Query 019880
Match_columns 334
No_of_seqs 271 out of 1301
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 05:16:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019880.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019880hhsearch_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 6.3E-40 1.4E-44 306.3 20.7 213 31-251 42-260 (317)
2 KOG1470 Phosphatidylinositol t 100.0 7.6E-39 1.6E-43 289.1 19.5 198 32-249 47-244 (324)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 1.4E-30 3.1E-35 218.7 10.9 154 84-247 3-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 2.7E-28 5.8E-33 204.6 14.6 150 87-248 8-157 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 1.3E-24 2.7E-29 180.9 12.9 145 90-247 11-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.5 2.8E-14 6.2E-19 118.6 6.6 141 90-250 4-146 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 99.1 4.3E-10 9.4E-15 77.0 6.3 54 4-58 1-55 (55)
8 KOG4406 CDC42 Rho GTPase-activ 98.0 4.5E-05 9.8E-10 71.4 9.4 126 95-236 89-215 (467)
9 PF00627 UBA: UBA/TS-N domain; 89.0 1.6 3.6E-05 26.6 5.2 25 31-55 13-37 (37)
10 PF14555 UBA_4: UBA-like domai 88.1 1.6 3.4E-05 27.8 4.8 24 32-55 13-36 (43)
11 PF02845 CUE: CUE domain; Int 80.8 4.7 0.0001 25.3 4.5 28 30-57 13-40 (42)
12 smart00546 CUE Domain that may 72.0 9.5 0.00021 24.0 4.2 27 30-56 14-40 (43)
13 cd00194 UBA Ubiquitin Associat 69.2 8.4 0.00018 23.3 3.4 26 31-56 12-37 (38)
14 smart00165 UBA Ubiquitin assoc 67.9 9.2 0.0002 23.0 3.4 25 31-55 12-36 (37)
15 PF06972 DUF1296: Protein of u 57.5 31 0.00068 23.6 4.6 26 32-57 19-44 (60)
16 PF08938 HBS1_N: HBS1 N-termin 42.7 12 0.00025 27.3 0.8 25 33-57 45-69 (79)
17 PF03474 DMA: DMRTA motif; In 39.3 58 0.0013 20.3 3.4 25 31-55 14-38 (39)
18 smart00804 TAP_C C-terminal do 37.1 65 0.0014 22.4 3.8 27 31-57 24-50 (63)
19 PF07862 Nif11: Nitrogen fixat 36.8 1E+02 0.0022 19.8 4.6 44 3-50 2-45 (49)
20 TIGR00116 tsf translation elon 33.3 89 0.0019 28.8 5.2 40 2-57 3-42 (290)
21 PF04838 Baculo_LEF5: Baculovi 32.2 29 0.00063 28.5 1.6 47 171-218 18-68 (159)
22 PF03641 Lysine_decarbox: Poss 29.7 90 0.0019 24.9 4.2 43 187-231 86-133 (133)
23 COG2961 ComJ Protein involved 29.5 33 0.00071 30.9 1.6 27 186-212 237-263 (279)
24 PRK12332 tsf elongation factor 29.1 1.3E+02 0.0028 26.1 5.2 40 2-57 3-42 (198)
25 PRK09377 tsf elongation factor 28.0 1.2E+02 0.0026 28.0 5.1 40 2-57 4-43 (290)
26 KOG2911 Uncharacterized conser 27.9 1.6E+02 0.0034 28.7 5.9 51 5-63 247-297 (439)
27 PF04378 RsmJ: Ribosomal RNA s 27.6 31 0.00068 31.0 1.2 30 185-214 205-234 (245)
28 PF02084 Bindin: Bindin; Inte 24.6 63 0.0014 28.4 2.4 41 2-45 101-141 (238)
29 PF11547 E3_UbLigase_EDD: E3 u 23.7 2.2E+02 0.0048 18.6 5.2 41 17-57 8-48 (53)
30 PF03943 TAP_C: TAP C-terminal 23.7 55 0.0012 21.6 1.5 27 31-57 12-38 (51)
31 COG1219 ClpX ATP-dependent pro 23.3 56 0.0012 30.8 2.0 22 34-55 144-165 (408)
32 COG2938 Uncharacterized conser 22.4 1.5E+02 0.0032 22.5 3.8 23 3-25 45-67 (94)
33 COG2994 HlyC ACP:hemolysin acy 22.2 1.9E+02 0.0041 23.6 4.5 17 95-111 58-74 (148)
34 CHL00098 tsf elongation factor 21.8 1.9E+02 0.0042 25.1 5.0 38 4-57 2-39 (200)
35 KOG1534 Putative transcription 20.3 3.8E+02 0.0083 23.8 6.3 106 124-235 75-193 (273)
No 1
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=6.3e-40 Score=306.26 Aligned_cols=213 Identities=34% Similarity=0.514 Sum_probs=188.9
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHcCcchhhcCCCCCHHHHHHHHhcccccccccCCCCCeEEEEeeCCc
Q 019880 31 GNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRIENDIDNILAKPILPAELYRAVRDSQLVGVSGYSKEGLPVIAVGVGLS 110 (334)
Q Consensus 31 ~~~d~~LlRFLra~~~dv~kA~~~l~~~l~wR~~~~id~i~~~~~~~~~l~~~l~~~~~~~~~g~Dk~G~pV~~~~~g~~ 110 (334)
..+|.+|+||||||+||+++|.+||.+++.||+++++|+++.+ +... ..+.++.+.+++|.|++|+||++.+.|..
