Query 020204
Match_columns 329
No_of_seqs 232 out of 1284
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 07:52:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020204.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020204hhsearch_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 7.2E-40 1.6E-44 304.3 19.3 213 33-253 42-260 (317)
2 KOG1470 Phosphatidylinositol t 100.0 3E-39 6.6E-44 290.1 18.8 197 34-250 47-243 (324)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 2.6E-30 5.6E-35 216.1 10.4 154 86-249 3-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 4E-28 8.7E-33 202.6 14.3 149 90-250 9-157 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 1.9E-24 4.1E-29 179.0 12.5 141 93-242 12-154 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.6 4.2E-15 9.2E-20 123.0 5.9 141 92-252 4-146 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 99.0 8.3E-10 1.8E-14 75.2 6.6 54 6-60 1-55 (55)
8 KOG4406 CDC42 Rho GTPase-activ 98.2 7.2E-06 1.6E-10 76.2 9.1 126 97-238 89-215 (467)
9 PF02845 CUE: CUE domain; Int 88.0 1.7 3.6E-05 27.3 4.9 28 32-59 13-40 (42)
10 PF14555 UBA_4: UBA-like domai 87.9 1.9 4.1E-05 27.3 5.0 25 34-58 13-37 (43)
11 smart00546 CUE Domain that may 80.3 3.4 7.4E-05 25.9 3.8 27 32-58 14-40 (43)
12 PF00627 UBA: UBA/TS-N domain; 77.6 4 8.6E-05 24.7 3.4 25 33-57 13-37 (37)
13 smart00165 UBA Ubiquitin assoc 74.4 5.3 0.00012 24.0 3.3 26 32-57 11-36 (37)
14 cd00194 UBA Ubiquitin Associat 73.2 6 0.00013 23.9 3.3 27 32-58 11-37 (38)
15 PF08938 HBS1_N: HBS1 N-termin 45.4 18 0.00038 26.2 2.1 25 35-59 45-69 (79)
16 TIGR02364 dha_pts dihydroxyace 44.8 50 0.0011 26.2 4.8 50 150-209 60-109 (125)
17 PF03474 DMA: DMRTA motif; In 43.0 46 0.001 20.6 3.3 24 34-57 15-38 (39)
18 smart00804 TAP_C C-terminal do 41.9 48 0.001 22.9 3.8 27 33-59 24-50 (63)
19 PRK09377 tsf elongation factor 40.2 59 0.0013 29.9 5.1 43 1-59 1-43 (290)
20 COG2938 Uncharacterized conser 40.0 49 0.0011 24.9 3.8 43 3-45 43-87 (94)
21 TIGR00116 tsf translation elon 36.5 72 0.0016 29.3 5.1 40 4-59 3-42 (290)
22 COG0264 Tsf Translation elonga 30.2 1.1E+02 0.0023 28.1 5.1 43 1-59 1-43 (296)
23 PF04378 RsmJ: Ribosomal RNA s 27.7 39 0.00085 30.2 1.8 29 188-216 206-234 (245)
24 COG2961 ComJ Protein involved 27.3 43 0.00093 30.0 2.0 27 188-214 237-263 (279)
25 KOG1534 Putative transcription 26.7 74 0.0016 28.0 3.2 86 148-237 95-193 (273)
26 PRK12332 tsf elongation factor 26.6 1.4E+02 0.003 25.8 5.0 40 4-59 3-42 (198)
27 PF03943 TAP_C: TAP C-terminal 26.0 39 0.00086 22.2 1.2 27 33-59 12-38 (51)
28 PF06972 DUF1296: Protein of u 25.9 1.6E+02 0.0034 20.1 4.0 26 34-59 19-44 (60)
29 PF03641 Lysine_decarbox: Poss 25.7 84 0.0018 25.0 3.3 43 189-233 86-133 (133)
30 CHL00098 tsf elongation factor 24.1 1.5E+02 0.0033 25.5 4.8 38 6-59 2-39 (200)
31 PF07862 Nif11: Nitrogen fixat 21.7 2.2E+02 0.0048 18.1 4.1 44 5-52 2-45 (49)
32 PF02954 HTH_8: Bacterial regu 21.1 1.4E+02 0.0031 18.3 3.0 23 35-57 6-28 (42)
33 cd08318 Death_NMPP84 Death dom 20.2 3.5E+02 0.0076 19.6 6.4 59 2-68 3-61 (86)
No 1
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=7.2e-40 Score=304.34 Aligned_cols=213 Identities=33% Similarity=0.483 Sum_probs=187.7
Q ss_pred CCChHHHHHHhhhcCCCHHHHHHHHHHHHHHHHhCCchhhccCCCCcHHHHHHhhhcccccccccCCCCCcEEEEecCCc
Q 020204 33 GYPTETLVRFLKARDGNVSKAHKMLMDCLHWRAQNEIDKILSKPIVPTELYRAVRDSQLIGMSGYSRESLPVFAVGVGLS 112 (329)
Q Consensus 33 ~~~d~~llRFL~a~~~dv~kA~~~l~~~l~wR~~~~id~i~~~~~~~~~~~~~l~~~~~~~~~g~Dk~G~pV~~~~~~~~ 112 (329)
..+|.+|+||||||+||+++|.+||.+++.||+++++|+++.+.... ..+.++.+.+.+|.|++|+|+++.+.|..
