Query 043459
Match_columns 243
No_of_seqs 129 out of 1174
Neff 9.6
Searched_HMMs 46136
Date Fri Mar 29 05:16:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043459.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043459hhsearch_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 3.7E-46 8E-51 302.8 19.7 221 16-240 27-248 (324)
2 KOG1471 Phosphatidylinositol t 100.0 8.2E-40 1.8E-44 275.6 20.9 229 8-238 16-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 4.4E-36 9.5E-41 228.5 8.2 152 82-234 3-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 6.8E-32 1.5E-36 205.2 15.0 143 92-236 14-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 100.0 2.7E-29 5.8E-34 189.9 14.1 146 87-234 10-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.8 1.4E-19 3.1E-24 136.2 2.5 141 88-238 4-147 (149)
7 PF03765 CRAL_TRIO_N: CRAL/TRI 99.0 2.4E-09 5.2E-14 66.2 5.9 47 15-61 1-55 (55)
8 KOG4406 CDC42 Rho GTPase-activ 98.9 1.2E-08 2.6E-13 85.6 10.2 131 86-225 80-213 (467)
9 PF14555 UBA_4: UBA-like domai 92.8 0.53 1.1E-05 27.0 5.2 36 16-59 2-37 (43)
10 PF02845 CUE: CUE domain; Int 90.5 0.97 2.1E-05 25.7 4.6 38 16-60 3-40 (42)
11 smart00546 CUE Domain that may 88.6 1.7 3.7E-05 24.8 4.7 37 16-59 4-40 (43)
12 PF06972 DUF1296: Protein of u 85.4 5.3 0.00011 24.5 5.6 43 11-60 2-44 (60)
13 smart00804 TAP_C C-terminal do 80.1 12 0.00026 23.4 6.4 48 7-62 5-52 (63)
14 PF08938 HBS1_N: HBS1 N-termin 79.8 0.37 8E-06 31.8 -0.9 55 5-61 15-70 (79)
15 PF11239 DUF3040: Protein of u 76.8 3.3 7.1E-05 27.4 3.0 23 9-31 2-24 (82)
16 KOG1838 Alpha/beta hydrolase [ 76.3 40 0.00087 29.6 10.1 85 96-194 123-216 (409)
17 PF11964 SpoIIAA-like: SpoIIAA 75.0 14 0.0003 25.3 6.0 76 114-197 11-87 (109)
18 PF00627 UBA: UBA/TS-N domain; 67.1 18 0.0004 19.6 5.2 35 15-58 3-37 (37)
19 PF04838 Baculo_LEF5: Baculovi 66.4 5.2 0.00011 29.5 2.2 49 159-208 16-68 (159)
20 TIGR02364 dha_pts dihydroxyace 64.3 32 0.00069 24.8 6.0 53 138-199 59-111 (125)
21 smart00165 UBA Ubiquitin assoc 62.2 17 0.00036 19.6 3.4 24 35-58 13-36 (37)
22 KOG2333 Uncharacterized conser 62.1 7.8 0.00017 34.5 2.9 65 1-65 130-194 (614)
23 COG2810 Predicted type IV rest 61.6 46 0.001 26.9 6.8 112 11-148 3-115 (284)
24 cd00194 UBA Ubiquitin Associat 61.3 18 0.00039 19.6 3.4 24 35-58 13-36 (38)
25 PF01740 STAS: STAS domain; I 54.0 25 0.00054 24.4 4.0 52 140-194 48-99 (117)
26 TIGR02886 spore_II_AA anti-sig 51.6 64 0.0014 21.9 5.7 52 141-195 40-91 (106)
27 PF03474 DMA: DMRTA motif; In 51.2 38 0.00083 19.0 3.5 24 35-58 15-38 (39)
28 PF14213 DUF4325: Domain of un 47.6 72 0.0016 20.3 5.7 51 140-192 17-69 (74)
29 PRK12751 cpxP periplasmic stre 45.9 81 0.0018 23.9 5.8 59 5-63 52-110 (162)
30 cd07322 PriL_PriS_Eukaryotic E 45.3 1.7E+02 0.0036 25.7 8.4 44 17-61 227-270 (390)
31 PRK10363 cpxP periplasmic repr 45.1 1.2E+02 0.0027 23.0 6.6 59 5-63 46-104 (166)