T Consensus 42 ~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~-~~~~---~~~~~~~~~~~~~~~~~g~~v~~~~~g~~ 117 (317)
T KOG1471|consen 42 YDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFED-FEED---DELLKYYPQGLHGVDKEGRPVYIERLGKI 117 (317)
T ss_pred CCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhc-cccc---hhhhhhccccccccCCCCCEEEEeccCCC
Confidence 4568899999999999999999999999999999999999875 2211 12334677889999999999999999987
Q ss_pred Ccc----cchHHHHHHHHHHHHHHHHHhcchhhhhhcCCCcceEEEEEeCCCCcccccch--hHHHHHHHHhhhccCccc
Q 019880 111 THD----KASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQ--IKLMTVITTIDDLNYPEK 184 (334)
Q Consensus 111 ~~~----~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~--~~~~~~i~~i~~~~YPer 184 (334)
+.. .....+++++++..+|.....+++.+.+..+++++|++.|+||+|+++++++. .+.++.++.+++++|||+
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 654 46778899999999998888888877777778999999999999999999964 568899999999999999
Q ss_pred ccceEEEcCChhhHHHHHHHcccCChhhhcceEEeCCCChhHHHhhCCCCCCCcccccCCCCccccc
Q 019880 185 TETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKIMDYASLPHFCRKEGSGSSRHI 251 (334)
Q Consensus 185 l~~i~ivN~P~~f~~~~~~vkpfL~~~t~~KI~i~~~~~~~~L~~~I~~~~LP~~~~~e~GG~~~~~ 251 (334)
++++||||+|++|+++|+++||||+++|++||+++++++.++|.++|++++||.+| ||++.+.
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 99999999999999999999999999999999977778999999999999999988 9998774
No 2
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=7.6e-39 Score=289.10 Aligned_cols=198 Identities=27% Similarity=0.444 Sum_probs=171.4
Q ss_pred CChHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHcCcchhhcCCCCCHHHHHHHHhcccccccccCCCCCeEEEEeeCCcC
Q 019880 32 NPTDTLVRFLKARDWNVSKAHKMLVDCLRWRIENDIDNILAKPILPAELYRAVRDSQLVGVSGYSKEGLPVIAVGVGLST 111 (334)
Q Consensus 32 ~~d~~LlRFLra~~~dv~kA~~~l~~~l~wR~~~~id~i~~~~~~~~~l~~~l~~~~~~~~~g~Dk~G~pV~~~~~g~~~ 111 (334)
++|++++||||||+||+++|.+||.++|.||+++++... +...++...+. .+..++.|+|++||||+|+++....
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 589999999999999999999999999999999998662 22455655554 4557788999999999999877665
Q ss_pred cccchHHHHHHHHHHHHHHHHHhcchhhhhhcCCCcceEEEEEeCCCCcccccchhHHHHHHHHhhhccCcccccceEEE
Q 019880 112 HDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQIKLMTVITTIDDLNYPEKTETYYIV 191 (334)
Q Consensus 112 ~~~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~~~~~~~i~~i~~~~YPerl~~i~iv 191 (334)
....+...+.+..++++|... ..++++.+++++++|++|+|+++++ +++.+.++.++|+||||||+..+++
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 666677788888888888643 3455677899999999999999887 8899999999999999999999999
Q ss_pred cCChhhHHHHHHHcccCChhhhcceEEeCCCChhHHHhhCCCCCCCcccccCCCCccc
Q 019880 192 NAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKIMDYASLPHFCRKEGSGSSR 249 (334)
Q Consensus 192 N~P~~f~~~~~~vkpfL~~~t~~KI~i~~~~~~~~L~~~I~~~~LP~~~~~e~GG~~~ 249 (334)
|+||+|..+|+++||||++.|++||+|+.+ .+.|.+|||+++||..+ ||+..