T Consensus 42 ~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~----~~~~~~~~~~~~~~~~~g~~v~~~~~g~~ 117 (317)
T KOG1471|consen 42 YDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEED----DELLKYYPQGLHGVDKEGRPVYIERLGKI 117 (317)
T ss_pred CCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccc----hhhhhhccccccccCCCCCEEEEeccCCC
Confidence 35688999999999999999999999999999999999998651111 22334677899999999999999999987
Q ss_pred Ccc----hhhHHHHHHHHHHHHHHHHhhcchhhhhhcCCCcceEEEEEEcCCCcccccch--HHHHHHHHHhhhccCccc
Q 020204 113 TFD----KASVHCYVQSHIQINEYRDRVILPSASAKHGRPITTCVKVLDMTGLKLSALSQ--IKLLTIISTVDDLNYPEK 186 (329)
Q Consensus 113 ~~~----~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~--~~~~~~i~~~~q~~YPe~ 186 (329)
+.. .....+++++++..+|...+.+++.+.+..+++++|++.|+||+|++++++.. ...++.++.++|+||||+
T Consensus 118 ~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~~q~~yPe~ 197 (317)
T KOG1471|consen 118 DPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKILQDNYPER 197 (317)
T ss_pred CcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHHHHHHHHHHHHHHHHHHhCHHh
Confidence 643 45678899999999999888888877776678999999999999999999854 478999999999999999
Q ss_pred cceEEEEcCChhHHHHHHHhhhcccccccccEEEcCCCChhHHhccCCCCCCCccccCCCCCccccC
Q 020204 187 TNTYYIVNVPYIFSACWKVVKPLLQERTRKKIQVLQGSGRDELLKIMDFESLPHFCRREDSGSSRSS 253 (329)
Q Consensus 187 l~~i~iIN~P~~~~~~~~ivkpfL~~~t~~Ki~~~~~~~~~~L~k~i~~~~LP~~~gge~GG~~~~~ 253 (329)
++++||||+|++|+++|+++||||+++|++||+++++++.++|.++|++++||.+| ||++.+.
T Consensus 198 l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~~~~~~L~k~i~~~~LP~~y----GG~~~~~ 260 (317)
T KOG1471|consen 198 LKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHSKDKESLLKYIPPEVLPEEY----GGTCGDL 260 (317)
T ss_pred hceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCCCchhhhhhhCCHhhCcccc----CCCcccc
Confidence 99999999999999999999999999999999977778999999999999999999 7776653
No 2
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=3e-39 Score=290.06 Aligned_cols=197 Identities=26% Similarity=0.405 Sum_probs=171.6
Q ss_pred CChHHHHHHhhhcCCCHHHHHHHHHHHHHHHHhCCchhhccCCCCcHHHHHHhhhcccccccccCCCCCcEEEEecCCcC
Q 020204 34 YPTETLVRFLKARDGNVSKAHKMLMDCLHWRAQNEIDKILSKPIVPTELYRAVRDSQLIGMSGYSRESLPVFAVGVGLST 113 (329)
Q Consensus 34 ~~d~~llRFL~a~~~dv~kA~~~l~~~l~wR~~~~id~i~~~~~~~~~~~~~l~~~~~~~~~g~Dk~G~pV~~~~~~~~~ 113 (329)
++|++++||||||+||+++|.+||.++|.||+++++... +...++..++. .+.+++.|+|++||||+|+++....
T Consensus 47 ~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~----~~~~Ev~~e~~-tGK~yi~G~D~~gRPVl~~~~~~~~ 121 (324)
T KOG1470|consen 47 CSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEV----IEADEVAAELE-TGKAYILGHDKDGRPVLYLRPRPHR 121 (324)
T ss_pred CcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccc----cCHHHHHHHhh-cCcEEEecccCCCCeEEEEecCCCC
Confidence 689999999999999999999999999999999987662 22345555554 4567888999999999999887766
Q ss_pred cchhhHHHHHHHHHHHHHHHHhhcchhhhhhcCCCcceEEEEEEcCCCcccccchHHHHHHHHHhhhccCccccceEEEE
Q 020204 114 FDKASVHCYVQSHIQINEYRDRVILPSASAKHGRPITTCVKVLDMTGLKLSALSQIKLLTIISTVDDLNYPEKTNTYYIV 193 (329)
Q Consensus 114 ~~~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~~~~~~~i~~~~q~~YPe~l~~i~iI 193 (329)
....+.....+..++++|.+. ..++.+++++++++|++|+++++.+ ++..+.+++++|+||||||+..+++
T Consensus 122 qn~~t~~~~~r~~Vy~mE~Ai--------~~lp~~qe~~~~L~D~~~fs~sN~d-~~~~k~~~~~lq~hYPErLg~a~l~ 192 (324)
T KOG1470|consen 122 QNTKTQKELERLLVYTLENAI--------LFLPPGQEQFVWLFDLTGFSMSNPD-IKFLKELLHILQDHYPERLGKALLV 192 (324)
T ss_pred CCCCCHHHHHHHHHHHHHHHH--------HhCCCCcceEEEEEecccCcccCCC-cHHHHHHHHHHHHhChHHhhhhhhc
Confidence 666778888899999988543 3446677899999999999999987 7899999999999999999999999
Q ss_pred cCChhHHHHHHHhhhcccccccccEEEcCCCChhHHhccCCCCCCCccccCCCCCcc
Q 020204 194 NVPYIFSACWKVVKPLLQERTRKKIQVLQGSGRDELLKIMDFESLPHFCRREDSGSS 250 (329)
Q Consensus 194 N~P~~~~~~~~ivkpfL~~~t~~Ki~~~~~~~~~~L~k~i~~~~LP~~~gge~GG~~ 250 (329)
|+||+|..+|+++||||++.|++||.|... ...|.+|||+++||..+ ||++
T Consensus 193 ~~P~iF~~~wkiikpflDp~t~~Kv~F~~~--~~~l~~~~d~~~l~s~~----GG~~ 243 (324)
T KOG1470|consen 193 NAPWIFQPFWKIIKPFLDPKTASKVKFVEP--KDDLSEYFDESQLPSLF----GGKL 243 (324)
T ss_pred CChHHHHHHHHHhhhccChhhhceeEEecC--hhHHHhhCCccccchhh----CCCc
Confidence 999999999999999999999999999874 56699999999999998 7754
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=2.6e-30 Score=216.06 Aligned_cols=154 Identities=29% Similarity=0.477 Sum_probs=124.8
Q ss_pred hhhcccccccccCCCCCcEEEEecCCcCcchhhHHHHHHHHHHHHHHHHhhcchhhhhhcCCCcceEEEEEEcCCCcccc