32 PRK02399 hypothetical protein; 44.1 2.2E+02 0.0048 25.1 8.8 80 114-199 313-403 (406)
33 KOG2267 Eukaryotic-type DNA pr 44.0 44 0.00096 29.1 4.5 78 16-104 289-366 (475)
34 cd07043 STAS_anti-anti-sigma_f 42.5 96 0.0021 20.3 5.5 52 141-195 39-90 (99)
35 PF03641 Lysine_decarbox: Poss 39.6 1E+02 0.0022 22.3 5.4 62 157-221 64-132 (133)
36 COG0052 RpsB Ribosomal protein 39.2 37 0.0008 27.6 3.2 66 169-237 30-103 (252)
37 PF11339 DUF3141: Protein of u 37.1 2.2E+02 0.0047 26.2 7.8 59 114-184 116-174 (581)
38 COG2961 ComJ Protein involved 35.2 21 0.00045 29.2 1.2 28 175-202 236-263 (279)
39 PF03943 TAP_C: TAP C-terminal 35.2 29 0.00064 20.6 1.6 26 35-60 13-38 (51)
40 cd01886 EF-G Elongation factor 34.4 1.4E+02 0.003 24.6 6.1 57 8-67 186-242 (270)
41 PF04378 RsmJ: Ribosomal RNA s 34.4 17 0.00036 29.6 0.6 32 172-203 202-233 (245)
42 TIGR00377 ant_ant_sig anti-ant 33.2 1.4E+02 0.003 20.1 5.1 52 140-195 43-95 (108)
43 PF07308 DUF1456: Protein of u 33.2 71 0.0015 20.3 3.2 28 19-46 33-61 (68)
44 cd06844 STAS Sulphate Transpor 31.5 1.6E+02 0.0035 19.7 5.8 53 140-195 39-91 (100)
45 COG4567 Response regulator con 30.6 1.1E+02 0.0024 23.1 4.2 58 2-61 104-168 (182)
46 PF02954 HTH_8: Bacterial regu 30.1 92 0.002 17.3 3.1 24 36-59 6-29 (42)
47 PF04552 Sigma54_DBD: Sigma-54 29.2 1.4E+02 0.003 22.6 4.7 44 18-62 106-150 (160)
48 cd07041 STAS_RsbR_RsbS_like Su 28.9 1.9E+02 0.0041 19.6 6.3 53 140-195 41-93 (109)
49 cd00870 PI3Ka_III Phosphoinosi 28.7 2.6E+02 0.0056 21.2 6.2 37 8-52 24-60 (166)
50 cd07042 STAS_SulP_like_sulfate 28.4 1.8E+02 0.0039 19.2 7.4 52 141-195 42-93 (107)
51 COG1219 ClpX ATP-dependent pro 28.0 46 0.00099 28.5 2.1 25 34-58 141-165 (408)
52 cd00872 PI3Ka_I Phosphoinositi 27.7 2.8E+02 0.006 21.2 6.2 45 9-61 18-62 (171)
53 KOG1534 Putative transcription 27.5 1.5E+02 0.0033 23.8 4.7 130 94-226 28-193 (273)
54 PF13466 STAS_2: STAS domain 26.1 1.8E+02 0.0038 18.4 5.7 51 141-194 27-77 (80)
55 cd08816 CARD_RIG-I_1 Caspase a 25.9 2.1E+02 0.0045 19.1 5.9 53 11-63 1-60 (89)
56 PF05762 VWA_CoxE: VWA domain 25.9 1.3E+02 0.0027 23.9 4.3 14 115-128 69-82 (222)
57 PRK14484 phosphotransferase ma 23.8 2.8E+02 0.0061 19.9 5.4 49 139-198 58-106 (124)
58 PRK10455 periplasmic protein; 22.3 3.4E+02 0.0074 20.5 5.8 54 7-60 54-107 (161)
59 PF04695 Pex14_N: Peroxisomal 20.8 3.4E+02 0.0074 19.7 6.1 46 14-61 2-47 (136)
60 COG1157 FliI Flagellar biosynt 20.6 1.9E+02 0.0041 25.7 4.5 60 5-72 361-424 (441)
61 PRK00095 mutL DNA mismatch rep 20.6 4.5E+02 0.0098 24.6 7.4 95 9-104 488-605 (617)
62 PF05704 Caps_synth: Capsular 20.3 64 0.0014 26.7 1.6 40 139-183 45-84 (276)
63 PF10400 Vir_act_alpha_C: Viru 20.1 2.4E+02 0.0052 18.3 4.2 33 35-67 3-35 (90)
64 PF09740 DUF2043: Uncharacteri 20.1 52 0.0011 23.1 0.9 12 89-100 91-106 (110)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=3.7e-46 Score=302.84 Aligned_cols=221 Identities=43% Similarity=0.697 Sum_probs=199.1
