Query 023175
Match_columns 286
No_of_seqs 152 out of 1539
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 08:59:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023175.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023175hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1470 Phosphatidylinositol t 100.0 9.1E-46 2E-50 323.1 20.6 205 65-277 45-251 (324)
2 KOG1471 Phosphatidylinositol t 100.0 4.9E-37 1.1E-41 276.8 20.0 230 32-272 13-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 3.4E-32 7.4E-37 220.9 6.8 151 113-268 3-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 1.4E-28 3.1E-33 199.4 13.9 142 123-270 14-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 99.9 3E-26 6.6E-31 184.3 12.8 145 118-268 9-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.5 1.9E-14 4.1E-19 115.6 6.1 138 120-271 5-146 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 98.9 3.5E-09 7.6E-14 70.2 5.9 52 42-93 1-55 (55)
8 KOG4406 CDC42 Rho GTPase-activ 98.3 7.2E-06 1.6E-10 74.2 10.7 119 117-241 80-202 (467)
9 PF14555 UBA_4: UBA-like domai 89.4 1.4 3E-05 27.1 5.1 24 68-91 14-37 (43)
10 PF02845 CUE: CUE domain; Int 86.5 3 6.4E-05 25.4 5.2 38 43-92 3-40 (42)
11 smart00546 CUE Domain that may 84.3 4 8.7E-05 24.9 5.1 26 66-91 15-40 (43)
12 PF06972 DUF1296: Protein of u 78.8 7.9 0.00017 25.6 5.0 41 40-92 4-44 (60)
13 PF00627 UBA: UBA/TS-N domain; 64.5 14 0.0003 21.6 3.6 23 68-90 15-37 (37)
14 smart00165 UBA Ubiquitin assoc 62.1 16 0.00035 21.2 3.6 24 67-90 13-36 (37)
15 cd00194 UBA Ubiquitin Associat 61.7 17 0.00036 21.2 3.6 25 67-91 13-37 (38)
16 KOG1838 Alpha/beta hydrolase [ 59.6 1.2E+02 0.0026 28.5 10.3 84 127-223 122-214 (409)
17 PF14213 DUF4325: Domain of un 59.0 36 0.00078 23.4 5.4 49 171-221 17-67 (74)
18 PF03474 DMA: DMRTA motif; In 58.2 22 0.00048 21.4 3.5 24 67-90 15-38 (39)
19 KOG2267 Eukaryotic-type DNA pr 57.5 29 0.00062 32.1 5.8 74 44-133 290-363 (475)
20 PF08938 HBS1_N: HBS1 N-termin 53.7 3.2 6.8E-05 29.3 -0.7 49 35-93 19-70 (79)
21 PF11964 SpoIIAA-like: SpoIIAA 52.8 63 0.0014 23.4 6.3 77 144-228 10-87 (109)
22 PF02084 Bindin: Bindin; Inte 50.6 20 0.00044 30.4 3.5 53 41-93 102-160 (238)
23 TIGR02364 dha_pts dihydroxyace 50.2 49 0.0011 25.5 5.4 63 159-230 49-111 (125)
24 smart00804 TAP_C C-terminal do 45.7 45 0.00098 22.4 4.0 28 66-93 24-51 (63)
25 PRK14484 phosphotransferase ma 42.2 74 0.0016 24.5 5.2 59 160-231 50-108 (124)
26 COG0052 RpsB Ribosomal protein 35.1 26 0.00056 30.4 1.9 83 200-284 30-118 (252)
27 KOG4329 DNA-binding protein [G 35.1 88 0.0019 28.8 5.2 36 57-93 234-269 (445)
28 cd07322 PriL_PriS_Eukaryotic E 34.1 2.6E+02 0.0056 26.1 8.4 45 43-93 226-270 (390)
29 KOG3561 Aryl-hydrocarbon recep 34.0 1.6E+02 0.0035 30.2 7.4 75 44-136 38-122 (803)
30 KOG1534 Putative transcription 33.2 1.6E+02 0.0034 25.4 6.1 63 154-219 75-145 (273)
31 PF09590 Env-gp36: Lentivirus 32.0 2E+02 0.0044 27.9 7.2 65 32-101 39-113 (591)
32 PF03943 TAP_C: TAP C-terminal 31.2 52 0.0011 21.0 2.4 26 67-92 13-38 (51)
33 COG2961 ComJ Protein involved 28.9 42 0.00092 29.3 2.1 26 207-232 237-262 (279)
34 PF04378 RsmJ: Ribosomal RNA s 28.7 33 0.00071 29.8 1.5 25 208-232 207-231 (245)
35 COG1219 ClpX ATP-dependent pro 26.7 49 0.0011 30.2 2.2 26 65-90 140-165 (408)
36 KOG0431 Auxilin-like protein a 26.5 1.2E+02 0.0026 28.9 5.0 78 39-127 339-420 (453)
37 PF11339 DUF3141: Protein of u 26.4 3.9E+02 0.0085 26.1 8.2 62 146-219 117-178 (581)
38 PF02954 HTH_8: Bacterial regu 26.2 1.2E+02 0.0025 18.2 3.3 22 69-90 7-28 (42)
39 KOG3824 Huntingtin interacting 24.8 1.3E+02 0.0028 27.4 4.4 49 82-130 333-381 (472)
40 cd01886 EF-G Elongation factor 23.4 2.7E+02 0.0058 24.4 6.3 57 37-101 188-244 (270)
41 PF11385 DUF3189: Protein of u 22.1 3.5E+02 0.0076 21.5 6.1 54 115-180 48-101 (148)
42 PF01740 STAS: STAS domain; I 20.8 1.2E+02 0.0026 22.3 3.1 48 172-222 49-96 (117)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=9.1e-46 Score=323.07 Aligned_cols=205 Identities=32% Similarity=0.544 Sum_probs=190.7
Q ss_pred CCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHcCCCC-CChhhhHHHHhcCceeeccCCCCCCCcEEEEEcCCCCCC
Q 023175 65 GRDDEDMILWFLKDRKFSIEESLAKLTKAIKWRQEFRVSE-LNEDSVRGIAESGKAYVHDFLDINERPVLIVVASKHLPA 143 (286)
Q Consensus 65 ~~~~d~~LlRFLra~~~dv~~A~~~l~~~~~wR~~~~~~~-l~~~~~~~~l~~~~~~~~g~~D~~Grpv~~~~~~~~~~~ 143 (286)
..++|.+++|||||++||+++|.++|.+++.||+.+++.. +..+++..++++|.+|++| .|++||||+|+++..+.++
T Consensus 45 ~~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~G-~D~~gRPVl~~~~~~~~qn 123 (324)
T KOG1470|consen 45 KWCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYILG-HDKDGRPVLYLRPRPHRQN 123 (324)
T ss_pred hcCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEec-ccCCCCeEEEEecCCCCCC
Confidence 5679999999999999999999999999999999999988 8888899999999999999 7999999999988888778
Q ss_pred CCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHhhhcccccccEEEEeCCcchHHHHH
Q 023175 144 VHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQ 223 (286)
Q Consensus 144 ~~~~~~~~r~~~~~lE~~~~~~~~~~~g~~vIiD~~g~s~~~~~~~~~k~~~~~lq~~yP~rl~~i~iiN~P~~f~~~w~ 223 (286)
..+.+...|+++|+||.++..++.+++++++++|++|+|++|++.+..+.++.++|+|||+||+.++++|+||+|..+|+
T Consensus 124 ~~t~~~~~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs~sN~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~wk 203 (324)
T KOG1470|consen 124 TKTQKELERLLVYTLENAILFLPPGQEQFVWLFDLTGFSMSNPDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPFWK 203 (324)
T ss_pred CCCHHHHHHHHHHHHHHHHHhCCCCcceEEEEEecccCcccCCCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHHHH
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhhhcccccc-cceeeccCCcchhhHHHHhhhhcCccccchhcCCCccchhhhcc
Q 023175 224 LTKPLLKSYA-SLKPSGRNISLKQRCQTTLESRLLVKSLHSCLAALAGLIFAQTV 277 (286)
Q Consensus 224 lvkpfL~~~t-~ki~~~~~~~~~~~~~~~l~~~i~~~~LP~~~GG~~~~~~~~~~ 277 (286)
++||||+++| +||.|+.+. ++ +.+++|+++||..|||+..+.+.+.+
T Consensus 204 iikpflDp~t~~Kv~F~~~~---~~----l~~~~d~~~l~s~~GG~~~~~y~~e~ 251 (324)
T KOG1470|consen 204 IIKPFLDPKTASKVKFVEPK---DD----LSEYFDESQLPSLFGGKLLFEYTHEE 251 (324)
T ss_pred HhhhccChhhhceeEEecCh---hH----HHhhCCccccchhhCCCcccccCCcc
Confidence 9999999999 599998764 22 67899999999999996666555443
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=4.9e-37 Score=276.82 Aligned_cols=230 Identities=22% Similarity=0.334 Sum_probs=183.9
Q ss_pred CCCCCChHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHcCCCCCChh-hh
Q 023175 32 KNCQSDPHESRKLVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKAIKWRQEFRVSELNED-SV 110 (286)
Q Consensus 32 ~e~~~~~e~~~~~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~~~wR~~~~~~~l~~~-~~ 110 (286)
.+.++.++..++.++++| |+..+ ++++ ....+|..|+|||||++||+++|.+++.+++.||+++..+.+..+ ..