Q 020204 86 VRDSQLIGMSGYSRESLPVFAVGVGLSTFDKASVHCYVQSHIQINEYRDRVILPSASAKHGRPITTCVKVLDMTGLKLSA 165 (329)
Q Consensus 86 l~~~~~~~~~g~Dk~G~pV~~~~~~~~~~~~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~ 165 (329)
+.++++.+++|+|++||||++++++++++.+.+.++++++.++++|...+.. +. +.+++++++|+|++|+++++
T Consensus 3 ~~~~~~~~~~g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~-~~-----~~~~~~~~~iiD~~g~~~~~ 76 (159)
T PF00650_consen 3 ILKSGPFYLHGRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRM-PE-----GGQVEGIVVIIDLSGFSLSN 76 (159)
T ss_dssp HHTTSCEEEEEE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTH-HH-----TSHHH-EEEEEE-TT--HHH
T ss_pred HHCCeeEEECCCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhh-cc-----cccceeEEEEEeCCCceEec
Confidence 4567889999999999999999999988887778899999999999876432 11 45678999999999999998
Q ss_pred cch--HHHHHHHHHhhhccCccccceEEEEcCChhHHHHHHHhhhcccccccccEEEcCCCC-hhHHhccCCCCCCCccc
Q 020204 166 LSQ--IKLLTIISTVDDLNYPEKTNTYYIVNVPYIFSACWKVVKPLLQERTRKKIQVLQGSG-RDELLKIMDFESLPHFC 242 (329)
Q Consensus 166 ~~~--~~~~~~i~~~~q~~YPe~l~~i~iIN~P~~~~~~~~ivkpfL~~~t~~Ki~~~~~~~-~~~L~k~i~~~~LP~~~ 242 (329)
++. ++.++.++.++|++||++++++||||+|++++++|++++|||+++|++||+++++.+ .++|.++||+++||.+|
T Consensus 77 ~~~~~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~~ 156 (159)
T PF00650_consen 77 FDWWPISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVEY 156 (159)
T ss_dssp HHCHHHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGGG
T ss_pred cccchhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchhc
Confidence 763 678999999999999999999999999999999999999999999999999996543 47899999999999999
Q ss_pred cCCCCCc
Q 020204 243 RREDSGS 249 (329)
Q Consensus 243 gge~GG~ 249 (329)
||+
T Consensus 157 ----GG~ 159 (159)
T PF00650_consen 157 ----GGT 159 (159)
T ss_dssp ----TSS
T ss_pred ----CCC
Confidence 664
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=4e-28 Score=202.59 Aligned_cols=149 Identities=27% Similarity=0.472 Sum_probs=133.5
Q ss_pred ccccccccCCCCCcEEEEecCCcCcchhhHHHHHHHHHHHHHHHHhhcchhhhhhcCCCcceEEEEEEcCCCcccccchH
Q 020204 90 QLIGMSGYSRESLPVFAVGVGLSTFDKASVHCYVQSHIQINEYRDRVILPSASAKHGRPITTCVKVLDMTGLKLSALSQI 169 (329)
Q Consensus 90 ~~~~~~g~Dk~G~pV~~~~~~~~~~~~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~~ 169 (329)
.+.++ |+|++||||++++++..+++..+.+++++++++.+|.+.+. ...+.+++++++|+|++|+++++++ +
T Consensus 9 ~~~~~-g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~------~~~~~~~~~~~~i~D~~~~~~~~~~-~ 80 (158)
T smart00516 9 IPGGR-GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQR------EKKTGGIEGFTVIFDLKGLSMSNPD-L 80 (158)
T ss_pred cCCCC-CCCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHH------HhcCCCeeeEEEEEECCCCCccccc-H
Confidence 34444 89999999999999998887888999999999999977542 1235577899999999999999965 6
Q ss_pred HHHHHHHHhhhccCccccceEEEEcCChhHHHHHHHhhhcccccccccEEEcCCCChhHHhccCCCCCCCccccCCCCCc
Q 020204 170 KLLTIISTVDDLNYPEKTNTYYIVNVPYIFSACWKVVKPLLQERTRKKIQVLQGSGRDELLKIMDFESLPHFCRREDSGS 249 (329)
Q Consensus 170 ~~~~~i~~~~q~~YPe~l~~i~iIN~P~~~~~~~~ivkpfL~~~t~~Ki~~~~~~~~~~L~k~i~~~~LP~~~gge~GG~ 249 (329)
+.++.++.+++.+||++++++||||+|++++++|+++++||++++++||+++++++.+.|.++||+++||.+| ||+
T Consensus 81 ~~lk~~~~~~~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~L~~~i~~~~lP~~~----GG~ 156 (158)
T smart00516 81 SVLRKILKILQDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGNDSKEELLEYIDPEQLPEEL----GGT 156 (158)
T ss_pred HHHHHHHHHHHHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCCCHHHHHhhCCHhhCcHhh----CCC
Confidence 8899999999999999999999999999999999999999999999999999876789999999999999999 777
Q ss_pred c
Q 020204 250 S 250 (329)
Q Consensus 250 ~ 250 (329)
+
T Consensus 157 ~ 157 (158)
T smart00516 157 L 157 (158)
T ss_pred C
Confidence 5
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=99.92 E-value=1.9e-24 Score=179.02 Aligned_cols=141 Identities=33% Similarity=0.516 Sum_probs=120.3
Q ss_pred cccccCCCCCcEEEEecCCcCcchh-hHHHHHHHHHHHHHHHHhhcchhhhhhcCCCcceEEEEEEcCCCcccccc-hHH
Q 020204 93 GMSGYSRESLPVFAVGVGLSTFDKA-SVHCYVQSHIQINEYRDRVILPSASAKHGRPITTCVKVLDMTGLKLSALS-QIK 170 (329)
Q Consensus 93 ~~~g~Dk~G~pV~~~~~~~~~~~~~-~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~-~~~ 170 (329)
+..|.|++||||++++.+..++... +.++++++.++.+|...+.. ....+++++|+|++|.+++++. .++
T Consensus 12 ~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~--------~~~~~~~~~i~D~~~~~~~~~~~~~~ 83 (157)
