------CC-CCH-HHHHHHHHHcCCCHHHHHHHHHc
Confidence 4566666655 32 344 47889999999999999998864
No 11
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=55.18 E-value=34 Score=23.88 Aligned_cols=38 Identities=13% Similarity=0.292 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHhcCCCHHHHHHHHHH
Q 012611 84 HAVDAFRRVLISEELLPARHDHYHMLLRFLKARKFDIAKATQMWAD 129 (460)
Q Consensus 84 ~~V~~lR~~L~~~~~LP~~~dD~~~LLRFLrArkfDvekA~k~L~~ 129 (460)
+.+++|++.. |. .++ ..+.+.|+++++|++.|.+.|.+
T Consensus 4 ~~v~~L~~mF------P~-l~~-~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 4 EALHDLKDMF------PN-LDE-EVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred HHHHHHHHHC------CC-CCH-HHHHHHHHHcCCCHHHHHHHHHc
Confidence 4566666654 33 344 36889999999999999988753
No 12
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=39.77 E-value=2.2e+02 Score=30.37 Aligned_cols=89 Identities=21% Similarity=0.327 Sum_probs=65.2
Q ss_pred CCCCcEEEEecCccCCccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCCCccCCCh------
Q 012611 167 KEGRPVYIERLGKVDPNKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGVGFKSLTK------ 240 (460)
Q Consensus 167 k~GRPVli~rlg~~d~~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~sl~~~~~------ 240 (460)
....|++++-.|--.- +.+.|+++++....+ + .=-++|++-.|++-..+..
T Consensus 122 ~~~~P~vvilpGltg~-------S~~~YVr~lv~~a~~-------------~---G~r~VVfN~RG~~g~~LtTpr~f~a 178 (409)
T KOG1838|consen 122 DGTDPIVVILPGLTGG-------SHESYVRHLVHEAQR-------------K---GYRVVVFNHRGLGGSKLTTPRLFTA 178 (409)
T ss_pred CCCCcEEEEecCCCCC-------ChhHHHHHHHHHHHh-------------C---CcEEEEECCCCCCCCccCCCceeec
Confidence 4566999999886432 577899988754422 1 1357788998876655531
Q ss_pred HHHHHHHHHHHHhhhcCCcccceEEEEecChHHHHHHHHH
Q 012611 241 SARELIMQVQKIDSDNYPETLCRMFIINAGQGFKLLWNSV 280 (460)
Q Consensus 241 ~~~~~ik~i~~ilq~~YPerL~~i~IINaP~~f~~lw~iv 280 (460)
-...-++.+++.+...||.+ +++.+-.+.+-+++||-+
T Consensus 179 g~t~Dl~~~v~~i~~~~P~a--~l~avG~S~Gg~iL~nYL 216 (409)
T KOG1838|consen 179 GWTEDLREVVNHIKKRYPQA--PLFAVGFSMGGNILTNYL 216 (409)
T ss_pred CCHHHHHHHHHHHHHhCCCC--ceEEEEecchHHHHHHHh
Confidence 12466888899999999998 899999999999998843
No 13
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=38.95 E-value=38 Score=30.53 Aligned_cols=76 Identities=14% Similarity=0.189 Sum_probs=40.3
Q ss_pred cccccchhhccCCCcccccc-cccccCCCCHHHHHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHhcCCCHHHHHHHHHH
Q 012611 51 SSKLKPSFKKKSRRKSVERV-PVSIEDVRNVEELHAVDAFRRVLISEELLPARHDHYHMLLRFLKARKFDIAKATQMWAD 129 (460)
Q Consensus 51 s~~~~~~~~k~~~r~~~~~~-~~~ied~~~~~E~~~V~~lR~~L~~~~~LP~~~dD~~~LLRFLrArkfDvekA~k~L~~ 129 (460)
..++++.|++||- ...+ .-.++++.+++++.+...+..........+. ..-.-+.+||..++|+.+.+.+.|..