T Consensus 13 ~~~~~~~~~~~~~i~~lr-~~~~~-~~l~---~~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~ 87 (317)
T KOG1471|consen 13 EELNEITESEEAVIAQLR-WLLQK-PHLP---NKYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEE 87 (317)
T ss_pred cccCCCcHHHHHHHHHHH-HHhhc-cCCC---CCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhcccc
Confidence 466776777788999999 66554 5665 247899999999999999999999999999999999998876654 11
Q ss_pred HHHH-hcCceeeccCCCCCCCcEEEEEcCCCCCC----CCChHHHHHHHH--------HHHHHHHHhCCCCcccEEEEEe
Q 023175 111 RGIA-ESGKAYVHDFLDINERPVLIVVASKHLPA----VHDPVEDEKLCV--------FFIEKALSKLPPGKEQILGIID 177 (286)
Q Consensus 111 ~~~l-~~~~~~~~g~~D~~Grpv~~~~~~~~~~~----~~~~~~~~r~~~--------~~lE~~~~~~~~~~~g~~vIiD 177 (286)
...+ .......+| .|++|+|+++.+.|..+.. .....+..++.+ ..+|......+.+++|++.|+|
T Consensus 88 ~~~~~~~~~~~~~~-~~~~g~~v~~~~~g~~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~D 166 (317)
T KOG1471|consen 88 DDELLKYYPQGLHG-VDKEGRPVYIERLGKIDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFD 166 (317)
T ss_pred chhhhhhccccccc-cCCCCCEEEEeccCCCCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEE
Confidence 1222 223456677 7999999999999987553 234455555544 4444444444567999999999
Q ss_pred CCCCCCCCC---CHHHHHHHHHHHhhhcccccccEEEEeCCcchHHHHHHhhhcccccc-cceeeccCCcchhhHHHHhh
Q 023175 178 LRGFGTENA---DLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLKSYA-SLKPSGRNISLKQRCQTTLE 253 (286)
Q Consensus 178 ~~g~s~~~~---~~~~~k~~~~~lq~~yP~rl~~i~iiN~P~~f~~~w~lvkpfL~~~t-~ki~~~~~~~~~~~~~~~l~ 253 (286)
++|++++|+ .+..++.++.++|++||++++++||||+|++|+++|+++||||+++| +||++.+ +...+.|.
T Consensus 167 l~G~~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~-----~~~~~~L~ 241 (317)
T KOG1471|consen 167 LKGVSLSHLLKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLH-----SKDKESLL 241 (317)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecC-----CCchhhhh
Confidence 999999987 36899999999999999999999999999999999999999999999 4888332 33456688
Q ss_pred hhcCccccchhcCCCccch
Q 023175 254 SRLLVKSLHSCLAALAGLI 272 (286)
Q Consensus 254 ~~i~~~~LP~~~GG~~~~~ 272 (286)
+.++++.||.+|||+++..
T Consensus 242 k~i~~~~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 242 KYIPPEVLPEEYGGTCGDL 260 (317)
T ss_pred hhCCHhhCccccCCCcccc
Confidence 9999999999999999875
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=3.4e-32 Score=220.92 Aligned_cols=151 Identities=26% Similarity=0.488 Sum_probs=125.4
Q ss_pred HHhcCceeeccCCCCCCCcEEEEEcCCCCCCCCChHHHHHHHHHHHHHHHHhCC--CCcccEEEEEeCCCCCCCCCC---
Q 023175 113 IAESGKAYVHDFLDINERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSKLP--PGKEQILGIIDLRGFGTENAD--- 187 (286)
Q Consensus 113 ~l~~~~~~~~g~~D~~Grpv~~~~~~~~~~~~~~~~~~~r~~~~~lE~~~~~~~--~~~~g~~vIiD~~g~s~~~~~--- 187 (286)
.++.+..+++| +|++||||++++++++++...+.+++.+++++.+|.+++.++ .+.+|+++|+|++|+++++++
T Consensus 3 ~~~~~~~~~~g-~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~ 81 (159)
T PF00650_consen 3 ILKSGPFYLHG-RDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFSLSNFDWWP 81 (159)
T ss_dssp HHTTSCEEEEE-E-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT--HHHHHCHH
T ss_pred HHCCeeEEECC-CCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCceEeccccch
Confidence 45678889999 799999999999999988888899999999999999986554 478999999999999999887
Q ss_pred HHHHHHHHHHHhhhcccccccEEEEeCCcchHHHHHHhhhcccccc-cceeeccCCcchhhHHHHhhhhcCccccchhcC
Q 023175 188 LKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLKSYA-SLKPSGRNISLKQRCQTTLESRLLVKSLHSCLA 266 (286)
Q Consensus 188 ~~~~k~~~~~lq~~yP~rl~~i~iiN~P~~f~~~w~lvkpfL~~~t-~ki~~~~~~~~~~~~~~~l~~~i~~~~LP~~~G 266 (286)
.+.++.+++++|++||+|++++|++|+|++|+++|++++|||+++| +||+++++. +....|.+++++++||.+||
T Consensus 82 ~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~----~~~~~l~~~i~~~~lP~~~G 157 (159)
T PF00650_consen 82 ISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGS----DWKAKLKEYIDPEQLPVEYG 157 (159)
T ss_dssp HHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTT----CHCHHHCCCSTGGGSBGGGT
T ss_pred hhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCc----ccHHHHHhhCCHhHCchhcC
Confidence 8999999999999999999999999999999999999999999999 599999653 33346889999999999999
Q ss_pred CC
Q 023175 267 AL 268 (286)
Q Consensus 267 G~ 268 (286)
|+
T Consensus 158 G~ 159 (159)
T PF00650_consen 158 GT 159 (159)
T ss_dssp SS
T ss_pred CC
Confidence 97
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=1.4e-28 Score=199.40 Aligned_cols=142 Identities=27% Similarity=0.383 Sum_probs=130.7
Q ss_pred cCCCCCCCcEEEEEcCCCCCCCCChHHHHHHHHHHHHHHHHh--CCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHhh
Q 023175 123 DFLDINERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSK--LPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYY 200 (286)
Q Consensus 123 g~~D~~Grpv~~~~~~~~~~~~~~~~~~~r~~~~~lE~~~~~--~~~~~~g~~vIiD~~g~s~~~~~~~~~k~~~~~lq~ 200 (286)
| +|++||||++++++++++...+.+++++++++.+|.+++. .+.+++|+++|+|++|++++|++++.++.+++++++
T Consensus 14 g-~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~lk~~~~~~~~ 92 (158)
T smart00516 14 G-YDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQREKKTGGIEGFTVIFDLKGLSMSNPDLSVLRKILKILQD 92 (158)
T ss_pred C-CCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHHHhcCCCeeeEEEEEECCCCCcccccHHHHHHHHHHHHH
Confidence 6 7999999999999998888899999999999999999876 567789999999999999999999999999999999
Q ss_pred hcccccccEEEEeCCcchHHHHHHhhhcccccc-cceeeccCCcchhhHHHHhhhhcCccccchhcCCCcc
Q 023175 201 YHPKRLGEVLFVEAPFVFKPFWQLTKPLLKSYA-SLKPSGRNISLKQRCQTTLESRLLVKSLHSCLAALAG 270 (286)
Q Consensus 201 ~yP~rl~~i~iiN~P~~f~~~w~lvkpfL~~~t-~ki~~~~~~~~~~~~~~~l~~~i~~~~LP~~~GG~~~ 270 (286)
+||+|++++||+|+|++++.+|+++++|+++++ +||+++++. ..+.|.+.+++++||++|||++.