T cd00170 12 YLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQED--------DEQVEGFVVIIDLKGLSLSHLLPDPS 83 (157)
T ss_pred ccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhhh--------hhcccceEEEEECCCCChhccchhHH
Confidence 3445699999999999996444332 33788999999999765421 1122589999999999999884 367
Q ss_pred HHHHHHHhhhccCccccceEEEEcCChhHHHHHHHhhhcccccccccEEEcCCCChhHHhccCCCCCCCccc
Q 020204 171 LLTIISTVDDLNYPEKTNTYYIVNVPYIFSACWKVVKPLLQERTRKKIQVLQGSGRDELLKIMDFESLPHFC 242 (329)
Q Consensus 171 ~~~~i~~~~q~~YPe~l~~i~iIN~P~~~~~~~~ivkpfL~~~t~~Ki~~~~~~~~~~L~k~i~~~~LP~~~ 242 (329)
.++.+..+++++||++++++||||+|+++.++|+++++|+++++++||++++++ .++|.+++|+++||.+|
T Consensus 84 ~~k~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~-~~~L~~~i~~~~Lp~~~ 154 (157)
T cd00170 84 LLKKILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD-KEELLKYIDKEQLPEEY 154 (157)
T ss_pred HHHHHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC-HHHHHhhCChhhCcHhh
Confidence 899999999999999999999999999999999999999999999999998754 89999999999999999
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.56 E-value=4.2e-15 Score=122.96 Aligned_cols=141 Identities=18% Similarity=0.218 Sum_probs=95.4
Q ss_pred ccccccCCCCCcEEEEecCCcCcchhhHHHHHHHHHHHHHHHHhhcchhhhhhcCCCcceEEEEEEcCCCcccccchHHH
Q 020204 92 IGMSGYSRESLPVFAVGVGLSTFDKASVHCYVQSHIQINEYRDRVILPSASAKHGRPITTCVKVLDMTGLKLSALSQIKL 171 (329)
Q Consensus 92 ~~~~g~Dk~G~pV~~~~~~~~~~~~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~~~~ 171 (329)
++..|+|++||||+++..... +...+.+.++.+.+..+. +.. ...++++|+|++|.+..+-+....
T Consensus 4 ~~~gG~d~~g~pV~~~~~~~~-~~~~~~~~ll~yl~~~l~-------~~~------~~~~f~vVid~~~~~~~~~~~~~~ 69 (149)
T PF13716_consen 4 FYPGGRDREGRPVVVFIASRL-PSSDDLERLLLYLLSTLS-------EEV------VDKPFSVVIDHTGFSRSSEPSLSW 69 (149)
T ss_dssp -EEEEEBTTS-EEEEEEGGG--C-TTHHHHHHHHHHHHH--------TTT------TTS-EEEEEE-TT--GGG---HHH
T ss_pred EEecccCCCcCEEEEEECCcC-cchhhHHHHHHHHHHhhh-------HHh------cCCCEEEEEEcCCCccccCCchHH
Confidence 355689999999999998776 544466666666554431 111 113699999999998877655778
Q ss_pred HHHHHHhhhccCccccceEEEEcCChhHHHHH-HHhhhcccccc-cccEEEcCCCChhHHhccCCCCCCCccccCCCCCc
Q 020204 172 LTIISTVDDLNYPEKTNTYYIVNVPYIFSACW-KVVKPLLQERT-RKKIQVLQGSGRDELLKIMDFESLPHFCRREDSGS 249 (329)
Q Consensus 172 ~~~i~~~~q~~YPe~l~~i~iIN~P~~~~~~~-~ivkpfL~~~t-~~Ki~~~~~~~~~~L~k~i~~~~LP~~~gge~GG~ 249 (329)
++.+..++...|+..++++||||++++++..+ .+.+++.+.+. ..||.++.+ .++|.++||+++||..+ ||+
T Consensus 70 l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s--l~~L~~~i~~~qL~~~l----p~~ 143 (149)
T PF13716_consen 70 LKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS--LSELSKHIDPSQLPESL----PGV 143 (149)
T ss_dssp HHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS--TCGGGGTSGGGG----------HH
T ss_pred HHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC--HHHHHhhCCHHHhcccC----CCE
Confidence 99999999999999999999999999999999 66677889988 999998874 89999999999999999 677
Q ss_pred ccc
Q 020204 250 SRS 252 (329)
Q Consensus 250 ~~~ 252 (329)
.++
T Consensus 144 ~~~ 146 (149)
T PF13716_consen 144 LQY 146 (149)
T ss_dssp H--
T ss_pred Eec
Confidence 654
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=99.03 E-value=8.3e-10 Score=75.21 Aligned_cols=54 Identities=28% Similarity=0.402 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHhhcChHHHHHH-hhhcCCCChHHHHHHhhhcCCCHHHHHHHHHHH
Q 020204 6 HEAVTQFQALMDQVDEPLKITF-QNIHRGYPTETLVRFLKARDGNVSKAHKMLMDC 60 (329)
Q Consensus 6 ~~~i~~lr~ll~~~~~~l~~~~-~~~~~~~~d~~llRFL~a~~~dv~kA~~~l~~~ 60 (329)
++++++|++.+.+..... ..+ ...+...+|.+|+||||||+||+++|.+||.+|
T Consensus 1 k~~l~~l~~~l~~~~~~~-~~~~~~~~~~~~d~~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 1 KQKLKQLREHLSELDEKA-PGLWDDEKEDHDDNFLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp HHHHHHHHHHHHH--GGG-THHHTTHTSS-SHHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhccch-hcccccccCCCCHHHHHHHHHHccCCHHHHHHHHHhC
Confidence 578999999999875432 111 224566789999999999999999999999875
No 8
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.20 E-value=7.2e-06 Score=76.17 Aligned_cols=126 Identities=15% Similarity=0.195 Sum_probs=94.7
Q ss_pred cCCCCCcEEEEecCCcCcchh-hHHHHHHHHHHHHHHHHhhcchhhhhhcCCCcceEEEEEEcCCCcccccchHHHHHHH
Q 020204 97 YSRESLPVFAVGVGLSTFDKA-SVHCYVQSHIQINEYRDRVILPSASAKHGRPITTCVKVLDMTGLKLSALSQIKLLTII 175 (329)
Q Consensus 97 ~Dk~G~pV~~~~~~~~~~~~~-~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~~~~~~~i 175 (329)
+|+.||+|+.+.+.+....+. .-..++++.++..++..+ . -++.|+=-.|+...+.+.+.++...