T Consensus 78 ~~~I~~~L~~kGi---~~~~I~~~l~~~~~d~~e~a~~~~~k~~~~~~~~~~--~~k~Ki~~~L~rkGF~~~~I~~~l~~ 152 (157)
T PRK00117 78 PRRIRQELRQKGV---DREIIEEALAELDIDWEELARELARKKFRRPLPDDA--KEKAKLVRFLARRGFSMDVIQRVLRN 152 (157)
T ss_pred HHHHHHHHHHcCC---CHHHHHHHHHHcCccHHHHHHHHHHHHcCCCCCCCH--HHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 3457788888874 2222 3445555422222222222222211111100 11246899999999999988877766
Q ss_pred HH
Q 012611 130 MI 131 (460)
Q Consensus 130 ~l 131 (460)
.+
T Consensus 153 ~~ 154 (157)
T PRK00117 153 AL 154 (157)
T ss_pred hh
Confidence 43
No 14
>PRK14136 recX recombination regulator RecX; Provisional
Probab=38.89 E-value=21 Score=36.25 Aligned_cols=23 Identities=30% Similarity=0.349 Sum_probs=19.2
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHH
Q 012611 107 HMLLRFLKARKFDIAKATQMWAD 129 (460)
Q Consensus 107 ~~LLRFLrArkfDvekA~k~L~~ 129 (460)
.-+.|||..+.|+.+...+.|..
T Consensus 279 ~K~iRfL~rRGFS~D~I~~vLk~ 301 (309)
T PRK14136 279 AKQARFLAARGFSSATIVKLLKV 301 (309)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHh
Confidence 56899999999999988777753
No 15
>COG4479 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.02 E-value=99 Score=24.60 Aligned_cols=54 Identities=11% Similarity=0.414 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHhc---CCCHHHHHHHHHHHHHHH
Q 012611 81 EELHAVDAFRRVLISEELLPARHDHYHMLLRFLKAR---KFDIAKATQMWADMIQWR 134 (460)
Q Consensus 81 ~E~~~V~~lR~~L~~~~~LP~~~dD~~~LLRFLrAr---kfDvekA~k~L~~~l~WR 134 (460)
.....+.+|-+..-.....|...+|++.+-+||... -|+...--..|++|+.|-
T Consensus 16 k~~d~~~~lAn~af~D~sFPK~t~Df~~is~YLE~~a~f~~~m~~FDeiwe~Yle~~ 72 (74)
T COG4479 16 KSKDDKTELANLAFDDHSFPKHTDDFHEISDYLETNADFLFNMSVFDEIWEEYLEHL 72 (74)
T ss_pred CCCChHHHHHHHHhhcccCCCCCccHHHHHHHHHhcCCcccchhhHHHHHHHHHHHh
Confidence 334555666677767777899999999999999865 356666667788888774
No 16
>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=34.29 E-value=1.4e+02 Score=23.04 Aligned_cols=39 Identities=18% Similarity=0.259 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHhcCCCHHHHHHHHHH
Q 012611 83 LHAVDAFRRVLISEELLPARHDHYHMLLRFLKARKFDIAKATQMWAD 129 (460)
Q Consensus 83 ~~~V~~lR~~L~~~~~LP~~~dD~~~LLRFLrArkfDvekA~k~L~~ 129 (460)
.+.|+.+++.. ..|.|. -+...|+-|+.|+..|.++|..
T Consensus 6 rk~VQ~iKEiv-------~~hse~-eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 6 RKTVQSIKEIV-------GCHSEE-EIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred HHHHHHHHHHh-------cCCCHH-HHHHHHHHhCCCHHHHHHHHHh
Confidence 45666777765 336674 5889999999999999999854
No 17
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=28.27 E-value=1.2e+02 Score=28.43 Aligned_cols=32 Identities=19% Similarity=0.282 Sum_probs=24.4
Q ss_pred CCCCCCcHHHHHHHHHhcCCCHHHHHHHHHHH
Q 012611 99 LPARHDHYHMLLRFLKARKFDIAKATQMWADM 130 (460)
Q Consensus 99 LP~~~dD~~~LLRFLrArkfDvekA~k~L~~~ 130 (460)
+|....+.+-+.|||..++|+.+.+...|...