T Consensus 93 ~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~-----~~~~L~~~i~~~~lP~~~GG~~~ 158 (158)
T smart00516 93 HYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGND-----SKEELLEYIDPEQLPEELGGTLD 158 (158)
T ss_pred HhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCC-----CHHHHHhhCCHhhCcHhhCCCCC
Confidence 999999999999999999999999999999998 599998752 24457788999999999999863
No 5
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.94 E-value=3e-26 Score=184.33 Aligned_cols=145 Identities=24% Similarity=0.288 Sum_probs=126.5
Q ss_pred ceeeccCCCCCCCcEEEEEcCCCCC-CCCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCC--CHHHHHHH
Q 023175 118 KAYVHDFLDINERPVLIVVASKHLP-AVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENA--DLKFLTFL 194 (286)
Q Consensus 118 ~~~~~g~~D~~Grpv~~~~~~~~~~-~~~~~~~~~r~~~~~lE~~~~~~~~~~~g~~vIiD~~g~s~~~~--~~~~~k~~ 194 (286)
.++..|++|++||||+++++++.+. ...+.++.+++.++.+|.+++.+..+.+|+++|+|++|.+++++ +.+.++.+
T Consensus 9 ~~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~~~k~~ 88 (157)
T cd00170 9 KVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQEDDEQVEGFVVIIDLKGLSLSHLLPDPSLLKKI 88 (157)
T ss_pred cccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhhhhhcccceEEEEECCCCChhccchhHHHHHHH
Confidence 3444444899999999999996433 34455889999999999998887776689999999999999998 78899999
Q ss_pred HHHHhhhcccccccEEEEeCCcchHHHHHHhhhcccccc-cceeeccCCcchhhHHHHhhhhcCccccchhcCCC
Q 023175 195 FDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLKSYA-SLKPSGRNISLKQRCQTTLESRLLVKSLHSCLAAL 268 (286)
Q Consensus 195 ~~~lq~~yP~rl~~i~iiN~P~~f~~~w~lvkpfL~~~t-~ki~~~~~~~~~~~~~~~l~~~i~~~~LP~~~GG~ 268 (286)
+++++++||++++++|++|+|++++.+|+++++|+++++ +||+++++. .+.|.+++++++||.+|||+
T Consensus 89 ~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~------~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 89 LKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD------KEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred HHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC------HHHHHhhCChhhCcHhhCCC
Confidence 999999999999999999999999999999999999998 599998642 44577899999999999996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.51 E-value=1.9e-14 Score=115.64 Aligned_cols=138 Identities=20% Similarity=0.315 Sum_probs=92.5
Q ss_pred eeccCCCCCCCcEEEEEcCCCCCCCCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCC-CHHHHHHHHHHH
Q 023175 120 YVHDFLDINERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENA-DLKFLTFLFDVF 198 (286)
Q Consensus 120 ~~~g~~D~~Grpv~~~~~~~~~~~~~~~~~~~r~~~~~lE~~~~~~~~~~~g~~vIiD~~g~s~~~~-~~~~~k~~~~~l 198 (286)
+..| +|++||||+++...+. + +.+++.+++.|++...... ....++++|+|++|.+..+. +...++.+.+.+
T Consensus 5 ~~gG-~d~~g~pV~~~~~~~~-~---~~~~~~~ll~yl~~~l~~~--~~~~~f~vVid~~~~~~~~~~~~~~l~~~~~~l 77 (149)
T PF13716_consen 5 YPGG-RDREGRPVVVFIASRL-P---SSDDLERLLLYLLSTLSEE--VVDKPFSVVIDHTGFSRSSEPSLSWLKQLYKLL 77 (149)
T ss_dssp EEEE-EBTTS-EEEEEEGGG--C----TTHHHHHHHHHHHHH-TT--TTTS-EEEEEE-TT--GGG---HHHHHHTTTSS
T ss_pred Eecc-cCCCcCEEEEEECCcC-c---chhhHHHHHHHHHHhhhHH--hcCCCEEEEEEcCCCccccCCchHHHHHHHHHH
Confidence 4445 8999999999997766 3 2336666777766654222 34567999999999997654 689999999999
Q ss_pred hhhcccccccEEEEeCCcchHHHH-HHhhhcccccc--cceeeccCCcchhhHHHHhhhhcCccccchhcCCCccc
Q 023175 199 YYYHPKRLGEVLFVEAPFVFKPFW-QLTKPLLKSYA--SLKPSGRNISLKQRCQTTLESRLLVKSLHSCLAALAGL 271 (286)
Q Consensus 199 q~~yP~rl~~i~iiN~P~~f~~~w-~lvkpfL~~~t--~ki~~~~~~~~~~~~~~~l~~~i~~~~LP~~~GG~~~~ 271 (286)
...|+..++++||+|++++++.++ .+.+++.+.+. +|+.++.+- ..|.+++++++||..+||+.+.
T Consensus 78 ~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~sl-------~~L~~~i~~~qL~~~lp~~~~~ 146 (149)
T PF13716_consen 78 PRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSSL-------SELSKHIDPSQLPESLPGVLQY 146 (149)
T ss_dssp -HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESST-------CGGGGTSGGGG------HHH--
T ss_pred HHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECCH-------HHHHhhCCHHHhcccCCCEEec
Confidence 999999999999999999999999 66677778875 488887543 3477899999999999987653
No 7
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=98.91 E-value=3.5e-09 Score=70.17 Aligned_cols=52 Identities=27% Similarity=0.466 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHhhcCC---CCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHH
Q 023175 42 RKLVLQVKERLEKDYNS---LPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKA 93 (286)
Q Consensus 42 ~~~i~~lr~~l~~~~~~---lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~ 93 (286)
++++++|++.++..... ++.......+|.+|+|||||++||+++|.++|.++
T Consensus 1 k~~l~~l~~~l~~~~~~~~~~~~~~~~~~~d~~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 1 KQKLKQLREHLSELDEKAPGLWDDEKEDHDDNFLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp HHHHHHHHHHHHH--GGGTHHHTTHTSS-SHHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhccchhcccccccCCCCHHHHHHHHHHccCCHHHHHHHHHhC
Confidence 36889999999873110 00011256799999999999999999999999875
No 8
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.28 E-value=7.2e-06 Score=74.17 Aligned_cols=119 Identities=18% Similarity=0.167 Sum_probs=91.6
Q ss_pred CceeeccC-CCCCCCcEEEEEcCCCCC-CCCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCCC-HHHHHH
Q 023175 117 GKAYVHDF-LDINERPVLIVVASKHLP-AVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENAD-LKFLTF 193 (286)
Q Consensus 117 ~~~~~~g~-~D~~Grpv~~~~~~~~~~-~~~~~~~~~r~~~~~lE~~~~~~~~~~~g~~vIiD~~g~s~~~~~-~~~~k~ 193 (286)
..+.+.|. .|+.||.|+++...+.-+ ++.+-..++++.++.+|..+++- ++.+.=-.|+...+.+ .+.+..