T Consensus 89 ~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~Ve--------~------DYt~vYfh~gl~s~nkp~l~~l~~a 154 (467)
T KOG4406|consen 89 KDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVE--------N------DYTLVYFHHGLPSDNKPYLQLLFDA 154 (467)
T ss_pred ccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHh--------c------cceeeehhcCCcccccchHHHHHHH
Confidence 699999999998887644321 222366777766664422 1 2455555567777777767666554
Q ss_pred HHhhhccCccccceEEEEcCChhHHHHHHHhhhcccccccccEEEcCCCChhHHhccCCCCCC
Q 020204 176 STVDDLNYPEKTNTYYIVNVPYIFSACWKVVKPLLQERTRKKIQVLQGSGRDELLKIMDFESL 238 (329)
Q Consensus 176 ~~~~q~~YPe~l~~i~iIN~P~~~~~~~~ivkpfL~~~t~~Ki~~~~~~~~~~L~k~i~~~~L 238 (329)
..-+..+|---++.+|+|.+-|+..++|+.+|||++.+..+||+.+. ..++|.+++.-+.|
T Consensus 155 Yke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n--~lseL~~~l~l~rL 215 (467)
T KOG4406|consen 155 YKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFN--SLSELFEALKLNRL 215 (467)
T ss_pred HHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEee--hHHHHHHhhhhhhh
Confidence 44455589999999999999999999999999999999999999887 49999999876654
No 9
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=88.04 E-value=1.7 Score=27.30 Aligned_cols=28 Identities=25% Similarity=0.408 Sum_probs=23.6
Q ss_pred CCCChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 32 RGYPTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 32 ~~~~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
++++...+.+-|.++++|++.|..+|-.
T Consensus 13 P~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 13 PDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp SSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 4578889999999999999999998754
No 10
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=87.86 E-value=1.9 Score=27.26 Aligned_cols=25 Identities=12% Similarity=0.271 Sum_probs=20.8
Q ss_pred CChHHHHHHhhhcCCCHHHHHHHHH
Q 020204 34 YPTETLVRFLKARDGNVSKAHKMLM 58 (329)
Q Consensus 34 ~~d~~llRFL~a~~~dv~kA~~~l~ 58 (329)
.++.....||.+++||++.|+..+-
T Consensus 13 ~~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 13 ADEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp SSHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred cCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4678889999999999999998754
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=80.31 E-value=3.4 Score=25.95 Aligned_cols=27 Identities=26% Similarity=0.377 Sum_probs=23.4
Q ss_pred CCCChHHHHHHhhhcCCCHHHHHHHHH
Q 020204 32 RGYPTETLVRFLKARDGNVSKAHKMLM 58 (329)
Q Consensus 32 ~~~~d~~llRFL~a~~~dv~kA~~~l~ 58 (329)
++.++..+.+.|+++++|++.|...|.
T Consensus 14 P~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 14 PNLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 346788999999999999999998875
No 12
>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=77.63 E-value=4 Score=24.74 Aligned_cols=25 Identities=36% Similarity=0.535 Sum_probs=21.6
Q ss_pred CCChHHHHHHhhhcCCCHHHHHHHH
Q 020204 33 GYPTETLVRFLKARDGNVSKAHKML 57 (329)
Q Consensus 33 ~~~d~~llRFL~a~~~dv~kA~~~l 57 (329)
|++.....+-|+++++|+++|...|
T Consensus 13 Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 13 GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 6888899999999999999998764
No 13
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=74.38 E-value=5.3 Score=23.98 Aligned_cols=26 Identities=35% Similarity=0.625 Sum_probs=23.0
Q ss_pred CCCChHHHHHHhhhcCCCHHHHHHHH
Q 020204 32 RGYPTETLVRFLKARDGNVSKAHKML 57 (329)
Q Consensus 32 ~~~~d~~llRFL~a~~~dv~kA~~~l 57 (329)
-+++.....+-|+++++|+++|...|
T Consensus 11 mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 11 MGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred cCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 47899999999999999999998764
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=73.18 E-value=6 Score=23.89 Aligned_cols=27 Identities=30% Similarity=0.494 Sum_probs=23.8
Q ss_pred CCCChHHHHHHhhhcCCCHHHHHHHHH
Q 020204 32 RGYPTETLVRFLKARDGNVSKAHKMLM 58 (329)
Q Consensus 32 ~~~~d~~llRFL~a~~~dv~kA~~~l~ 58 (329)
-+++.....+-|+++++|+++|...|.