T Consensus 133 ~~~~~~~k~Ki~r~L~~rGFs~~~i~~~l~~~ 164 (174)
T COG2137 133 KPPDKKEKAKIQRFLLRRGFSYEVIKEALNEA 164 (174)
T ss_pred cCcchhHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 44444555789999999999999887777553
No 18
>PRK14137 recX recombination regulator RecX; Provisional
Probab=26.02 E-value=1.4e+02 Score=28.37 Aligned_cols=27 Identities=19% Similarity=0.105 Sum_probs=22.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 012611 107 HMLLRFLKARKFDIAKATQMWADMIQW 133 (460)
Q Consensus 107 ~~LLRFLrArkfDvekA~k~L~~~l~W 133 (460)
.-+.+||..++|+.+.+...|...+.-
T Consensus 156 ~K~~~~L~rRGFs~~~I~~al~~~~~~ 182 (195)
T PRK14137 156 ASAYAFLARRGFSGAVIWPAIREVAAL 182 (195)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHh
Confidence 468999999999999998888875543
No 19
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=25.68 E-value=7e+02 Score=25.11 Aligned_cols=44 Identities=20% Similarity=0.295 Sum_probs=29.8
Q ss_pred hCCcCceEEEEeCCCCCccCCChHHHHHHHHHHHHhhhcCCcccc
Q 012611 218 KRHIDSSTTILDVQGVGFKSLTKSARELIMQVQKIDSDNYPETLC 262 (460)
Q Consensus 218 ~~~i~~~tiIiD~~G~sl~~~~~~~~~~ik~i~~ilq~~YPerL~ 262 (460)
...+...-+|+|- |+|+..-......+++.+-.+-.-.||-.++
T Consensus 174 ~~GI~~~~IilDP-GiGF~k~~~~n~~ll~~l~~l~~lg~Pilvg 217 (282)
T PRK11613 174 AAGIAKEKLLLDP-GFGFGKNLSHNYQLLARLAEFHHFNLPLLVG 217 (282)
T ss_pred HcCCChhhEEEeC-CCCcCCCHHHHHHHHHHHHHHHhCCCCEEEE
Confidence 3456666889999 6777543345677888887766667776544
No 20
>PRK09261 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated
Probab=23.38 E-value=4.9e+02 Score=27.13 Aligned_cols=67 Identities=18% Similarity=0.277 Sum_probs=39.9
Q ss_pred cccccccCCCCCCcEEEEecCccCCccccccc-cHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCCCc
Q 012611 158 YPQGYHGMDKEGRPVYIERLGKVDPNKLTQVT-TMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGVGF 235 (460)
Q Consensus 158 ~~~~~~G~Dk~GRPVli~rlg~~d~~~l~~~~-s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~sl 235 (460)
.+|.+.|.|++|++.++.-.|+-|..-.++-. +...|-+..+......+. +... ..-+|+|++.-+-
T Consensus 205 ~~H~fl~~~~~G~~~~i~t~GN~~~hlilRGg~~~pNy~~~~i~~~~~~l~----------k~~l-~~~v~VD~SH~ns 272 (349)
T PRK09261 205 APHHFLGITKDGRSAIVSTTGNPDCHVILRGGNKGPNYDAESVAEAKERLE----------KAGL-PPRIMIDCSHANS 272 (349)
T ss_pred CCceeeecCCCCcEEEEECCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHH----------HcCC-CCCEEEECCCccc
Confidence 47778899999999999988887765443322 233333333333222222 1112 4678999987543
No 21
>TIGR00034 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase.
Probab=23.36 E-value=1.6e+02 Score=30.66 Aligned_cols=68 Identities=15% Similarity=0.185 Sum_probs=40.3
Q ss_pred hcccccccCCCCCCcEEEEecCccCCccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCCCc
Q 012611 157 YYPQGYHGMDKEGRPVYIERLGKVDPNKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGVGF 235 (460)
Q Consensus 157 ~~~~~~~G~Dk~GRPVli~rlg~~d~~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~sl 235 (460)
..+|++.|.+++|++.++.-.|+-|.--..+-.....|-+..+......++ ..+.. -.+|+|++.-+-
T Consensus 199 ~~~H~fl~~~~~G~~~~i~t~GN~~~hlilRGg~~pNy~~~di~~~~~~l~----------~~~lp-~~vmVD~SH~ns 266 (344)
T TIGR00034 199 AAPHYFLSVTKDGQMAIVQTSGNPDGHIILRGGKKPNYSAADVAAAKKQLE----------KAGLP-PHLMIDFSHGNS 266 (344)
T ss_pred hCCceeeecCCCCcEEEEECCCCCCEEEEecCCCCCCCCHHHHHHHHHHHH----------HcCCC-CeEEEeCCCccc
Confidence 468889999999999999988887654333321113333333333333222 12222 458999987543
No 22
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=23.27 E-value=1.4e+02 Score=31.09 Aligned_cols=18 Identities=33% Similarity=0.779 Sum_probs=16.2
Q ss_pred HHHHHHHHhcCCCHHHHH
Q 012611 107 HMLLRFLKARKFDIAKAT 124 (460)
Q Consensus 107 ~~LLRFLrArkfDvekA~ 124 (460)
..|+|-|.+++|||++|.
T Consensus 145 NillkLlqaadydV~rAe 162 (408)
T COG1219 145 NILLKLLQAADYDVERAE 162 (408)
T ss_pred HHHHHHHHHcccCHHHHh
Confidence 579999999999999884
No 23
>PF04378 RsmJ: Ribosomal RNA small subunit methyltransferase D, RsmJ; InterPro: IPR007473 This is a bacterial protein of unknown function, possibly secreted.; PDB: 2OO3_A.