T Consensus 80 ei~qvi~~~~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~Ve~D------Yt~vYfh~gl~s~nkp~l~~l~~ 153 (467)
T KOG4406|consen 80 EILQVIGDAKDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVEND------YTLVYFHHGLPSDNKPYLQLLFD 153 (467)
T ss_pred heeeeccCcccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHhcc------ceeeehhcCCcccccchHHHHHH
Confidence 44455553 599999999999888643 23333347888999999887652 5666666787777775 566666
Q ss_pred HHHHHhhhcccccccEEEEeCCcchHHHHHHhhhcccccc-cceeeccC
Q 023175 194 LFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLKSYA-SLKPSGRN 241 (286)
Q Consensus 194 ~~~~lq~~yP~rl~~i~iiN~P~~f~~~w~lvkpfL~~~t-~ki~~~~~ 241 (286)
...-+-.+|---++.+|+|++.|+.+++|+++|||++.|. +|++.+..
T Consensus 154 aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n~ 202 (467)
T KOG4406|consen 154 AYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFNS 202 (467)
T ss_pred HHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEeeh
Confidence 6666777788889999999999999999999999999995 78887754
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=89.40 E-value=1.4 Score=27.10 Aligned_cols=24 Identities=21% Similarity=0.494 Sum_probs=20.4
Q ss_pred CHHHHHHHHhhcCCCHHHHHHHHH
Q 023175 68 DEDMILWFLKDRKFSIEESLAKLT 91 (286)
Q Consensus 68 ~d~~LlRFLra~~~dv~~A~~~l~ 91 (286)
++.....||..++||++.|+..+-
T Consensus 14 ~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 14 DEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp SHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578899999999999999998764
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=86.46 E-value=3 Score=25.41 Aligned_cols=38 Identities=21% Similarity=0.291 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHH
Q 023175 43 KLVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTK 92 (286)
Q Consensus 43 ~~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~ 92 (286)
+.|++|++.+ | ..+...+..-|..+++|++.|...|-+
T Consensus 3 ~~v~~L~~mF----P--------~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMF----P--------DLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHS----S--------SS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHC----C--------CCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 4556666654 2 457889999999999999999998754
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=84.27 E-value=4 Score=24.92 Aligned_cols=26 Identities=23% Similarity=0.299 Sum_probs=22.9
Q ss_pred CCCHHHHHHHHhhcCCCHHHHHHHHH
Q 023175 66 RDDEDMILWFLKDRKFSIEESLAKLT 91 (286)
Q Consensus 66 ~~~d~~LlRFLra~~~dv~~A~~~l~ 91 (286)
..++..+.+-|+++++|++.|.+.|-
T Consensus 15 ~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 15 NLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45788999999999999999998875
No 12
>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=78.81 E-value=7.9 Score=25.59 Aligned_cols=41 Identities=29% Similarity=0.362 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHH
Q 023175 40 ESRKLVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTK 92 (286)
Q Consensus 40 ~~~~~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~ 92 (286)
...+.|+.+|+.... .+|..+..-|+-|+.|+.+|+++|-.
T Consensus 4 ~~rk~VQ~iKEiv~~------------hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 4 ASRKTVQSIKEIVGC------------HSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred HHHHHHHHHHHHhcC------------CCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 444566666665532 46888999999999999999999865
No 13
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=64.52 E-value=14 Score=21.63 Aligned_cols=23 Identities=13% Similarity=0.059 Sum_probs=19.1
Q ss_pred CHHHHHHHHhhcCCCHHHHHHHH
Q 023175 68 DEDMILWFLKDRKFSIEESLAKL 90 (286)
Q Consensus 68 ~d~~LlRFLra~~~dv~~A~~~l 90 (286)
+.....+-|+.+++|+++|.+.|
T Consensus 15 ~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 15 SREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp -HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHHHHHHhC
Confidence 45679999999999999998754
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=62.10 E-value=16 Score=21.16 Aligned_cols=24 Identities=17% Similarity=0.081 Sum_probs=20.2
Q ss_pred CCHHHHHHHHhhcCCCHHHHHHHH
Q 023175 67 DDEDMILWFLKDRKFSIEESLAKL 90 (286)
Q Consensus 67 ~~d~~LlRFLra~~~dv~~A~~~l 90 (286)
.+.....+-|+.+++|+++|...|
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 356689999999999999998754
No 15
>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=61.74 E-value=17 Score=21.22 Aligned_cols=25 Identities=12% Similarity=0.033 Sum_probs=21.2
Q ss_pred CCHHHHHHHHhhcCCCHHHHHHHHH
Q 023175 67 DDEDMILWFLKDRKFSIEESLAKLT 91 (286)
Q Consensus 67 ~~d~~LlRFLra~~~dv~~A~~~l~ 91 (286)
.+.....+-|+.+++|+++|...|.
T Consensus 13 f~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 13 FSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 3578899999999999999987653
No 16
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=59.58 E-value=1.2e+02 Score=28.49 Aligned_cols=84 Identities=11% Similarity=0.042 Sum_probs=59.8
Q ss_pred CCCCcEEEEEcCCCCCCCCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCC---------CHHHHHHHHHH
Q 023175 127 INERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENA---------DLKFLTFLFDV 197 (286)
Q Consensus 127 ~~Grpv~~~~~~~~~~~~~~~~~~~r~~~~~lE~~~~~~~~~~~g~~vIiD~~g~s~~~~---------~~~~~k~~~~~ 197 (286)
....|++++-+|... .+.+.++|+++..... . .=-+||++-+|++-..+ +..-++.+++.