T Consensus 193 ~~P~iF~~~wkiikpflDp~t~~Kv~F~~~--~~~l~~~~d~~~l~s~~----GG~~~ 244 (324)
T KOG1470|consen 193 NAPWIFQPFWKIIKPFLDPKTASKVKFVEP--KDDLSEYFDESQLPSLF----GGKLL 244 (324)
T ss_pred CChHHHHHHHHHhhhccChhhhceeEEecC--hhHHHhhCCccccchhh----CCCcc
Confidence 999999999999999999999999999873 56699999999999987 89653
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=1.4e-30 Score=218.70 Aligned_cols=154 Identities=28% Similarity=0.476 Sum_probs=125.3
Q ss_pred HHhcccccccccCCCCCeEEEEeeCCcCcccchHHHHHHHHHHHHHHHHHhcchhhhhhcCCCcceEEEEEeCCCCcccc
Q 019880 84 VRDSQLVGVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSA 163 (334)
Q Consensus 84 l~~~~~~~~~g~Dk~G~pV~~~~~g~~~~~~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~ 163 (334)
+.++++.+++|+|++||||+++++++++..+.+.+++++..++++|...+.. +. +.+++++++|+|++|+++++
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 4677889999999999999999999988887778899999999999865421 11 45788999999999999998
Q ss_pred cch--hHHHHHHHHhhhccCcccccceEEEcCChhhHHHHHHHcccCChhhhcceEEeCCC-ChhHHHhhCCCCCCCccc
Q 019880 164 LNQ--IKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGN-GRDELLKIMDYASLPHFC 240 (334)
Q Consensus 164 ~~~--~~~~~~i~~i~~~~YPerl~~i~ivN~P~~f~~~~~~vkpfL~~~t~~KI~i~~~~-~~~~L~~~I~~~~LP~~~ 240 (334)
++. +++++.++.+++++||++++++|++|+|++|+++|++++|||+++|++||++++++ +.++|.++||+++||.+|
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 864 67889999999999999999999999999999999999999999999999999654 347899999999999988
Q ss_pred ccCCCCc
Q 019880 241 RKEGSGS 247 (334)
Q Consensus 241 ~~e~GG~ 247 (334)
||+
T Consensus 157 ----GG~ 159 (159)
T PF00650_consen 157 ----GGT 159 (159)
T ss_dssp ----TSS
T ss_pred ----CCC
Confidence 886
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=2.7e-28 Score=204.61 Aligned_cols=150 Identities=27% Similarity=0.462 Sum_probs=134.4
Q ss_pred cccccccccCCCCCeEEEEeeCCcCcccchHHHHHHHHHHHHHHHHHhcchhhhhhcCCCcceEEEEEeCCCCcccccch
Q 019880 87 SQLVGVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQ 166 (334)
Q Consensus 87 ~~~~~~~g~Dk~G~pV~~~~~g~~~~~~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~ 166 (334)
+.+.++ |+|++||||++++++.++.+..+.+++++++++.+|...+. .....+++++++|+|++|+++++++
T Consensus 8 ~~~~~~-g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~------~~~~~~~~~~~~i~D~~~~~~~~~~- 79 (158)
T smart00516 8 YIPGGR-GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQR------EKKTGGIEGFTVIFDLKGLSMSNPD- 79 (158)
T ss_pred hcCCCC-CCCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHH------HhcCCCeeeEEEEEECCCCCccccc-
Confidence 344555 89999999999999998888889999999999999976532 2245578999999999999999865
Q ss_pred hHHHHHHHHhhhccCcccccceEEEcCChhhHHHHHHHcccCChhhhcceEEeCCCChhHHHhhCCCCCCCcccccCCCC
Q 019880 167 IKLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKIMDYASLPHFCRKEGSG 246 (334)
Q Consensus 167 ~~~~~~i~~i~~~~YPerl~~i~ivN~P~~f~~~~~~vkpfL~~~t~~KI~i~~~~~~~~L~~~I~~~~LP~~~~~e~GG 246 (334)
++.++.+..+++.+||++++++||+|+|++++++|+++++||++++++||+++++++.+.|.++||+++||.+| ||
T Consensus 80 ~~~lk~~~~~~~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~L~~~i~~~~lP~~~----GG 155 (158)
T smart00516 80 LSVLRKILKILQDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGNDSKEELLEYIDPEQLPEEL----GG 155 (158)
T ss_pred HHHHHHHHHHHHHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCCCHHHHHhhCCHhhCcHhh----CC
Confidence 78899999999999999999999999999999999999999999999999999876789999999999999988 99
Q ss_pred cc
Q 019880 247 SS 248 (334)
Q Consensus 247 ~~ 248 (334)
++
T Consensus 156 ~~ 157 (158)
T smart00516 156 TL 157 (158)
T ss_pred CC
Confidence 86
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=1.3e-24 Score=180.93 Aligned_cols=145 Identities=32% Similarity=0.512 Sum_probs=122.6
Q ss_pred ccccccCCCCCeEEEEeeCCcCccc-chHHHHHHHHHHHHHHHHHhcchhhhhhcCCCcceEEEEEeCCCCcccccc-hh
Q 019880 90 VGVSGYSKEGLPVIAVGVGLSTHDK-ASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALN-QI 167 (334)
Q Consensus 90 ~~~~g~Dk~G~pV~~~~~g~~~~~~-~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~-~~ 167 (334)
.+..|.|++||||++++++..++.. ...++++++.++.+|...+. .....+++++|+|++|++++++. .+
T Consensus 11 ~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~--------~~~~~~~~~~i~D~~~~~~~~~~~~~ 82 (157)