T Consensus 11 mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 11 MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 478999999999999999999987763
No 15
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=45.36 E-value=18 Score=26.17 Aligned_cols=25 Identities=28% Similarity=0.232 Sum_probs=21.0
Q ss_pred ChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 35 PTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 35 ~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
++..|..=|..+.|||++|+..|.+
T Consensus 45 ~e~~i~eal~~~~fDvekAl~~Ll~ 69 (79)
T PF08938_consen 45 PEEQIKEALWHYYFDVEKALDYLLS 69 (79)
T ss_dssp -CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred CHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 7789999999999999999999876
No 16
>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=44.84 E-value=50 Score=26.17 Aligned_cols=50 Identities=14% Similarity=0.196 Sum_probs=35.0
Q ss_pred ceEEEEEEcCCCcccccchHHHHHHHHHhhhccCccccceEEEEcCChhHHHHHHHhhhc
Q 020204 150 TTCVKVLDMTGLKLSALSQIKLLTIISTVDDLNYPEKTNTYYIVNVPYIFSACWKVVKPL 209 (329)
Q Consensus 150 ~~~v~IiDl~g~~l~~~~~~~~~~~i~~~~q~~YPe~l~~i~iIN~P~~~~~~~~ivkpf 209 (329)
.+++++.|+ |-+..+. ...+.+++ ++....+..+|+|.+..++-..+..-
T Consensus 60 dgVlvl~DL-Ggs~~n~------e~a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~ 109 (125)
T TIGR02364 60 DGVLIFYDL-GSAVMNA------EMAVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQ 109 (125)
T ss_pred CCEEEEEcC-CCcHhHH------HHHHHHhc---cccccEEEEechhHHHHHHHHHHHHc
Confidence 489999999 6555331 11223322 45668899999999999998887653
No 17
>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=42.96 E-value=46 Score=20.64 Aligned_cols=24 Identities=21% Similarity=0.260 Sum_probs=20.3
Q ss_pred CChHHHHHHhhhcCCCHHHHHHHH
Q 020204 34 YPTETLVRFLKARDGNVSKAHKML 57 (329)
Q Consensus 34 ~~d~~llRFL~a~~~dv~kA~~~l 57 (329)
.....|-.-|+.|++|+-+|.+.+
T Consensus 15 ~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 15 QKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CChHHHHHHHHHcCCcHHHHHHHh
Confidence 456788889999999999998864
No 18
>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=41.93 E-value=48 Score=22.88 Aligned_cols=27 Identities=19% Similarity=0.183 Sum_probs=23.9
Q ss_pred CCChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 33 GYPTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 33 ~~~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
+.+-.+-.++|...+||.+.|.+.+.+
T Consensus 24 gmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 24 GMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 467789999999999999999999775
No 19
>PRK09377 tsf elongation factor Ts; Provisional
Probab=40.22 E-value=59 Score=29.85 Aligned_cols=43 Identities=19% Similarity=0.245 Sum_probs=33.3
Q ss_pred CCcchHHHHHHHHHHHhhcChHHHHHHhhhcCCCChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 1 MVTVSHEAVTQFQALMDQVDEPLKITFQNIHRGYPTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 1 ~~~~~~~~i~~lr~ll~~~~~~l~~~~~~~~~~~~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
|-..+.+.|++||+....- =..+-+=|..+++|+++|.+.|++
T Consensus 1 m~~is~~~IK~LR~~Tgag----------------m~dCKkAL~e~~gD~ekAi~~Lrk 43 (290)
T PRK09377 1 MAAITAALVKELRERTGAG----------------MMDCKKALTEADGDIEKAIEWLRK 43 (290)
T ss_pred CCccCHHHHHHHHHHHCCC----------------HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4567889999999876542 235566778899999999999875
No 20
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=40.03 E-value=49 Score=24.89 Aligned_cols=43 Identities=21% Similarity=0.247 Sum_probs=25.6
Q ss_pred cchHHHHHHHHHHHhhcChHHHHHHh--hhcCCCChHHHHHHhhh
Q 020204 3 TVSHEAVTQFQALMDQVDEPLKITFQ--NIHRGYPTETLVRFLKA 45 (329)
Q Consensus 3 ~~~~~~i~~lr~ll~~~~~~l~~~~~--~~~~~~~d~~llRFL~a 45 (329)
..+++++.+|.++|+..+..|-.|+- ..+++..+.-+++-+++
T Consensus 43 ~lsd~el~~f~~LLe~~D~dL~~Wi~g~~~~~~~~~~~mv~~I~~ 87 (94)
T COG2938 43 SLSDEELDEFERLLECEDNDLFNWIMGHGEPPDAELTPMVRKIQA 87 (94)
T ss_pred hCCHHHHHHHHHHHcCCcHHHHHHHhCCCCCCcHHHHHHHHHHHH
Confidence 45778888888888877766666662 22333334444444443
No 21
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=36.51 E-value=72 Score=29.30 Aligned_cols=40 Identities=18% Similarity=0.195 Sum_probs=30.9
Q ss_pred chHHHHHHHHHHHhhcChHHHHHHhhhcCCCChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 4 VSHEAVTQFQALMDQVDEPLKITFQNIHRGYPTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 4 ~~~~~i~~lr~ll~~~~~~l~~~~~~~~~~~~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
.+.+.|++||+....-. ..+-+=|..+++|+++|.+.|+.