T Consensus 122 ~~~~P~vvilpGltg---~S~~~YVr~lv~~a~~---~-----G~r~VVfN~RG~~g~~LtTpr~f~ag~t~Dl~~~v~~ 190 (409)
T KOG1838|consen 122 DGTDPIVVILPGLTG---GSHESYVRHLVHEAQR---K-----GYRVVVFNHRGLGGSKLTTPRLFTAGWTEDLREVVNH 190 (409)
T ss_pred CCCCcEEEEecCCCC---CChhHHHHHHHHHHHh---C-----CcEEEEECCCCCCCCccCCCceeecCCHHHHHHHHHH
Confidence 356699999988643 3566788877665421 1 13578899999774443 35789999999
Q ss_pred HhhhcccccccEEEEeCCcchHHHHH
Q 023175 198 FYYYHPKRLGEVLFVEAPFVFKPFWQ 223 (286)
Q Consensus 198 lq~~yP~rl~~i~iiN~P~~f~~~w~ 223 (286)
+...||.+ +++.+--+.--+++++
T Consensus 191 i~~~~P~a--~l~avG~S~Gg~iL~n 214 (409)
T KOG1838|consen 191 IKKRYPQA--PLFAVGFSMGGNILTN 214 (409)
T ss_pred HHHhCCCC--ceEEEEecchHHHHHH
Confidence 99999998 7777776666666654
No 17
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=59.04 E-value=36 Score=23.38 Aligned_cols=49 Identities=18% Similarity=0.157 Sum_probs=34.9
Q ss_pred cEEEEEeCCCCCCCCCCHHHHHHHHHHHhhhcc--cccccEEEEeCCcchHHH
Q 023175 171 QILGIIDLRGFGTENADLKFLTFLFDVFYYYHP--KRLGEVLFVEAPFVFKPF 221 (286)
Q Consensus 171 g~~vIiD~~g~s~~~~~~~~~k~~~~~lq~~yP--~rl~~i~iiN~P~~f~~~ 221 (286)
|-.+++|++|+ ..+..+++-.++..+...|+ +.-+++.++|+......+
T Consensus 17 ~~~V~lDF~gv--~~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~ 67 (74)
T PF14213_consen 17 GEKVVLDFEGV--ESITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEM 67 (74)
T ss_pred CCeEEEECCCc--ccccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHH
Confidence 33489999998 44557778888877777777 345678888877665433
No 18
>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=58.17 E-value=22 Score=21.45 Aligned_cols=24 Identities=4% Similarity=0.191 Sum_probs=20.3
Q ss_pred CCHHHHHHHHhhcCCCHHHHHHHH
Q 023175 67 DDEDMILWFLKDRKFSIEESLAKL 90 (286)
Q Consensus 67 ~~d~~LlRFLra~~~dv~~A~~~l 90 (286)
.....|-.-|++|++|+-+|.+.+
T Consensus 15 ~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 15 QKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CChHHHHHHHHHcCCcHHHHHHHh
Confidence 356778999999999999998865
No 19
>KOG2267 consensus Eukaryotic-type DNA primase, large subunit [Replication, recombination and repair]
Probab=57.51 E-value=29 Score=32.14 Aligned_cols=74 Identities=20% Similarity=0.205 Sum_probs=48.9
Q ss_pred HHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHcCCCCCChhhhHHHHhcCceeecc
Q 023175 44 LVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKAIKWRQEFRVSELNEDSVRGIAESGKAYVHD 123 (286)
Q Consensus 44 ~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~~~wR~~~~~~~l~~~~~~~~l~~~~~~~~g 123 (286)
++.+|.+.|.++ .||. ......+--||.+.+..+++|.+.++. +|.- +++.+.+.+++.-.+-.-.
T Consensus 290 Cmk~lhe~LrkN-hHLr-----y~gR~qygLFLKgiGLS~deal~fwr~------sFtk-~~t~dkFdKEY~YnIRh~Y- 355 (475)
T KOG2267|consen 290 CMKQLHERLRKN-HHLR-----YGGRQQYGLFLKGIGLSVDEALAFWRG------SFTK-KMTRDKFDKEYRYNIRHNY- 355 (475)
T ss_pred HHHHHHHHHhhc-cccc-----ccchhhhhhhhhccCcCHHHHHHHHHH------HHhc-cCChhHhchhhceeheecc-
Confidence 788999999886 5774 456777889999999999999987544 4432 4455555555433322222
Q ss_pred CCCCCCCcEE
Q 023175 124 FLDINERPVL 133 (286)
Q Consensus 124 ~~D~~Grpv~ 133 (286)
-++|+++=
T Consensus 356 --GlEGkR~n 363 (475)
T KOG2267|consen 356 --GLEGKRAN 363 (475)
T ss_pred --cccccccc
Confidence 34555543
No 20
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=53.70 E-value=3.2 Score=29.29 Aligned_cols=49 Identities=24% Similarity=0.236 Sum_probs=31.1
Q ss_pred CCChHHHH---HHHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHH
Q 023175 35 QSDPHESR---KLVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKA 93 (286)
Q Consensus 35 ~~~~e~~~---~~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~ 93 (286)
.++|+++. .++.++|+.|.... . ++..|..-|..++||+++|+..|.+.
T Consensus 19 ~Ls~ed~~~L~~~l~~vr~~Lg~~~--------~--~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 19 ELSPEDQAQLYSCLPQVREVLGDYV--------P--PEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp H-TCHHHHHHCHHCCCHHHHCCCCC------------CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred cCCHHHHHHHHHHHHHHHHHHcccC--------C--CHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 45565543 25555565554321 1 56779999999999999999988764
No 21
>PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A.
Probab=52.83 E-value=63 Score=23.45 Aligned_cols=77 Identities=13% Similarity=0.042 Sum_probs=53.7
Q ss_pred CCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCC-CCCCCCCCHHHHHHHHHHHhhhcccccccEEEEeCCcchHHHH
Q 023175 144 VHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLR-GFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFW 222 (286)
Q Consensus 144 ~~~~~~~~r~~~~~lE~~~~~~~~~~~g~~vIiD~~-g~s~~~~~~~~~k~~~~~lq~~yP~rl~~i~iiN~P~~f~~~w 222 (286)
..+.+++.+ +.-.++..+. ....+.+++|++ ++ .++++.......++... +...++++=+|-.+.+...+-
T Consensus 10 ~~t~ed~~~-~~~~~~~~~~----~~~~~~ll~d~~~~~--~~~~~~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~~~ 81 (109)
T PF11964_consen 10 KLTEEDYKE-LLPALEELIA----DHGKIRLLVDLRRDF--EGWSPEARWEDAKFGLK-HLKHFRRIAVVGDSEWIRMIA 81 (109)
T ss_dssp EE-HHHHHH-HHHHHHHHHT----TSSSEEEEEEEC-CE--EEEHHHHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHHHH
T ss_pred eeCHHHHHH-HHHHHHHHHh----cCCceEEEEEecCcc--CCCCHHHHHHHHHhchh-hhcccCEEEEEECcHHHHHHH
Confidence 356777777 4444554433 345689999998 65 34456666666655444 788899999999999999999
Q ss_pred HHhhhc
Q 023175 223 QLTKPL 228 (286)
Q Consensus 223 ~lvkpf 228 (286)
+++.+|
T Consensus 82 ~~~~~~ 87 (109)
T PF11964_consen 82 NFFAAF 87 (109)
T ss_dssp HHHHHH
T ss_pred HHHHhc
Confidence 999997
No 22
>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=50.62 E-value=20 Score=30.37 Aligned_cols=53 Identities=25% Similarity=0.214 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcC------CCHHHHHHHHHHH
Q 023175 41 SRKLVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRK------FSIEESLAKLTKA 93 (286)
Q Consensus 41 ~~~~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~------~dv~~A~~~l~~~ 93 (286)
-.+..+.+|..|..+...||+..++..|-..|||-||-+. .|.+--.+.|...
T Consensus 102 SAKvm~~ikavLgaTKiDLPVDINDPYDlGLLLRhLRHHSNLLAnIgdP~VreqVLsAM 160 (238)
T PF02084_consen 102 SAKVMEDIKAVLGATKIDLPVDINDPYDLGLLLRHLRHHSNLLANIGDPEVREQVLSAM 160 (238)
T ss_pred cHHHHHHHHHHhcccccccccccCChhhHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence 3456788889998888899988888888899999999764 3555555555444
No 23
>TIGR02364 dha_pts dihydroxyacetone kinase, phosphotransfer subunit. In E. coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits. This protein, which resembles proteins of PTS transport systems, is found with its gene adjacent to
Probab=50.23 E-value=49 Score=25.46 Aligned_cols=63 Identities=22% Similarity=0.273 Sum_probs=41.0
Q ss_pred HHHHHhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHhhhcccccccEEEEeCCcchHHHHHHhhhccc
Q 023175 159 EKALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLK 230 (286)
Q Consensus 159 E~~~~~~~~~~~g~~vIiD~~g~s~~~~~~~~~k~~~~~lq~~yP~rl~~i~iiN~P~~f~~~w~lvkpfL~ 230 (286)
+.++.+.....+|++++.|+ |-+..|. ...+.++. ++..+.+..+|+|.+...+-..+..-..