Q ss_pred HHHHHHHHHHhhhC-CCCCCCChHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhcCCCCCCCCCCchhhhhcCCceeccCC
Q 043459 16 TKIRLMRALVEKQD-PSSKEVDDPTLRRFLRARDLDVEKASGMFLKYLKWRQTFVPNGSISLSEVPNELSQNKMFMQGFD 94 (243)
Q Consensus 16 ~~l~~lr~~l~~~~-~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~~~~R~~~~~~~~~~~~~~~~~l~~~~~~~~g~d 94 (243)
+.+.++++.+.... ......+|.+++|||||++||+++|.+++.+++.||+.+++...+..+++..++..|.+|+.|+|
T Consensus 27 ~k~~~~~~~~~pl~~~~~~~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~G~D 106 (324)
T KOG1470|consen 27 DKINSVKKLLGPLTEKESKWCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYILGHD 106 (324)
T ss_pred HHHHHHHHhhcchhhhhHhcCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEeccc
Confidence 45566665553321 12346799999999999999999999999999999999988765677789999999999999999
Q ss_pred CCCCcEEEEeCccccccccCCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecCCCCCCCccHHHHHHHHHHHhhccccc
Q 043459 95 KKGRPIATVLGARHFQNKLGGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPER 174 (243)
Q Consensus 95 ~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~r 174 (243)
++||||+|++++...++. .+.++..|+++|+||.++..++.+++++++++|++|+|++|+|.+..+.++.++|+|||+|
T Consensus 107 ~~gRPVl~~~~~~~~qn~-~t~~~~~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs~sN~d~~~~k~~~~~lq~hYPEr 185 (324)
T KOG1470|consen 107 KDGRPVLYLRPRPHRQNT-KTQKELERLLVYTLENAILFLPPGQEQFVWLFDLTGFSMSNPDIKFLKELLHILQDHYPER 185 (324)
T ss_pred CCCCeEEEEecCCCCCCC-CCHHHHHHHHHHHHHHHHHhCCCCcceEEEEEecccCcccCCCcHHHHHHHHHHHHhChHH
Confidence 999999999888777777 7899999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceEEEeCChHHHHHHHHHcccCChhhhhceEEecCcchHHHHHhcCCCCCCccccCCCCCCccC
Q 043459 175 LGKLFIVHAPYIFMTVWKIVYPFIDNNTKKKIVFVQDKKLKSTLLEEIDESQIPEIYGGQLPLVPI 240 (243)
Q Consensus 175 l~~i~ivn~p~~~~~~~~~ik~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~~~~~~~ 240 (243)
|+..+++|+||+|..+|+++|||++++|++||+|+.+. ..+.+|||+++||..+||+..+...
T Consensus 186 Lg~a~l~~~P~iF~~~wkiikpflDp~t~~Kv~F~~~~---~~l~~~~d~~~l~s~~GG~~~~~y~ 248 (324)
T KOG1470|consen 186 LGKALLVNAPWIFQPFWKIIKPFLDPKTASKVKFVEPK---DDLSEYFDESQLPSLFGGKLLFEYT 248 (324)
T ss_pred hhhhhhcCChHHHHHHHHHhhhccChhhhceeEEecCh---hHHHhhCCccccchhhCCCcccccC
Confidence 99999999999999999999999999999999999875 4699999999999999998776543
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=8.2e-40 Score=275.55 Aligned_cols=229 Identities=35% Similarity=0.485 Sum_probs=187.3
Q ss_pred CCCCHHHHHHHHHHHHHHhhhCCCC-CCCChHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhcCCCCCCCCCCchhhhhc-
Q 043459 8 SNIDEKEETKIRLMRALVEKQDPSS-KEVDDPTLRRFLRARDLDVEKASGMFLKYLKWRQTFVPNGSISLSEVPNELSQ- 85 (243)
Q Consensus 8 ~~l~~~~~~~l~~lr~~l~~~~~~~-~~~~d~~llrfL~~~~~d~~~a~~~l~~~~~~R~~~~~~~~~~~~~~~~~l~~- 85 (243)
.++++.+++.++++| |+..++..+ ...+|.+|+||||+++||+++|.+++.+++.||.+++.+......+..+.+..