T cd00170 11 GYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQE--------DDEQVEGFVVIIDLKGLSLSHLLPDP 82 (157)
T ss_pred cccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhh--------hhhcccceEEEEECCCCChhccchhH
Confidence 3344569999999999999644433 33478889988888875432 12233699999999999999884 46
Q ss_pred HHHHHHHHhhhccCcccccceEEEcCChhhHHHHHHHcccCChhhhcceEEeCCCChhHHHhhCCCCCCCcccccCCCCc
Q 019880 168 KLMTVITTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKIMDYASLPHFCRKEGSGS 247 (334)
Q Consensus 168 ~~~~~i~~i~~~~YPerl~~i~ivN~P~~f~~~~~~vkpfL~~~t~~KI~i~~~~~~~~L~~~I~~~~LP~~~~~e~GG~ 247 (334)
+.++.+..+++.+||++++++|++|+|+++.++|+++++|+++++++||++++++ .++|.++|++++||.+| ||+
T Consensus 83 ~~~k~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~-~~~L~~~i~~~~Lp~~~----GG~ 157 (157)
T cd00170 83 SLLKKILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD-KEELLKYIDKEQLPEEY----GGT 157 (157)
T ss_pred HHHHHHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC-HHHHHhhCChhhCcHhh----CCC
Confidence 7899999999999999999999999999999999999999999999999998754 88999999999999988 885
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.50 E-value=2.8e-14 Score=118.57 Aligned_cols=141 Identities=16% Similarity=0.231 Sum_probs=94.1
Q ss_pred ccccccCCCCCeEEEEeeCCcCcccchHHHHHHHHHHHHHHHHHhcchhhhhhcCCCcceEEEEEeCCCCcccccchhHH
Q 019880 90 VGVSGYSKEGLPVIAVGVGLSTHDKASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQIKL 169 (334)
Q Consensus 90 ~~~~g~Dk~G~pV~~~~~g~~~~~~~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~~~~ 169 (334)
++..|+|++|+||+++..... +.....+.++.+.+..+. +. ....++++|+|++|.+..+-.....
T Consensus 4 ~~~gG~d~~g~pV~~~~~~~~-~~~~~~~~ll~yl~~~l~-------~~------~~~~~f~vVid~~~~~~~~~~~~~~ 69 (149)
T PF13716_consen 4 FYPGGRDREGRPVVVFIASRL-PSSDDLERLLLYLLSTLS-------EE------VVDKPFSVVIDHTGFSRSSEPSLSW 69 (149)
T ss_dssp -EEEEEBTTS-EEEEEEGGG--C-TTHHHHHHHHHHHHH--------TT------TTTS-EEEEEE-TT--GGG---HHH
T ss_pred EEecccCCCcCEEEEEECCcC-cchhhHHHHHHHHHHhhh-------HH------hcCCCEEEEEEcCCCccccCCchHH
Confidence 345689999999999997776 443455555554433221 11 1224699999999998876655778
Q ss_pred HHHHHHhhhccCcccccceEEEcCChhhHHHH-HHHcccCChhh-hcceEEeCCCChhHHHhhCCCCCCCcccccCCCCc
Q 019880 170 MTVITTIDDLNYPEKTETYYIVNAPYIFSACW-KVVKPLLQERT-RRKMQVLQGNGRDELLKIMDYASLPHFCRKEGSGS 247 (334)
Q Consensus 170 ~~~i~~i~~~~YPerl~~i~ivN~P~~f~~~~-~~vkpfL~~~t-~~KI~i~~~~~~~~L~~~I~~~~LP~~~~~e~GG~ 247 (334)
++.+..++...|+..++++||+|++++++.+. .+.+++.+.+. ..||.++. ..++|.++||+++||..+ ||+
T Consensus 70 l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~--sl~~L~~~i~~~qL~~~l----p~~ 143 (149)
T PF13716_consen 70 LKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVS--SLSELSKHIDPSQLPESL----PGV 143 (149)
T ss_dssp HHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEES--STCGGGGTSGGGG----------HH
T ss_pred HHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEEC--CHHHHHhhCCHHHhcccC----CCE
Confidence 89999999999999999999999999999999 66678889988 89999887 489999999999999998 888
Q ss_pred ccc
Q 019880 248 SRH 250 (334)
Q Consensus 248 ~~~ 250 (334)
..+
T Consensus 144 ~~~ 146 (149)
T PF13716_consen 144 LQY 146 (149)
T ss_dssp H--
T ss_pred Eec
Confidence 765
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=99.06 E-value=4.3e-10 Score=77.03 Aligned_cols=54 Identities=30% Similarity=0.564 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHhhccHHHHHHh-hhhcCCCChHHHHHHHhhcCCCHHHHHHHHHHH
Q 019880 4 QEEIKQFQTLMEDLDDSLKETF-KNVHQGNPTDTLVRFLKARDWNVSKAHKMLVDC 58 (334)
Q Consensus 4 ~~~i~~lr~~l~~~~~~l~~~~-~~~~~~~~d~~LlRFLra~~~dv~kA~~~l~~~ 58 (334)
++++++|++.+.+..... ..+ ...+...+|.+|+||||||+||+++|.+||++|
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 578999999999864322 111 234567789999999999999999999999875
No 8
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=97.96 E-value=4.5e-05 Score=71.39 Aligned_cols=126 Identities=17% Similarity=0.212 Sum_probs=91.6
Q ss_pred cCCCCCeEEEEeeCCcCccc-chHHHHHHHHHHHHHHHHHhcchhhhhhcCCCcceEEEEEeCCCCcccccchhHHHHHH
Q 019880 95 YSKEGLPVIAVGVGLSTHDK-ASVNYYVQSHIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLKLSALNQIKLMTVI 173 (334)
Q Consensus 95 ~Dk~G~pV~~~~~g~~~~~~-~~~~~~l~~~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~l~~~~~~~~~~~i 173 (334)
+|+.||+|+++.+.++.... ..-..++++.++..++.. ++ -++.+.=-.|+...+.+.+.++...