Probab=22.09 E-value=54 Score=32.40 Aligned_cols=26 Identities=19% Similarity=0.211 Sum_probs=18.0
Q ss_pred ceEEEEecChHHHHHHHHHhhccChh
Q 012611 262 CRMFIINAGQGFKLLWNSVRRFLDPK 287 (460)
Q Consensus 262 ~~i~IINaP~~f~~lw~ivKpFLd~k 287 (460)
..|+|||+||.+.-...-+-++|.+.
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 46999999999987777666665543
No 24
>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=21.94 E-value=1.9e+02 Score=25.36 Aligned_cols=43 Identities=19% Similarity=0.380 Sum_probs=34.4
Q ss_pred eEEEEecChHHHHHHHHH-----hhccChhhhcceEEcCCcchHHHHhhc
Q 012611 263 RMFIINAGQGFKLLWNSV-----RRFLDPKTTSKIHVLGNKYQSKLLEII 307 (460)
Q Consensus 263 ~i~IINaP~~f~~lw~iv-----KpFLd~kt~~KI~~l~~~~~~~L~e~I 307 (460)
.+.++|..-+++-++.++ ..|+++.....++++.+ .+++.++|
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~--~~e~~~~i 133 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDD--PEEALEYI 133 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESS--HHHHHHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCC--HHHHHhhC
Confidence 699999876777777776 58999999999999866 46776654
No 25
>PRK12822 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional
Probab=21.24 E-value=3.2e+02 Score=28.54 Aligned_cols=67 Identities=12% Similarity=0.003 Sum_probs=40.3
Q ss_pred cccccccCCCCCCcEEEEecCccCCccccccccHHHHHHHHHHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCCCc
Q 012611 158 YPQGYHGMDKEGRPVYIERLGKVDPNKLTQVTTMDRYLRYHVQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGVGF 235 (460)
Q Consensus 158 ~~~~~~G~Dk~GRPVli~rlg~~d~~~l~~~~s~~~~ir~~v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~sl 235 (460)
.||.+.|.|++|++.++.-.|+-|..-+++-.....|-...+......+. +..+. -.++||++.-+-
T Consensus 205 ~pH~Fl~i~~~G~~aiv~T~GN~~~HvILRGg~~PNY~~~~v~~a~~~l~----------~~~l~-~~vmVDcSH~NS 271 (356)
T PRK12822 205 SPHLVTVPGLTGCISTLLSDGNPHGHIILRGGREPNYGLSDVTKASKLLH----------DEGLN-HRLIIDCSHGNS 271 (356)
T ss_pred CCCeEEecCCCCcEEEEEcCCCCCceEEEeCCCCCCCCHHHHHHHHHHHH----------HCCCC-CcEEEECCCccC
Confidence 57888999999999999999988776555432222222222222222222 11222 458899987654
No 26
>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=20.97 E-value=1.3e+02 Score=19.96 Aligned_cols=21 Identities=14% Similarity=0.199 Sum_probs=18.4
Q ss_pred HHHHHHHHhcCCCHHHHHHHH
Q 012611 107 HMLLRFLKARKFDIAKATQMW 127 (460)
Q Consensus 107 ~~LLRFLrArkfDvekA~k~L 127 (460)
+..++-|+++++|+++|...|
T Consensus 16 ~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 16 EEARKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHHHHHhCCCHHHHHHHH
Confidence 468999999999999998765
No 27
>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=20.68 E-value=5e+02 Score=27.43 Aligned_cols=45 Identities=20% Similarity=0.288 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHhcCCCHHHHHHHHHHH
Q 012611 84 HAVDAFRRVLISEELLPARHDHYHMLLRFLKARKFDIAKATQMWADM 130 (460)
Q Consensus 84 ~~V~~lR~~L~~~~~LP~~~dD~~~LLRFLrArkfDvekA~k~L~~~ 130 (460)
-.+..+-+.|....||+ |..-.-|--||++.+.+++.|.+.|+..