T Consensus 3 isa~~IK~LRe~Tgagm----------------~dCKkAL~e~~gDiekAi~~LRk 42 (290)
T TIGR00116 3 ITAQLVKELRERTGAGM----------------MDCKKALTEANGDFEKAIKNLRE 42 (290)
T ss_pred CCHHHHHHHHHHHCCCH----------------HHHHHHHHHcCCCHHHHHHHHHH
Confidence 67888999998765432 34556678899999999998876
No 22
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=30.20 E-value=1.1e+02 Score=28.10 Aligned_cols=43 Identities=16% Similarity=0.228 Sum_probs=33.2
Q ss_pred CCcchHHHHHHHHHHHhhcChHHHHHHhhhcCCCChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 1 MVTVSHEAVTQFQALMDQVDEPLKITFQNIHRGYPTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 1 ~~~~~~~~i~~lr~ll~~~~~~l~~~~~~~~~~~~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
|-.++.+.|++||+....-- ..+-+=|-..++|+++|.+.|+.
T Consensus 1 m~~ita~~VKeLRe~TgAGM----------------mdCKkAL~E~~Gd~EkAie~LR~ 43 (296)
T COG0264 1 MAEITAALVKELREKTGAGM----------------MDCKKALEEANGDIEKAIEWLRE 43 (296)
T ss_pred CCcccHHHHHHHHHHhCCcH----------------HHHHHHHHHcCCCHHHHHHHHHH
Confidence 66788999999998775432 24556677889999999988775
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=27.70 E-value=39 Score=30.19 Aligned_cols=29 Identities=21% Similarity=0.376 Sum_probs=22.0
Q ss_pred ceEEEEcCChhHHHHHHHhhhcccccccc
Q 020204 188 NTYYIVNVPYIFSACWKVVKPLLQERTRK 216 (329)
Q Consensus 188 ~~i~iIN~P~~~~~~~~ivkpfL~~~t~~ 216 (329)
..++|||+||-+....+-+-|+|.+....
T Consensus 206 SGm~iiNPPw~l~~~l~~~l~~L~~~L~~ 234 (245)
T PF04378_consen 206 SGMLIINPPWTLDEELEEILPWLAETLAQ 234 (245)
T ss_dssp EEEEEES--TTHHHHHHHHHHHHHHHSST
T ss_pred ceEEEEcCCccHHHHHHHHHHHHHHHhCc
Confidence 57999999999999888888887765544
No 24
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=27.34 E-value=43 Score=30.04 Aligned_cols=27 Identities=15% Similarity=0.313 Sum_probs=23.0
Q ss_pred ceEEEEcCChhHHHHHHHhhhcccccc
Q 020204 188 NTYYIVNVPYIFSACWKVVKPLLQERT 214 (329)
Q Consensus 188 ~~i~iIN~P~~~~~~~~ivkpfL~~~t 214 (329)
..++|||+||-+.--...+-|+|....
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~L 263 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTLL 263 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHHh
Confidence 469999999999999999988887543
No 25
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=26.67 E-value=74 Score=27.98 Aligned_cols=86 Identities=14% Similarity=0.278 Sum_probs=47.7
Q ss_pred CcceEEEEEEcCCCc--ccccchHHHHHHHHHhhhccCccccceEE------EEcCChhHHHHHHHhhhccccc-----c
Q 020204 148 PITTCVKVLDMTGLK--LSALSQIKLLTIISTVDDLNYPEKTNTYY------IVNVPYIFSACWKVVKPLLQER-----T 214 (329)
Q Consensus 148 ~~~~~v~IiDl~g~~--l~~~~~~~~~~~i~~~~q~~YPe~l~~i~------iIN~P~~~~~~~~ivkpfL~~~-----t 214 (329)
..+.-.+|+||-|-= +.|++ +++++..-++. .-.++-.+| +|....+++.+.+.++.++.=+ .
T Consensus 95 d~eddylifDcPGQIELytH~p---Vm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~KfiSG~lsAlsAMi~lE~P~INv 170 (273)
T KOG1534|consen 95 DVEDDYLIFDCPGQIELYTHLP---VMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTKFISGCLSALSAMISLEVPHINV 170 (273)
T ss_pred CccCCEEEEeCCCeeEEeecCh---hHHHHHHHHhc-ccCceeEEEEeccchhhhHHHHHHHHHHHHHHHHHhcCcchhh
Confidence 456778999997742 34544 45555544443 223344444 4555566777777666655433 2
Q ss_pred cccEEEcCCCChhHHhccCCCCC
Q 020204 215 RKKIQVLQGSGRDELLKIMDFES 237 (329)
Q Consensus 215 ~~Ki~~~~~~~~~~L~k~i~~~~ 237 (329)
..|.-.+++.++++|.++.+++.
T Consensus 171 lsKMDLlk~~~k~~l~~Fl~~d~ 193 (273)
T KOG1534|consen 171 LSKMDLLKDKNKKELERFLNPDE 193 (273)
T ss_pred hhHHHHhhhhhHHHHHHhcCCch
Confidence 33444444444566666666543
No 26
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=26.57 E-value=1.4e+02 Score=25.76 Aligned_cols=40 Identities=15% Similarity=0.207 Sum_probs=30.5
Q ss_pred chHHHHHHHHHHHhhcChHHHHHHhhhcCCCChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 4 VSHEAVTQFQALMDQVDEPLKITFQNIHRGYPTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 4 ~~~~~i~~lr~ll~~~~~~l~~~~~~~~~~~~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
++.+.|++||+....-. ..+-+=|..+++|+++|...|+.