T Consensus 89 ~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~V--------e~------DYt~vYfh~gl~s~nkp~l~~l~~a 154 (467)
T KOG4406|consen 89 KDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYV--------EN------DYTLVYFHHGLPSDNKPYLQLLFDA 154 (467)
T ss_pred ccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHH--------hc------cceeeehhcCCcccccchHHHHHHH
Confidence 59999999999887765422 112225666555555421 11 1344444467776666666666554
Q ss_pred HHhhhccCcccccceEEEcCChhhHHHHHHHcccCChhhhcceEEeCCCChhHHHhhCCCCCC
Q 019880 174 TTIDDLNYPEKTETYYIVNAPYIFSACWKVVKPLLQERTRRKMQVLQGNGRDELLKIMDYASL 236 (334)
Q Consensus 174 ~~i~~~~YPerl~~i~ivN~P~~f~~~~~~vkpfL~~~t~~KI~i~~~~~~~~L~~~I~~~~L 236 (334)
..-+..+|---++.+|+|.+-|+..++|+.+|||++.+..+||+-+. ..++|.+++.-+.|
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 55555689999999999999999999999999999999999999876 59999999876655
No 9
>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=89.05 E-value=1.6 Score=26.64 Aligned_cols=25 Identities=28% Similarity=0.274 Sum_probs=20.9
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHH
Q 019880 31 GNPTDTLVRFLKARDWNVSKAHKML 55 (334)
Q Consensus 31 ~~~d~~LlRFLra~~~dv~kA~~~l 55 (334)
+++.....+-|+++++|+++|...|
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 5777788999999999999998764
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=88.10 E-value=1.6 Score=27.81 Aligned_cols=24 Identities=21% Similarity=0.566 Sum_probs=19.6
Q ss_pred CChHHHHHHHhhcCCCHHHHHHHH
Q 019880 32 NPTDTLVRFLKARDWNVSKAHKML 55 (334)
Q Consensus 32 ~~d~~LlRFLra~~~dv~kA~~~l 55 (334)
.++..-..||.+++||++.|+...
T Consensus 13 ~~~~~A~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 13 ADEDVAIQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp SSHHHHHHHHHHTTT-HHHHHHHH
T ss_pred cCHHHHHHHHHHcCCCHHHHHHHH
Confidence 355688999999999999999875
No 11
>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=80.77 E-value=4.7 Score=25.35 Aligned_cols=28 Identities=18% Similarity=0.233 Sum_probs=23.9
Q ss_pred CCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 30 QGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 30 ~~~~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
.+++...+.+-|+++++|++.|..+|-.
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 4678889999999999999999998854
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=72.02 E-value=9.5 Score=24.00 Aligned_cols=27 Identities=19% Similarity=0.195 Sum_probs=23.7
Q ss_pred CCCChHHHHHHHhhcCCCHHHHHHHHH
Q 019880 30 QGNPTDTLVRFLKARDWNVSKAHKMLV 56 (334)
Q Consensus 30 ~~~~d~~LlRFLra~~~dv~kA~~~l~ 56 (334)
.+.++..+.+.|+++++|++.|...|.
T Consensus 14 P~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 14 PNLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 457788999999999999999998875
No 13
>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=69.23 E-value=8.4 Score=23.35 Aligned_cols=26 Identities=27% Similarity=0.354 Sum_probs=23.1
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHH
Q 019880 31 GNPTDTLVRFLKARDWNVSKAHKMLV 56 (334)
Q Consensus 31 ~~~d~~LlRFLra~~~dv~kA~~~l~ 56 (334)
+++.....+-|+++++|+++|...|.
T Consensus 12 Gf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 12 GFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 68888999999999999999987763
No 14
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=67.92 E-value=9.2 Score=23.03 Aligned_cols=25 Identities=28% Similarity=0.410 Sum_probs=22.2
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHH
Q 019880 31 GNPTDTLVRFLKARDWNVSKAHKML 55 (334)
Q Consensus 31 ~~~d~~LlRFLra~~~dv~kA~~~l 55 (334)
+++.....+-|+++++|+++|...|
T Consensus 12 Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 12 GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 6888899999999999999998754
No 15
>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=57.50 E-value=31 Score=23.57 Aligned_cols=26 Identities=15% Similarity=0.284 Sum_probs=23.6
Q ss_pred CChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 32 NPTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 32 ~~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
.+|+.++--|+-|+.|+.+|.+.|..