T Consensus 16 ~~~~~~~~~~i~~lr-~~~~~~~l~~~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~~~~~~ 94 (317)
T KOG1471|consen 16 NEITESEEAVIAQLR-WLLQKPHLPNKYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDDELLKY 94 (317)
T ss_pred CCCcHHHHHHHHHHH-HHhhccCCCCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccchhhhhh
Confidence 456788899999999 777763333 26899999999999999999999999999999999877664443222233332
Q ss_pred CCceeccCCCCCCcEEEEeCcccccccc-----------CCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecCCCCCCC
Q 043459 86 NKMFMQGFDKKGRPIATVLGARHFQNKL-----------GGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLKGWGYSN 154 (243)
Q Consensus 86 ~~~~~~g~d~~Grpv~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~g~~~~~ 154 (243)
.....+|.|++|+||.+.+.+..+...+ ....++.+.+...+|........+++|++.|+|++|+++++
T Consensus 95 ~~~~~~~~~~~g~~v~~~~~g~~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~ 174 (317)
T KOG1471|consen 95 YPQGLHGVDKEGRPVYIERLGKIDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSH 174 (317)
T ss_pred ccccccccCCCCCEEEEeccCCCCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchh
Confidence 2345789999999999999998876552 22344455555555655555556789999999999999998
Q ss_pred c---cHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHcccCChhhhhceEEecCcchHHHHHhcCCCCCCcccc
Q 043459 155 S---DLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVYPFIDNNTKKKIVFVQDKKLKSTLLEEIDESQIPEIY 231 (243)
Q Consensus 155 ~---~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~ 231 (243)
+ ....+++++.+++++||++++++||||+|++++++|+++||||+++|++||++.++ ++.++|.++|+++.||.+|
T Consensus 175 ~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~-~~~~~L~k~i~~~~LP~~y 253 (317)
T KOG1471|consen 175 LLKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHS-KDKESLLKYIPPEVLPEEY 253 (317)
T ss_pred HHHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCC-CchhhhhhhCCHhhCcccc
Confidence 7 57789999999999999999999999999999999999999999999999995443 4578999999999999999
Q ss_pred CCCCCCc
Q 043459 232 GGQLPLV 238 (243)
Q Consensus 232 GG~~~~~ 238 (243)
||++.+.
T Consensus 254 GG~~~~~ 260 (317)
T KOG1471|consen 254 GGTCGDL 260 (317)
T ss_pred CCCcccc
Confidence 9999985
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=100.00 E-value=4.4e-36 Score=228.50 Aligned_cols=152 Identities=41% Similarity=0.707 Sum_probs=129.5
Q ss_pred hhhcCCceeccCCCCCCcEEEEeCccccccccCCHHHHHHHHHHHHHHHHhhCC--CCCceEEEEEecCCCCCCCcc---
Q 043459 82 ELSQNKMFMQGFDKKGRPIATVLGARHFQNKLGGLEEFKRFVVYILDKICSRMP--PGQEKFVVIGDLKGWGYSNSD--- 156 (243)
Q Consensus 82 ~l~~~~~~~~g~d~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~--~~~~~~~iI~D~~g~~~~~~~--- 156 (243)
..+.+..+++|+|++||||++++++++++.. .+.+++.+++++.+|.+++.+. .+.+|+++|+|++|+++++++
T Consensus 3 ~~~~~~~~~~g~D~~gr~v~~~~~~~~~~~~-~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~ 81 (159)
T PF00650_consen 3 ILKSGPFYLHGRDKDGRPVIYIRLGRFDPKK-FSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFSLSNFDWWP 81 (159)
T ss_dssp HHTTSCEEEEEE-TTS-EEEEEEGTT--HHT-S-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT--HHHHHCHH
T ss_pred HHCCeeEEECCCCCCcCEEEEEEcccCCCCc-CCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCceEeccccch
Confidence 3456778999999999999999999999888 7889999999999999886554 467999999999999999987
Q ss_pred HHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHcccCChhhhhceEEecCcchHHHHHhcCCCCCCccccCCC
Q 043459 157 LRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVYPFIDNNTKKKIVFVQDKKLKSTLLEEIDESQIPEIYGGQ 234 (243)
Q Consensus 157 ~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~ 234 (243)
.+.++.++++++++||+|++++||+|+|++++++|+++++|+++++++||+++++.++.++|.++||+++||.+|||+
T Consensus 82 ~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~~GG~ 159 (159)
T PF00650_consen 82 ISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVEYGGT 159 (159)
T ss_dssp HHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGGGTSS
T ss_pred hhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchhcCCC
Confidence 899999999999999999999999999999999999999999999999999997767767999999999999999997
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=100.00 E-value=6.8e-32 Score=205.16 Aligned_cols=143 Identities=48% Similarity=0.785 Sum_probs=134.7
Q ss_pred cCCCCCCcEEEEeCccccccccCCHHHHHHHHHHHHHHHHhh--CCCCCceEEEEEecCCCCCCCccHHHHHHHHHHHhh
Q 043459 92 GFDKKGRPIATVLGARHFQNKLGGLEEFKRFVVYILDKICSR--MPPGQEKFVVIGDLKGWGYSNSDLRAYLGALSILQD 169 (243)
Q Consensus 92 g~d~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~--~~~~~~~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~ 169 (243)
|.|++||||++++++++++.. .+.+++++++++.+|.+... .+.+..|+++|+|++|+++++++++.++.+++.++.