T Consensus 3 i~a~~ik~LR~~tga~~----------------~~ck~AL~~~~gd~~~A~~~lr~ 42 (198)
T PRK12332 3 ITAKLVKELREKTGAGM----------------MDCKKALEEANGDMEKAIEWLRE 42 (198)
T ss_pred CCHHHHHHHHHHHCCCH----------------HHHHHHHHHcCCCHHHHHHHHHH
Confidence 56788999998765422 34556678899999999999886
No 27
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=25.97 E-value=39 Score=22.15 Aligned_cols=27 Identities=15% Similarity=0.160 Sum_probs=20.9
Q ss_pred CCChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 33 GYPTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 33 ~~~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
+.+-.+-.++|...+||.++|.+.+..
T Consensus 12 gmn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 12 GMNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp SS-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 355678899999999999999988664
No 28
>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=25.94 E-value=1.6e+02 Score=20.11 Aligned_cols=26 Identities=19% Similarity=0.232 Sum_probs=23.3
Q ss_pred CChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 34 YPTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 34 ~~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
.+|+-++--|+-|+.|+.+|++.|..
T Consensus 19 hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 19 HSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 57899999999999999999998764
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=25.68 E-value=84 Score=24.98 Aligned_cols=43 Identities=7% Similarity=0.233 Sum_probs=35.0
Q ss_pred eEEEEcCChhHHHHHHHh-----hhcccccccccEEEcCCCChhHHhccC
Q 020204 189 TYYIVNVPYIFSACWKVV-----KPLLQERTRKKIQVLQGSGRDELLKIM 233 (329)
Q Consensus 189 ~i~iIN~P~~~~~~~~iv-----kpfL~~~t~~Ki~~~~~~~~~~L~k~i 233 (329)
.++++|..-+++-++..+ ..|++++....+.++.+ .+++.++|
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 699999887888888877 56899999999999774 77776653
No 30
>CHL00098 tsf elongation factor Ts
Probab=24.08 E-value=1.5e+02 Score=25.55 Aligned_cols=38 Identities=18% Similarity=0.190 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhhcChHHHHHHhhhcCCCChHHHHHHhhhcCCCHHHHHHHHHH
Q 020204 6 HEAVTQFQALMDQVDEPLKITFQNIHRGYPTETLVRFLKARDGNVSKAHKMLMD 59 (329)
Q Consensus 6 ~~~i~~lr~ll~~~~~~l~~~~~~~~~~~~d~~llRFL~a~~~dv~kA~~~l~~ 59 (329)
.+.|++||+....- =..+-+=|..+++|+++|.+.|+.
T Consensus 2 a~~ik~LR~~Tgag----------------~~dck~AL~e~~gd~~~A~~~Lr~ 39 (200)
T CHL00098 2 AELVKELRDKTGAG----------------MMDCKKALQEANGDFEKALESLRQ 39 (200)
T ss_pred HHHHHHHHHHHCCC----------------HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 46788888776532 234566678899999999988876
No 31
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=21.72 E-value=2.2e+02 Score=18.05 Aligned_cols=44 Identities=14% Similarity=0.182 Sum_probs=28.0
Q ss_pred hHHHHHHHHHHHhhcChHHHHHHhhhcCCCChHHHHHHhhhcCCCHHH
Q 020204 5 SHEAVTQFQALMDQVDEPLKITFQNIHRGYPTETLVRFLKARDGNVSK 52 (329)
Q Consensus 5 ~~~~i~~lr~ll~~~~~~l~~~~~~~~~~~~d~~llRFL~a~~~dv~k 52 (329)
+.+.++.|-+.++.. ..++..+..+ -+...++++.+..+|++..
T Consensus 2 S~~~l~~Fl~~~~~d-~~l~~~l~~~---~~~~e~~~lA~~~Gy~ft~ 45 (49)
T PF07862_consen 2 SIESLKAFLEKVKSD-PELREQLKAC---QNPEEVVALAREAGYDFTE 45 (49)
T ss_pred CHHHHHHHHHHHhcC-HHHHHHHHhc---CCHHHHHHHHHHcCCCCCH
Confidence 345566666666543 3566655322 2667888899988888654
No 32
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=21.06 E-value=1.4e+02 Score=18.30 Aligned_cols=23 Identities=35% Similarity=0.476 Sum_probs=19.0
Q ss_pred ChHHHHHHhhhcCCCHHHHHHHH
Q 020204 35 PTETLVRFLKARDGNVSKAHKML 57 (329)
Q Consensus 35 ~d~~llRFL~a~~~dv~kA~~~l 57 (329)
....+..-|..++||+.+|.+.|
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH
Confidence 45688888999999999999887
No 33
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.17 E-value=3.5e+02 Score=19.63 Aligned_cols=59 Identities=15% Similarity=0.237 Sum_probs=40.2
Q ss_pred CcchHHHHHHHHHHHhhcChHHHHHHhhhcCCCChHHHHHHhhhcCCCHHHHHHHHHHHHHHHHhCC
Q 020204 2 VTVSHEAVTQFQALMDQVDEPLKITFQNIHRGYPTETLVRFLKARDGNVSKAHKMLMDCLHWRAQNE 68 (329)
Q Consensus 2 ~~~~~~~i~~lr~ll~~~~~~l~~~~~~~~~~~~d~~llRFL~a~~~dv~kA~~~l~~~l~wR~~~~ 68 (329)
.+++++.+..+...+...=..|.. +-++++..+.++=.-+....+.+.+|| ..||...|
T Consensus 3 ~~~t~~~l~~ia~~iG~~Wk~Lar-----~LGls~~dI~~i~~~~~~~~eq~~~mL---~~W~~r~g 61 (86)
T cd08318 3 KPVTGEQITVFANKLGEDWKTLAP-----HLEMKDKEIRAIESDSEDIKMQAKQLL---VAWQDREG 61 (86)
T ss_pred CCCCHHHHHHHHHHHhhhHHHHHH-----HcCCCHHHHHHHHhcCCCHHHHHHHHH---HHHHHhcC
Confidence 367888888888887755444443 457888888777654443356677775 46999887
Done!