T Consensus 19 hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 19 HSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 58889999999999999999999865
No 16
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=42.74 E-value=12 Score=27.30 Aligned_cols=25 Identities=24% Similarity=0.324 Sum_probs=21.2
Q ss_pred ChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 33 PTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 33 ~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
++..|..=|..+.|||++|+..|++
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 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=39.31 E-value=58 Score=20.33 Aligned_cols=25 Identities=16% Similarity=0.126 Sum_probs=21.0
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHH
Q 019880 31 GNPTDTLVRFLKARDWNVSKAHKML 55 (334)
Q Consensus 31 ~~~d~~LlRFLra~~~dv~kA~~~l 55 (334)
......|-.-|+.|++|+-+|.+.+
T Consensus 14 ~~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 14 HQKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CCChHHHHHHHHHcCCcHHHHHHHh
Confidence 3456788899999999999998875
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=37.11 E-value=65 Score=22.37 Aligned_cols=27 Identities=19% Similarity=0.379 Sum_probs=24.2
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 31 GNPTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 31 ~~~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
+.+-.+-.++|...+||.+.|.+.+.+
T Consensus 24 gmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 24 GMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 567789999999999999999998866
No 19
>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=36.83 E-value=1e+02 Score=19.82 Aligned_cols=44 Identities=16% Similarity=0.338 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHhhccHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHH
Q 019880 3 HQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSK 50 (334)
Q Consensus 3 ~~~~i~~lr~~l~~~~~~l~~~~~~~~~~~~d~~LlRFLra~~~dv~k 50 (334)
|.+.++.|-+.+... ..|+..+.... +..-++++.+..+|++..
T Consensus 2 S~~~l~~Fl~~~~~d-~~l~~~l~~~~---~~~e~~~lA~~~Gy~ft~ 45 (49)
T PF07862_consen 2 SIESLKAFLEKVKSD-PELREQLKACQ---NPEEVVALAREAGYDFTE 45 (49)
T ss_pred CHHHHHHHHHHHhcC-HHHHHHHHhcC---CHHHHHHHHHHcCCCCCH
Confidence 556777777777655 45776664322 667888999999988754
No 20
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=33.29 E-value=89 Score=28.84 Aligned_cols=40 Identities=15% Similarity=0.046 Sum_probs=30.8
Q ss_pred chHHHHHHHHHHHhhccHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 2 ~~~~~i~~lr~~l~~~~~~l~~~~~~~~~~~~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
++.+.|++||+.....- ..+-+=|..+++|+++|.+.|+.
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 67889999998765532 24456677889999999998876
No 21
>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=32.25 E-value=29 Score=28.46 Aligned_cols=47 Identities=19% Similarity=0.451 Sum_probs=38.8
Q ss_pred HHHHHhhhccCccccc--ceEEEcCChhhHHHHHHHcccCCh--hhhcceEE
Q 019880 171 TVITTIDDLNYPEKTE--TYYIVNAPYIFSACWKVVKPLLQE--RTRRKMQV 218 (334)
Q Consensus 171 ~~i~~i~~~~YPerl~--~i~ivN~P~~f~~~~~~vkpfL~~--~t~~KI~i 218 (334)
..++..+-.+||.-|+ ..-++|..-.|+++|+-+ |-++. +-|+.|++
T Consensus 18 ~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRL 68 (159)
T PF04838_consen 18 KELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRL 68 (159)
T ss_pred HHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhh
Confidence 3556677789999999 888999999999999987 77777 67777775
No 22
>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=29.65 E-value=90 Score=24.94 Aligned_cols=43 Identities=7% Similarity=0.197 Sum_probs=35.2
Q ss_pred ceEEEcCChhhHHHHHHH-----cccCChhhhcceEEeCCCChhHHHhhC
Q 019880 187 TYYIVNAPYIFSACWKVV-----KPLLQERTRRKMQVLQGNGRDELLKIM 231 (334)
Q Consensus 187 ~i~ivN~P~~f~~~~~~v-----kpfL~~~t~~KI~i~~~~~~~~L~~~I 231 (334)
.++++|..-++..+++.+ .-|+++.....+.++. +.+++.++|
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d--~~~e~~~~i 133 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVD--DPEEALEYI 133 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEES--SHHHHHHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeC--CHHHHHhhC
Confidence 699999887778888876 5799999999999986 478877664
No 23
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=29.54 E-value=33 Score=30.89 Aligned_cols=27 Identities=15% Similarity=0.330 Sum_probs=22.6
Q ss_pred cceEEEcCChhhHHHHHHHcccCChhh
Q 019880 186 ETYYIVNAPYIFSACWKVVKPLLQERT 212 (334)
Q Consensus 186 ~~i~ivN~P~~f~~~~~~vkpfL~~~t 212 (334)
..++|||+||.+..-...+-|+|....
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~L 263 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTLL 263 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHHh
Confidence 469999999999998888888876543
No 24
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=29.10 E-value=1.3e+02 Score=26.13 Aligned_cols=40 Identities=13% Similarity=0.057 Sum_probs=30.5
Q ss_pred chHHHHHHHHHHHhhccHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 2 ~~~~~i~~lr~~l~~~~~~l~~~~~~~~~~~~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
++.+.|++||+.....- ..+-+=|..+++|+++|...|+.