T Consensus 226 ~Cm~~l~~~l~~~~hL~--h~gR~ql~lFLk~iGl~~~e~l~~~~~~ 270 (390)
T cd07322 226 LCMRQLHEALRKNHHLK--HGGRLQLGLFLKGIGLSLEEALKFWRSE 270 (390)
T ss_pred HHHHHHHHHHhcCCCCC--chhHHHHHHHHHhCCCCHHHHHHHHHHh
Confidence 57788888888888885 3333467889999999999999988775
No 28
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=20.67 E-value=2.6e+02 Score=27.50 Aligned_cols=105 Identities=13% Similarity=0.184 Sum_probs=56.2
Q ss_pred HHHHHHHHHhhcchhhhhhhCCcCceEEEEeCCCC-Cc-cCCChHHHHHHHHHHHHhhhcCCcccceEEEEecChHHH--
Q 012611 199 VQEFEKCFAIKFPACSIAAKRHIDSSTTILDVQGV-GF-KSLTKSARELIMQVQKIDSDNYPETLCRMFIINAGQGFK-- 274 (460)
Q Consensus 199 v~~lE~~~~~~~pa~s~~~~~~i~~~tiIiD~~G~-sl-~~~~~~~~~~ik~i~~ilq~~YPerL~~i~IINaP~~f~-- 274 (460)
+++||.++....-. ....+..+.-.+|+|+-|- -+ .|++ ++++++.-++. .=.++..+|++..++++.
T Consensus 76 v~cmEyl~~NldwL--~~~~Gd~eddylifDcPGQIELytH~p-----Vm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~ 147 (273)
T KOG1534|consen 76 VYCMEYLLENLDWL--EEEIGDVEDDYLIFDCPGQIELYTHLP-----VMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDST 147 (273)
T ss_pred hhHHHHHHHHHHHH--HhhccCccCCEEEEeCCCeeEEeecCh-----hHHHHHHHHhc-ccCceeEEEEeccchhhhHH
Confidence 45555554432110 0134678889999999884 22 3443 55566666665 445778888888877543
Q ss_pred ----HHHHHHhhccCh-----hhhcceEEcCCcchHHHHhhcCCCC
Q 012611 275 ----LLWNSVRRFLDP-----KTTSKIHVLGNKYQSKLLEIIDASE 311 (460)
Q Consensus 275 ----~lw~ivKpFLd~-----kt~~KI~~l~~~~~~~L~e~Id~~~ 311 (460)
.++..+..++.= ...+|.-++.+..++.|.++.+++.
T Consensus 148 KfiSG~lsAlsAMi~lE~P~INvlsKMDLlk~~~k~~l~~Fl~~d~ 193 (273)
T KOG1534|consen 148 KFISGCLSALSAMISLEVPHINVLSKMDLLKDKNKKELERFLNPDE 193 (273)
T ss_pred HHHHHHHHHHHHHHHhcCcchhhhhHHHHhhhhhHHHHHHhcCCch
Confidence 333333333221 1233444444433455666665543
No 29
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=20.49 E-value=73 Score=31.72 Aligned_cols=26 Identities=15% Similarity=0.175 Sum_probs=21.1
Q ss_pred ceEEEEecChHHHHHHHHHhhccChh
Q 012611 262 CRMFIINAGQGFKLLWNSVRRFLDPK 287 (460)
Q Consensus 262 ~~i~IINaP~~f~~lw~ivKpFLd~k 287 (460)
..|+|||+||-+.--...+-|||...
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~ 262 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTL 262 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHH
Confidence 47999999999988888887776543
No 30
>PRK14136 recX recombination regulator RecX; Provisional
Probab=20.44 E-value=2.8e+02 Score=28.40 Aligned_cols=58 Identities=21% Similarity=0.225 Sum_probs=36.2
Q ss_pred hhhhhhHHhhhcccccch---hhccCCCcccccccccccCCCCHHHHHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHh
Q 012611 40 MRNLKKKAIKASSKLKPS---FKKKSRRKSVERVPVSIEDVRNVEELHAVDAFRRVLISEELLPARHDHYHMLLRFLKA 115 (460)
Q Consensus 40 ~~~~~~~~~~~s~~~~~~---~~k~~~r~~~~~~~~~ied~~~~~E~~~V~~lR~~L~~~~~LP~~~dD~~~LLRFLrA 115 (460)
..+|+.+|++.=++=.|| |+.|-+++- .+.+.|++.-+.|..+.+| ||..+.-.|++.
T Consensus 161 ~~~lk~kAL~lLSrReRSe~ELr~KL~kkG--------------~~ee~IE~VIerLke~gYL----DDeRFAesyVr~ 221 (309)
T PRK14136 161 ARSLKGRALGYLSRREYSRAELARKLAPYA--------------DESDSVEPLLDALEREGWL----SDARFAESLVHR 221 (309)
T ss_pred HHHHHHHHHHHhhcccccHHHHHHHHHHcC--------------CCHHHHHHHHHHHHHcCCc----CHHHHHHHHHHH
Confidence 568999999776665555 233322221 1235677777777777665 776666667655
Done!