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~-~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~lk~~~~~~~~ 92 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKS-VTLEELLRYLVYVLEKILQREKKTGGIEGFTVIFDLKGLSMSNPDLSVLRKILKILQD 92 (158)
T ss_pred CCCCCcCEEEEEeccccccCc-CCHHHHHHHHHHHHHHHHHHHhcCCCeeeEEEEEECCCCCcccccHHHHHHHHHHHHH
Confidence 799999999999999998888 89999999999999998876 566779999999999999999999999999999999
Q ss_pred cccccccceEEEeCChHHHHHHHHHcccCChhhhhceEEecCcchHHHHHhcCCCCCCccccCCCCC
Q 043459 170 YYPERLGKLFIVHAPYIFMTVWKIVYPFIDNNTKKKIVFVQDKKLKSTLLEEIDESQIPEIYGGQLP 236 (243)
Q Consensus 170 ~yP~rl~~i~ivn~p~~~~~~~~~ik~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~~~ 236 (243)
+||++++++||+|+|++++++|+++++|+++++++||+++++ ++.++|.+++|+++||.+|||++.
T Consensus 93 ~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~-~~~~~L~~~i~~~~lP~~~GG~~~ 158 (158)
T smart00516 93 HYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGN-DSKEELLEYIDPEQLPEELGGTLD 158 (158)
T ss_pred HhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCC-CCHHHHHhhCCHhhCcHhhCCCCC
Confidence 999999999999999999999999999999999999999986 445799999999999999999974
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=99.96 E-value=2.7e-29 Score=189.92 Aligned_cols=146 Identities=42% Similarity=0.681 Sum_probs=130.6
Q ss_pred CceeccCCCCCCcEEEEeCccccccccCCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecCCCCCCCc--cHHHHHHHH
Q 043459 87 KMFMQGFDKKGRPIATVLGARHFQNKLGGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLKGWGYSNS--DLRAYLGAL 164 (243)
Q Consensus 87 ~~~~~g~d~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~g~~~~~~--~~~~~k~~~ 164 (243)
..+..|+|++||||++++++..+.....+.++++++.++.+|.++........|+++|+|++|.+++++ +.+.+++++
T Consensus 10 ~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~~~k~~~ 89 (157)
T cd00170 10 VGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQEDDEQVEGFVVIIDLKGLSLSHLLPDPSLLKKIL 89 (157)
T ss_pred ccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhhhhhcccceEEEEECCCCChhccchhHHHHHHHH
Confidence 334556799999999999996554442455899999999999998876666689999999999999998 788999999
Q ss_pred HHHhhcccccccceEEEeCChHHHHHHHHHcccCChhhhhceEEecCcchHHHHHhcCCCCCCccccCCC
Q 043459 165 SILQDYYPERLGKLFIVHAPYIFMTVWKIVYPFIDNNTKKKIVFVQDKKLKSTLLEEIDESQIPEIYGGQ 234 (243)
Q Consensus 165 ~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~ 234 (243)
++++++||++++++||+|+|++++.+|+++++|+++++++||+++++. .++|.+++|+++||.+|||+
T Consensus 90 ~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~--~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 90 KILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD--KEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred HHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC--HHHHHhhCChhhCcHhhCCC
Confidence 999999999999999999999999999999999999999999999863 47999999999999999996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.76 E-value=1.4e-19 Score=136.15 Aligned_cols=141 Identities=28% Similarity=0.485 Sum_probs=96.2
Q ss_pred ceeccCCCCCCcEEEEeCccccccccCCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecCCCCCCCc-cHHHHHHHHHH
Q 043459 88 MFMQGFDKKGRPIATVLGARHFQNKLGGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLKGWGYSNS-DLRAYLGALSI 166 (243)
Q Consensus 88 ~~~~g~d~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~g~~~~~~-~~~~~k~~~~~ 166 (243)
++..|+|++||||+++...+. ++. .+.+.++.+++..++ .. ....++++|+|++|.+..+- +++.++++.+.