T Consensus 49 ~~ai~~~~~~~dgVlvl~DL-Ggs~~n~-----e~a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~~g 111 (125)
T TIGR02364 49 IEAIEKADNEADGVLIFYDL-GSAVMNA-----EMAVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQVG 111 (125)
T ss_pred HHHHHHhcCCCCCEEEEEcC-CCcHhHH-----HHHHHHhc---cccccEEEEechhHHHHHHHHHHHHcCC
Confidence 33444443335799999999 7664331 11222322 3556889999999999988888776444
No 24
>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=45.69 E-value=45 Score=22.38 Aligned_cols=28 Identities=18% Similarity=0.286 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHhhcCCCHHHHHHHHHHH
Q 023175 66 RDDEDMILWFLKDRKFSIEESLAKLTKA 93 (286)
Q Consensus 66 ~~~d~~LlRFLra~~~dv~~A~~~l~~~ 93 (286)
..+-.|-.++|...+||.+.|.+.+.+-
T Consensus 24 gmn~~~s~~cLe~~~Wd~~~Al~~F~~l 51 (63)
T smart00804 24 GMNAEYSQMCLEDNNWDYERALKNFTEL 51 (63)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3578899999999999999999988764
No 25
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=42.16 E-value=74 Score=24.50 Aligned_cols=59 Identities=19% Similarity=0.282 Sum_probs=38.1
Q ss_pred HHHHhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHhhhcccccccEEEEeCCcchHHHHHHhhhcccc
Q 023175 160 KALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFWQLTKPLLKS 231 (286)
Q Consensus 160 ~~~~~~~~~~~g~~vIiD~~g~s~~~~~~~~~k~~~~~lq~~yP~rl~~i~iiN~P~~f~~~w~lvkpfL~~ 231 (286)
.++++... +|++++.|+ |-+..| ....+..+ .+- ++++++++|.+=..+-..+......
T Consensus 50 ~ai~~~~~--dGVlVltDL-Gssp~n-----~~~a~e~~----~~~-~~v~~~daPlVEGa~~Aav~~~~g~ 108 (124)
T PRK14484 50 EAIEKNES--DGVLIFFDL-GSAEMN-----AEMAIEML----DGE-KKIIIIDAPIVEGAFTAAVLLSAGA 108 (124)
T ss_pred HHHHhcCc--CCeEEEEeC-CChHHH-----HHHHHHhc----CCC-CcEEEECCcHHHHHHHHHHHHcCCC
Confidence 34445444 899999999 766444 22223333 222 8999999998877777776655443
No 26
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=35.14 E-value=26 Score=30.41 Aligned_cols=83 Identities=7% Similarity=0.057 Sum_probs=52.3
Q ss_pred hhcccccccEEEEeCCcchH---HHHHHhhhcccccccceeeccCCcchhhHHHHhhhhcCccccchh-cCCCccc--hh
Q 023175 200 YYHPKRLGEVLFVEAPFVFK---PFWQLTKPLLKSYASLKPSGRNISLKQRCQTTLESRLLVKSLHSC-LAALAGL--IF 273 (286)
Q Consensus 200 ~~yP~rl~~i~iiN~P~~f~---~~w~lvkpfL~~~t~ki~~~~~~~~~~~~~~~l~~~i~~~~LP~~-~GG~~~~--~~ 273 (286)
--|.+| +.|||||.-.... ..++.++-.... -.+|-|+++.....+..+...+....-.+... +||++.. ..
T Consensus 30 fIf~~R-ngihIIDL~kT~~~l~~A~~~v~~~~~~-~g~ILfVgTK~~a~~~V~~~A~r~g~~yV~~RwLgG~LTN~~ti 107 (252)
T COG0052 30 FIFGER-NGIHIIDLQKTLERLREAYKFLRRIAAN-GGKILFVGTKKQAQEPVKEFAERTGAYYVNGRWLGGMLTNFKTI 107 (252)
T ss_pred cceeec-CCcEEEEHHHHHHHHHHHHHHHHHHHcC-CCEEEEEechHHHHHHHHHHHHHhCCceecCcccCccccCchhH
Confidence 357899 9999999754433 233333333211 13788998875555556666666666666665 7998876 44
Q ss_pred hhccceehhhc
Q 023175 274 AQTVKTYYFVE 284 (286)
Q Consensus 274 ~~~~~~~~~~~ 284 (286)
.+++.++.-+|
T Consensus 108 ~~si~rl~~lE 118 (252)
T COG0052 108 RKSIKRLKELE 118 (252)
T ss_pred HHHHHHHHHHH
Confidence 46677766544
No 27
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=35.07 E-value=88 Score=28.76 Aligned_cols=36 Identities=28% Similarity=0.377 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHH
Q 023175 57 NSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKA 93 (286)
Q Consensus 57 ~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~ 93 (286)
+.+|.|. ..-|+.-.|--|.-|+||+++|+++++-.
T Consensus 234 p~~P~gt-~vkDnEqAL~~LvkcnfDteeAlrr~rfn 269 (445)
T KOG4329|consen 234 PCPPEGT-EVKDNEQALYELVKCNFDTEEALRRLRFN 269 (445)
T ss_pred CCCCccc-cccccHHHHHHHHHcCCcHHHHHHhcCCc
Confidence 4455443 33456677778999999999999877543
No 28
>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=34.09 E-value=2.6e+02 Score=26.12 Aligned_cols=45 Identities=27% Similarity=0.280 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHH
Q 023175 43 KLVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKA 93 (286)
Q Consensus 43 ~~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~ 93 (286)
-++..+.+.+.+. .+|+ ......|--||.+.+.++++|.+.++..
T Consensus 226 ~Cm~~l~~~l~~~-~hL~-----h~gR~ql~lFLk~iGl~~~e~l~~~~~~ 270 (390)
T cd07322 226 LCMRQLHEALRKN-HHLK-----HGGRLQLGLFLKGIGLSLEEALKFWRSE 270 (390)
T ss_pred HHHHHHHHHHhcC-CCCC-----chhHHHHHHHHHhCCCCHHHHHHHHHHh
Confidence 3777888888765 5775 5678889999999999999999987665
No 29
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=34.00 E-value=1.6e+02 Score=30.19 Aligned_cols=75 Identities=20% Similarity=0.291 Sum_probs=42.1
Q ss_pred HHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHH-------HHcCCCCCChhhhHHHH--
Q 023175 44 LVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKAIKWR-------QEFRVSELNEDSVRGIA-- 114 (286)
Q Consensus 44 ~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~~~wR-------~~~~~~~l~~~~~~~~l-- 114 (286)
.|+||-+++-.. ..+. ...|...+||+ |++.|+..-..- ..+.+..++.+++...+
T Consensus 38 yI~ELs~Mvp~~-~~~~----RK~DK~tVLr~----------aV~~lr~~k~~~~~~~~~~~d~KpSflS~~eL~~LmLe 102 (803)
T KOG3561|consen 38 YIEELSEMVPTN-ASLS----RKPDKLTVLRM----------AVDHLRLIKEQESENSSIDQDYKPSFLSNDELTHLILE 102 (803)
T ss_pred HHHHHHHhhhcc-hhcc----cCchHHHHHHH----------HHHHHHHHhhhhcccccccccccccccchHHHHHHHHH
Confidence 455555555432 1222 45566777776 555555554431 12334456666665532
Q ss_pred -hcCceeeccCCCCCCCcEEEEE
Q 023175 115 -ESGKAYVHDFLDINERPVLIVV 136 (286)
Q Consensus 115 -~~~~~~~~g~~D~~Grpv~~~~ 136 (286)
-.|.+|+.+ +| |+.|+|-.