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 56788889988765532 24556678899999999999876
No 25
>PRK09377 tsf elongation factor Ts; Provisional
Probab=28.05 E-value=1.2e+02 Score=27.96 Aligned_cols=40 Identities=15% Similarity=0.072 Sum_probs=31.0
Q ss_pred chHHHHHHHHHHHhhccHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 2 ~~~~~i~~lr~~l~~~~~~l~~~~~~~~~~~~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
++.+.|++||+..... =..+-+=|..+++|+++|.+.|++
T Consensus 4 is~~~IK~LR~~Tgag----------------m~dCKkAL~e~~gD~ekAi~~Lrk 43 (290)
T PRK09377 4 ITAALVKELRERTGAG----------------MMDCKKALTEADGDIEKAIEWLRK 43 (290)
T ss_pred cCHHHHHHHHHHHCCC----------------HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6788899998876543 224566788899999999999876
No 26
>KOG2911 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.94 E-value=1.6e+02 Score=28.69 Aligned_cols=51 Identities=18% Similarity=0.253 Sum_probs=35.6
Q ss_pred HHHHHHHHHHhhccHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHHHHHHHH
Q 019880 5 EEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVDCLRWRI 63 (334)
Q Consensus 5 ~~i~~lr~~l~~~~~~l~~~~~~~~~~~~d~~LlRFLra~~~dv~kA~~~l~~~l~wR~ 63 (334)
.+|+.|++.+++..+.+|+.+. .-+...-++|||+++ .+.+.+.+....+.
T Consensus 247 kqie~L~qeie~~~~~~r~~~k----~g~K~iA~~ylr~rk----~~eK~~er~~~~l~ 297 (439)
T KOG2911|consen 247 KQIEFLEQEIEKSKEKLRQALK----EGKKQIAITYLRARK----LLEKDLERKVSSLN 297 (439)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH----hcchHHHHHHHHHHH----HHHhhHHHHHHHHH
Confidence 4678889999999888887764 245667899999998 44444444444433
No 27
>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=27.63 E-value=31 Score=30.97 Aligned_cols=30 Identities=20% Similarity=0.367 Sum_probs=21.8
Q ss_pred ccceEEEcCChhhHHHHHHHcccCChhhhc
Q 019880 185 TETYYIVNAPYIFSACWKVVKPLLQERTRR 214 (334)
Q Consensus 185 l~~i~ivN~P~~f~~~~~~vkpfL~~~t~~ 214 (334)
=..++|||+||-+....+-+-|+|.+....
T Consensus 205 GSGm~iiNPPw~l~~~l~~~l~~L~~~L~~ 234 (245)
T PF04378_consen 205 GSGMLIINPPWTLDEELEEILPWLAETLAQ 234 (245)
T ss_dssp EEEEEEES--TTHHHHHHHHHHHHHHHSST
T ss_pred cceEEEEcCCccHHHHHHHHHHHHHHHhCc
Confidence 356999999999998888888877665443
No 28
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=24.61 E-value=63 Score=28.42 Aligned_cols=41 Identities=10% Similarity=0.208 Sum_probs=29.9
Q ss_pred chHHHHHHHHHHHhhccHHHHHHhhhhcCCCChHHHHHHHhhcC
Q 019880 2 AHQEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARD 45 (334)
Q Consensus 2 ~~~~~i~~lr~~l~~~~~~l~~~~~~~~~~~~d~~LlRFLra~~ 45 (334)
||++.++.+|+.|...+..|.- ++.+.||=-.|||-||-..
T Consensus 101 ISAKvm~~ikavLgaTKiDLPV---DINDPYDlGLLLRhLRHHS 141 (238)
T PF02084_consen 101 ISAKVMEDIKAVLGATKIDLPV---DINDPYDLGLLLRHLRHHS 141 (238)
T ss_pred ccHHHHHHHHHHhccccccccc---ccCChhhHHHHHHHHHHHH
Confidence 6788888999988887665542 2345666679999998653
No 29
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=23.73 E-value=2.2e+02 Score=18.62 Aligned_cols=41 Identities=22% Similarity=0.332 Sum_probs=28.3
Q ss_pred ccHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 17 LDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 17 ~~~~l~~~~~~~~~~~~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
.|+.|-...+.+-++-+...+.|=|+..+.||..|+.-|..
T Consensus 8 vPedlI~q~q~VLqgksR~vIirELqrTnLdVN~AvNNlLs 48 (53)
T PF11547_consen 8 VPEDLINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLLS 48 (53)
T ss_dssp S-HHHHHHHHHHSTTS-HHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHcCCcHHHHHHHHHHhcccHHHHHHHHhc
Confidence 34444444455557788889999999999999999877643
No 30
>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=23.66 E-value=55 Score=21.58 Aligned_cols=27 Identities=15% Similarity=0.350 Sum_probs=21.5
Q ss_pred CCChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 31 GNPTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 31 ~~~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
+.+-.+-.++|...+||.++|.+.+..