T Consensus 4 ~~~gG~d~~g~pV~~~~~~~~-~~~-~~~~~ll~yl~~~l~---~~--~~~~~f~vVid~~~~~~~~~~~~~~l~~~~~~ 76 (149)
T PF13716_consen 4 FYPGGRDREGRPVVVFIASRL-PSS-DDLERLLLYLLSTLS---EE--VVDKPFSVVIDHTGFSRSSEPSLSWLKQLYKL 76 (149)
T ss_dssp -EEEEEBTTS-EEEEEEGGG--C-T-THHHHHHHHHHHHH----TT--TTTS-EEEEEE-TT--GGG---HHHHHHTTTS
T ss_pred EEecccCCCcCEEEEEECCcC-cch-hhHHHHHHHHHHhhh---HH--hcCCCEEEEEEcCCCccccCCchHHHHHHHHH
Confidence 356789999999999998777 554 445555555555542 22 23356999999999887654 78999999999
Q ss_pred HhhcccccccceEEEeCChHHHHHH-HHHcccCChhh-hhceEEecCcchHHHHHhcCCCCCCccccCCCCCCc
Q 043459 167 LQDYYPERLGKLFIVHAPYIFMTVW-KIVYPFIDNNT-KKKIVFVQDKKLKSTLLEEIDESQIPEIYGGQLPLV 238 (243)
Q Consensus 167 ~~~~yP~rl~~i~ivn~p~~~~~~~-~~ik~~l~~~~-~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~~~~~ 238 (243)
+...|+.+++++||+||+++++... .+.+++.+.+. ..|+.++++- ++|.++||+++||.++||+.++.
T Consensus 77 l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~sl---~~L~~~i~~~qL~~~lp~~~~~d 147 (149)
T PF13716_consen 77 LPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSSL---SELSKHIDPSQLPESLPGVLQYD 147 (149)
T ss_dssp S-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESST---CGGGGTSGGGG------HHH---
T ss_pred HHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECCH---HHHHhhCCHHHhcccCCCEEecC
Confidence 9999999999999999999999999 56667778888 8999998764 79999999999999999987754
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=98.95 E-value=2.4e-09 Score=66.16 Aligned_cols=47 Identities=40% Similarity=0.559 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHhhh--------CCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHH
Q 043459 15 ETKIRLMRALVEKQ--------DPSSKEVDDPTLRRFLRARDLDVEKASGMFLKY 61 (243)
Q Consensus 15 ~~~l~~lr~~l~~~--------~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~ 61 (243)
++++++|++.|+.. .......+|.+++|||||++||+++|.++|.++
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 57899999999984 233456899999999999999999999999875
No 8
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.90 E-value=1.2e-08 Score=85.62 Aligned_cols=131 Identities=22% Similarity=0.389 Sum_probs=105.3
Q ss_pred CCceecc--CCCCCCcEEEEeCccccccccCCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecCCCCCCCc-cHHHHHH
Q 043459 86 NKMFMQG--FDKKGRPIATVLGARHFQNKLGGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLKGWGYSNS-DLRAYLG 162 (243)
Q Consensus 86 ~~~~~~g--~d~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~g~~~~~~-~~~~~k~ 162 (243)
+.+...| .|++||.|+.+-+.++.+.+-.+-..++++..+.+|...+. .+++++-..|+...+. .++++..