T Consensus 103 AlDGF~fvV~-cd--G~IvyVSe 122 (803)
T KOG3561|consen 103 ALDGFLFVVN-CD--GRIVYVSE 122 (803)
T ss_pred HhcCeEEEEe-cC--ceEEEEec
Confidence 358888888 77 88887653
No 30
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=33.24 E-value=1.6e+02 Score=25.35 Aligned_cols=63 Identities=17% Similarity=0.189 Sum_probs=42.3
Q ss_pred HHHHHHHHHHhCC------CCcccEEEEEeCCCCC--CCCCCHHHHHHHHHHHhhhcccccccEEEEeCCcchH
Q 023175 154 CVFFIEKALSKLP------PGKEQILGIIDLRGFG--TENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFK 219 (286)
Q Consensus 154 ~~~~lE~~~~~~~------~~~~g~~vIiD~~g~s--~~~~~~~~~k~~~~~lq~~yP~rl~~i~iiN~P~~f~ 219 (286)
++|++|..+...+ ...++--+|+||-|-= ..| ..++++++.-++. .=.++..+|++..+++.+
T Consensus 75 Lv~cmEyl~~NldwL~~~~Gd~eddylifDcPGQIELytH--~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD 145 (273)
T KOG1534|consen 75 LVYCMEYLLENLDWLEEEIGDVEDDYLIFDCPGQIELYTH--LPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVD 145 (273)
T ss_pred chhHHHHHHHHHHHHHhhccCccCCEEEEeCCCeeEEeec--ChhHHHHHHHHhc-ccCceeEEEEeccchhhh
Confidence 6778887766332 2356777899998854 455 4566777777766 336778888888776653
No 31
>PF09590 Env-gp36: Lentivirus surface glycoprotein; InterPro: IPR018582 The proteins in this family are envelope glycoproteins from feline immunodeficiency retrovirus. The process of lentiviral envelope glycoprotein-mediated fusion of membranes is essential for viral entry and syncytia formation [].
Probab=32.02 E-value=2e+02 Score=27.85 Aligned_cols=65 Identities=11% Similarity=0.186 Sum_probs=43.8
Q ss_pred CCCCCChHHHHH-------HHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHH---HHHcC
Q 023175 32 KNCQSDPHESRK-------LVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKAIKW---RQEFR 101 (286)
Q Consensus 32 ~e~~~~~e~~~~-------~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~~~w---R~~~~ 101 (286)
.+.+.||+++++ .++++|+.+.+- .+..+ .-.+.-=.|||+..+.++-.-+..+-.++.. |.+.+
T Consensus 39 R~pGiT~~eKqe~ckiLQp~Lq~iK~e~~Eg--kl~~~---~~GK~rr~R~lrysd~~v~~~~~l~~g~~~Yl~~r~~lG 113 (591)
T PF09590_consen 39 RVPGITPQEKQEYCKILQPKLQEIKQEMQEG--KLEEG---NAGKFRRARYLRYSDEQVLSIVYLFVGYCRYLYDRNKLG 113 (591)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc--ccccC---CcchhhhhhHhhhhHHHHHHHHHHHhhhhhcccchhhcC
Confidence 455777776655 677777777542 33222 2233456899999999999888888877777 55555
No 32
>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=31.18 E-value=52 Score=20.97 Aligned_cols=26 Identities=12% Similarity=0.202 Sum_probs=20.5
Q ss_pred CCHHHHHHHHhhcCCCHHHHHHHHHH
Q 023175 67 DDEDMILWFLKDRKFSIEESLAKLTK 92 (286)
Q Consensus 67 ~~d~~LlRFLra~~~dv~~A~~~l~~ 92 (286)
.+-.+-.++|..++||.++|...+..
T Consensus 13 mn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 13 MNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp S-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 35568899999999999999988764
No 33
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=28.86 E-value=42 Score=29.27 Aligned_cols=26 Identities=12% Similarity=0.394 Sum_probs=22.8
Q ss_pred ccEEEEeCCcchHHHHHHhhhccccc
Q 023175 207 GEVLFVEAPFVFKPFWQLTKPLLKSY 232 (286)
Q Consensus 207 ~~i~iiN~P~~f~~~w~lvkpfL~~~ 232 (286)
..++|||+||-+..-...+-|+|...
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~ 262 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTL 262 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHH
Confidence 36999999999999999999998774
No 34
>PF04378 RsmJ: Ribosomal RNA small subunit methyltransferase D, RsmJ; InterPro: IPR007473 This is a bacterial protein of unknown function, possibly secreted.; PDB: 2OO3_A.
Probab=28.70 E-value=33 Score=29.82 Aligned_cols=25 Identities=16% Similarity=0.317 Sum_probs=19.3
Q ss_pred cEEEEeCCcchHHHHHHhhhccccc
Q 023175 208 EVLFVEAPFVFKPFWQLTKPLLKSY 232 (286)
Q Consensus 208 ~i~iiN~P~~f~~~w~lvkpfL~~~ 232 (286)
.++|||+||-+.-..+-+-|+|.+.
T Consensus 207 Gm~iiNPPw~l~~~l~~~l~~L~~~ 231 (245)
T PF04378_consen 207 GMLIINPPWTLDEELEEILPWLAET 231 (245)
T ss_dssp EEEEES--TTHHHHHHHHHHHHHHH
T ss_pred eEEEEcCCccHHHHHHHHHHHHHHH
Confidence 6999999999998888887877664
No 35
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=26.74 E-value=49 Score=30.16 Aligned_cols=26 Identities=23% Similarity=0.509 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHhhcCCCHHHHHHHH
Q 023175 65 GRDDEDMILWFLKDRKFSIEESLAKL 90 (286)
Q Consensus 65 ~~~~d~~LlRFLra~~~dv~~A~~~l 90 (286)
..+-+..|+|-|.+++||+++|.+-|
T Consensus 140 GEDVENillkLlqaadydV~rAerGI 165 (408)
T COG1219 140 GEDVENILLKLLQAADYDVERAERGI 165 (408)
T ss_pred chhHHHHHHHHHHHcccCHHHHhCCe
Confidence 34456889999999999999998754
No 36
>KOG0431 consensus Auxilin-like protein and related proteins containing DnaJ domain [General function prediction only]
Probab=26.47 E-value=1.2e+02 Score=28.92 Aligned_cols=78 Identities=12% Similarity=0.135 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHcCC----CCCChhhhHHHH
Q 023175 39 HESRKLVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKAIKWRQEFRV----SELNEDSVRGIA 114 (286)
Q Consensus 39 e~~~~~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~~~wR~~~~~----~~l~~~~~~~~l 114 (286)
.+..+.++++|+-+.+.. ..-|.-+.||.-+...|+-.=+.-|..-+-|-..|.. |=+++..|++.+
T Consensus 339 ~k~~~~~ae~~~e~~r~~---------e~~d~~I~~W~~GKE~NIRALLSTLh~VLW~es~WqpVsltDLVtp~~VKKaY 409 (453)
T KOG0431|consen 339 EKRPREIAEMRKELSRLM---------EPLDEEIRRWSEGKEGNIRALLSTLHYVLWPESGWQPVSLTDLVTPAQVKKAY 409 (453)
T ss_pred hhhHHHHHHHHHHHHhhc---------chHHHHHHHhcccccccHHHHHHHHhHhhcCccCcccCchhhccCHHHHHHHH
Confidence 355556777765443321 2247889999999999998888777766655233432 335678999999
Q ss_pred hcCceeeccCCCC
Q 023175 115 ESGKAYVHDFLDI 127 (286)
Q Consensus 115 ~~~~~~~~g~~D~ 127 (286)
+..++++|+ ||
T Consensus 410 rKA~L~VHP--DK 420 (453)
T KOG0431|consen 410 RKAVLCVHP--DK 420 (453)
T ss_pred HhhhheeCc--cc
Confidence 988889997 66
No 37
>PF11339 DUF3141: Protein of unknown function (DUF3141); InterPro: IPR024501 This family of proteins appears to be predominantly expressed in Proteobacteria. Their function is unknown.