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 456678999999999999999998754
No 31
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=23.34 E-value=56 Score=30.78 Aligned_cols=22 Identities=27% Similarity=0.628 Sum_probs=19.4
Q ss_pred hHHHHHHHhhcCCCHHHHHHHH
Q 019880 34 TDTLVRFLKARDWNVSKAHKML 55 (334)
Q Consensus 34 d~~LlRFLra~~~dv~kA~~~l 55 (334)
+..|+|.|.|++|||++|.+-+
T Consensus 144 ENillkLlqaadydV~rAerGI 165 (408)
T COG1219 144 ENILLKLLQAADYDVERAERGI 165 (408)
T ss_pred HHHHHHHHHHcccCHHHHhCCe
Confidence 5689999999999999998654
No 32
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=22.36 E-value=1.5e+02 Score=22.46 Aligned_cols=23 Identities=30% Similarity=0.469 Sum_probs=14.0
Q ss_pred hHHHHHHHHHHHhhccHHHHHHh
Q 019880 3 HQEEIKQFQTLMEDLDDSLKETF 25 (334)
Q Consensus 3 ~~~~i~~lr~~l~~~~~~l~~~~ 25 (334)
+++.+.++.++++..+..|-.|+
T Consensus 45 sd~el~~f~~LLe~~D~dL~~Wi 67 (94)
T COG2938 45 SDEELDEFERLLECEDNDLFNWI 67 (94)
T ss_pred CHHHHHHHHHHHcCCcHHHHHHH
Confidence 45566666666666655555555
No 33
>COG2994 HlyC ACP:hemolysin acyltransferase (hemolysin-activating protein) [Posttranslational modification, protein turnover, chaperones]
Probab=22.23 E-value=1.9e+02 Score=23.65 Aligned_cols=17 Identities=12% Similarity=0.335 Sum_probs=13.9
Q ss_pred cCCCCCeEEEEeeCCcC
Q 019880 95 YSKEGLPVIAVGVGLST 111 (334)
Q Consensus 95 ~Dk~G~pV~~~~~g~~~ 111 (334)
+|++|+||.++.-.-++
T Consensus 58 ~de~g~Piaf~~WA~vd 74 (148)
T COG2994 58 FDEHGRPIAFCTWAFVD 74 (148)
T ss_pred EcCCCCeeEEEEEeecC
Confidence 58999999998876643
No 34
>CHL00098 tsf elongation factor Ts
Probab=21.79 E-value=1.9e+02 Score=25.05 Aligned_cols=38 Identities=16% Similarity=0.086 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhhccHHHHHHhhhhcCCCChHHHHHHHhhcCCCHHHHHHHHHH
Q 019880 4 QEEIKQFQTLMEDLDDSLKETFKNVHQGNPTDTLVRFLKARDWNVSKAHKMLVD 57 (334)
Q Consensus 4 ~~~i~~lr~~l~~~~~~l~~~~~~~~~~~~d~~LlRFLra~~~dv~kA~~~l~~ 57 (334)
.+.|++||+..... =..+-+=|..+++|+++|.+.|+.
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 46788888775543 224566788899999999988876
No 35
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=20.26 E-value=3.8e+02 Score=23.82 Aligned_cols=106 Identities=14% Similarity=0.242 Sum_probs=56.2
Q ss_pred HHHHHHHHHHhcchhhhhhcCCCcceEEEEEeCCCCc--ccccchhHHHHHHHHhhhccCcccccceEEEc------CCh
Q 019880 124 HIQMNEYRDRVVLPSASKKHGRYIGTSLKVLDMTGLK--LSALNQIKLMTVITTIDDLNYPEKTETYYIVN------APY 195 (334)
Q Consensus 124 ~i~~~E~~~~~~l~~~~~~~~~~~~~~v~IiDl~g~~--l~~~~~~~~~~~i~~i~~~~YPerl~~i~ivN------~P~ 195 (334)
.++++||...-+ +-.....| ..+.-.+|+||-|-= ..| +.+++.+..-++. .--++..+|++. ...
T Consensus 75 Lv~cmEyl~~Nl-dwL~~~~G-d~eddylifDcPGQIELytH---~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~K 148 (273)
T KOG1534|consen 75 LVYCMEYLLENL-DWLEEEIG-DVEDDYLIFDCPGQIELYTH---LPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTK 148 (273)
T ss_pred chhHHHHHHHHH-HHHHhhcc-CccCCEEEEeCCCeeEEeec---ChhHHHHHHHHhc-ccCceeEEEEeccchhhhHHH
Confidence 355666654322 11112223 456668899997632 233 3345555544443 233455556555 455
Q ss_pred hhHHHHHHHcccCCh-----hhhcceEEeCCCChhHHHhhCCCCC
Q 019880 196 IFSACWKVVKPLLQE-----RTRRKMQVLQGNGRDELLKIMDYAS 235 (334)
Q Consensus 196 ~f~~~~~~vkpfL~~-----~t~~KI~i~~~~~~~~L~~~I~~~~ 235 (334)
+|+.++..+..++.- ...+|.-++++..+++|.++.+++.
T Consensus 149 fiSG~lsAlsAMi~lE~P~INvlsKMDLlk~~~k~~l~~Fl~~d~ 193 (273)
T KOG1534|consen 149 FISGCLSALSAMISLEVPHINVLSKMDLLKDKNKKELERFLNPDE 193 (273)
T ss_pred HHHHHHHHHHHHHHhcCcchhhhhHHHHhhhhhHHHHHHhcCCch
Confidence 666666655554332 2445555555555677777777553
Done!