Probab=26.41 E-value=3.9e+02 Score=26.15 Aligned_cols=62 Identities=15% Similarity=0.209 Sum_probs=42.8
Q ss_pred ChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCCCCCCCCCHHHHHHHHHHHhhhcccccccEEEEeCCcchH
Q 023175 146 DPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFK 219 (286)
Q Consensus 146 ~~~~~~r~~~~~lE~~~~~~~~~~~g~~vIiD~~g~s~~~~~~~~~k~~~~~lq~~yP~rl~~i~iiN~P~~f~ 219 (286)
+.+|+.+.....+|.+...-+.. ..-++|=+|.| --.+.++...+|+.++-+.+--+|.-+.
T Consensus 117 Tl~DV~~ae~~Fv~~V~~~hp~~-~kp~liGnCQg-----------GWa~~mlAA~~Pd~~gplvlaGaPlsyw 178 (581)
T PF11339_consen 117 TLEDVMRAEAAFVEEVAERHPDA-PKPNLIGNCQG-----------GWAAMMLAALRPDLVGPLVLAGAPLSYW 178 (581)
T ss_pred cHHHHHHHHHHHHHHHHHhCCCC-CCceEEeccHH-----------HHHHHHHHhcCcCccCceeecCCCcccc
Confidence 66777777777777776554432 26777777775 2244567888899999888888876554
No 38
>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=26.23 E-value=1.2e+02 Score=18.21 Aligned_cols=22 Identities=14% Similarity=0.073 Sum_probs=18.5
Q ss_pred HHHHHHHHhhcCCCHHHHHHHH
Q 023175 69 EDMILWFLKDRKFSIEESLAKL 90 (286)
Q Consensus 69 d~~LlRFLra~~~dv~~A~~~l 90 (286)
..++..-|..++||+.+|++.|
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 4678889999999999999987
No 39
>KOG3824 consensus Huntingtin interacting protein HYPE [General function prediction only]
Probab=24.82 E-value=1.3e+02 Score=27.37 Aligned_cols=49 Identities=20% Similarity=0.293 Sum_probs=33.8
Q ss_pred CHHHHHHHHHHHHHHHHHcCCCCCChhhhHHHHhcCceeeccCCCCCCC
Q 023175 82 SIEESLAKLTKAIKWRQEFRVSELNEDSVRGIAESGKAYVHDFLDINER 130 (286)
Q Consensus 82 dv~~A~~~l~~~~~wR~~~~~~~l~~~~~~~~l~~~~~~~~g~~D~~Gr 130 (286)
..+...++++++..|-..-..-.+.+-+....-.-..+++|++.|-+||
T Consensus 333 ~P~dv~~qmq~fv~WLNsE~~~tlhPve~AAlAHYKLV~iHPF~DGNGR 381 (472)
T KOG3824|consen 333 SPEDVMEQMQDFVDWLNSESTLTLHPVERAALAHYKLVLIHPFTDGNGR 381 (472)
T ss_pred ChHHHHHHHHHHHHHhccccccccChHHHHHHhhheeEEEeccccCCch
Confidence 3556777888999997654444555544443334467889999999998
No 40
>cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta
Probab=23.36 E-value=2.7e+02 Score=24.39 Aligned_cols=57 Identities=16% Similarity=0.179 Sum_probs=44.3
Q ss_pred ChHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHcC
Q 023175 37 DPHESRKLVLQVKERLEKDYNSLPVGKNGRDDEDMILWFLKDRKFSIEESLAKLTKAIKWRQEFR 101 (286)
Q Consensus 37 ~~e~~~~~i~~lr~~l~~~~~~lp~~~~~~~~d~~LlRFLra~~~dv~~A~~~l~~~~~wR~~~~ 101 (286)
-|++..+.+++.|+.|-+.- ...||..+-|||..-..+.++-.+.|++.+.-++-++
T Consensus 188 ip~~~~~~~~~~r~~l~e~v--------ae~dd~L~e~yl~~~~~~~~el~~~l~~~~~~~~~~P 244 (270)
T cd01886 188 IPEDLLEEAEEAREELIETL--------AEFDDELMEKYLEGEEITEEEIKAAIRKGTIANKIVP 244 (270)
T ss_pred CCHHHHHHHHHHHHHHHHHH--------hcCCHHHHHHHhCCCCCCHHHHHHHHHHHHHcCcEEE
Confidence 35566677888888886642 3458999999999999999999999888877655554
No 41
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=22.07 E-value=3.5e+02 Score=21.50 Aligned_cols=54 Identities=13% Similarity=0.105 Sum_probs=35.1
Q ss_pred hcCceeeccCCCCCCCcEEEEEcCCCCCCCCChHHHHHHHHHHHHHHHHhCCCCcccEEEEEeCCC
Q 023175 115 ESGKAYVHDFLDINERPVLIVVASKHLPAVHDPVEDEKLCVFFIEKALSKLPPGKEQILGIIDLRG 180 (286)
Q Consensus 115 ~~~~~~~~g~~D~~Grpv~~~~~~~~~~~~~~~~~~~r~~~~~lE~~~~~~~~~~~g~~vIiD~~g 180 (286)
..|..+..| .|..|+.|+.+-.+. ..+.+.+++.-+++.. .. .++=++++|+..
T Consensus 48 d~G~l~y~G-~De~gn~VY~lG~~~------~~~~~~~al~~l~~i~--~~---~~~~i~~vdt~~ 101 (148)
T PF11385_consen 48 DIGRLIYMG-TDEYGNEVYILGRKN------NGKIVERALKSLLEIL--GI---ENEEIILVDTSP 101 (148)
T ss_pred cCceEEEEE-EcCCCCEEEEEecCC------hHHHHHHHHHHHHHHh--CC---CCCcEEEEeccc
Confidence 457888899 899999999887553 2344555655555443 11 134477888764
No 42
>PF01740 STAS: STAS domain; InterPro: IPR002645 The STAS (Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. The establishment of differential gene expression in sporulating Bacillus subtilis involves four protein components one of which is SpoIIAA (P10727 from SWISSPROT). The four components regulate the sporulation sigma factor F. Early in sporulation, SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase SpoIIAB (P10728 from SWISSPROT). The site at which this protein is a conserved serine. SpoIIAB is an anti-sigma factor that in its free form inhibits F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases Sigma F activity []. The STAS domain is found in the anti-sigma factor antagonist SpoIIAA.; PDB: 3T6O_B 3LKL_B 1H4Z_A 1H4Y_B 1H4X_B 3NY7_A 3OIZ_A 1T6R_A 1VC1_B 1SBO_A ....
Probab=20.77 E-value=1.2e+02 Score=22.28 Aligned_cols=48 Identities=17% Similarity=0.130 Sum_probs=33.6
Q ss_pred EEEEEeCCCCCCCCCCHHHHHHHHHHHhhhcccccccEEEEeCCcchHHHH
Q 023175 172 ILGIIDLRGFGTENADLKFLTFLFDVFYYYHPKRLGEVLFVEAPFVFKPFW 222 (286)
Q Consensus 172 ~~vIiD~~g~s~~~~~~~~~k~~~~~lq~~yP~rl~~i~iiN~P~~f~~~w 222 (286)
-.+|+||+++ ..++...+..+.++.+..- .+=..++++|.+.-....+
T Consensus 49 ~~vIlD~s~v--~~iDssgi~~L~~~~~~~~-~~g~~~~l~~~~~~v~~~l 96 (117)
T PF01740_consen 49 KNVILDMSGV--SFIDSSGIQALVDIIKELR-RRGVQLVLVGLNPDVRRIL 96 (117)
T ss_dssp SEEEEEETTE--SEESHHHHHHHHHHHHHHH-HTTCEEEEESHHHHHHHHH
T ss_pred eEEEEEEEeC--CcCCHHHHHHHHHHHHHHH-HCCCEEEEEECCHHHHHHH
Confidence 5889999986 5566666666666655555 5667889998866655443
Done!