T Consensus 80 ei~qvi~~~~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~Ve~------DYt~vYfh~gl~s~nkp~l~~l~~ 153 (467)
T KOG4406|consen 80 EILQVIGDAKDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVEN------DYTLVYFHHGLPSDNKPYLQLLFD 153 (467)
T ss_pred heeeeccCcccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHhc------cceeeehhcCCcccccchHHHHHH
Confidence 4444444 59999999999888877654122234888999999988876 3999999999887776 3666666
Q ss_pred HHHHHhhcccccccceEEEeCChHHHHHHHHHcccCChhhhhceEEecCcchHHHHHhcCCCC
Q 043459 163 ALSILQDYYPERLGKLFIVHAPYIFMTVWKIVYPFIDNNTKKKIVFVQDKKLKSTLLEEIDES 225 (243)
Q Consensus 163 ~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~ 225 (243)
...-+..+|--.++.+|+|++.|+.+++|+++||+++.|..+||..++. .++|.+++.-+
T Consensus 154 aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n~---lseL~~~l~l~ 213 (467)
T KOG4406|consen 154 AYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFNS---LSELFEALKLN 213 (467)
T ss_pred HHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEeeh---HHHHHHhhhhh
Confidence 6666777899999999999999999999999999999999999998865 47888887643
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=92.78 E-value=0.53 Score=26.99 Aligned_cols=36 Identities=22% Similarity=0.410 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHH
Q 043459 16 TKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFL 59 (243)
Q Consensus 16 ~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~ 59 (243)
+.|.+|.+... .++.....||.+++||++.|+..+-
T Consensus 2 e~i~~F~~iTg--------~~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 2 EKIAQFMSITG--------ADEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp HHHHHHHHHH---------SSHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHHHC--------cCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45666666543 3778999999999999999998753
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=90.51 E-value=0.97 Score=25.69 Aligned_cols=38 Identities=24% Similarity=0.456 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHH
Q 043459 16 TKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLK 60 (243)
Q Consensus 16 ~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~ 60 (243)
+.+++|++.. | ..+...+..-|.++++|++.|...|-.
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 4566666665 3 378999999999999999999998753
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=88.62 E-value=1.7 Score=24.76 Aligned_cols=37 Identities=19% Similarity=0.415 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHH
Q 043459 16 TKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFL 59 (243)
Q Consensus 16 ~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~ 59 (243)
+.+.+|++.+ | ..++..+.+-|+++++|++.|...|-
T Consensus 4 ~~v~~L~~mF----P---~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 4 EALHDLKDMF----P---NLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred HHHHHHHHHC----C---CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4556666654 3 37899999999999999999998874
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=85.38 E-value=5.3 Score=24.54 Aligned_cols=43 Identities=12% Similarity=0.249 Sum_probs=32.7
Q ss_pred CHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHH
Q 043459 11 DEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLK 60 (243)
Q Consensus 11 ~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~ 60 (243)
++.-++.++.+++.... .+|..++.-|+-|+.|..+|+++|..
T Consensus 2 P~~~rk~VQ~iKEiv~~-------hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 2 PAASRKTVQSIKEIVGC-------HSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred ChHHHHHHHHHHHHhcC-------CCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 34445556666665433 48999999999999999999999865
No 13
>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=80.11 E-value=12 Score=23.44 Aligned_cols=48 Identities=15% Similarity=0.213 Sum_probs=38.5
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHHH
Q 043459 7 KSNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKYL 62 (243)
Q Consensus 7 ~~~l~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~~ 62 (243)
.+++++.+++.+.+|...- .++-.|-.++|...+||.++|.+.+.+--
T Consensus 5 ~~~~~~~q~~~v~~~~~~T--------gmn~~~s~~cLe~~~Wd~~~Al~~F~~lk 52 (63)
T smart00804 5 KPTLSPEQQEMVQAFSAQT--------GMNAEYSQMCLEDNNWDYERALKNFTELK 52 (63)
T ss_pred CCCCCHHHHHHHHHHHHHH--------CCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4577888888888777642 26889999999999999999999877643
No 14
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=79.79 E-value=0.37 Score=31.78 Aligned_cols=55 Identities=16% Similarity=0.167 Sum_probs=36.9
Q ss_pred ccCCCCCHHHHHHHHHHHHHHhhhCCCCCCC-ChHHHHHHHHhcCCCHHHHHHHHHHH
Q 043459 5 YMKSNIDEKEETKIRLMRALVEKQDPSSKEV-DDPTLRRFLRARDLDVEKASGMFLKY 61 (243)
Q Consensus 5 ~~~~~l~~~~~~~l~~lr~~l~~~~~~~~~~-~d~~llrfL~~~~~d~~~a~~~l~~~ 61 (243)
+....||+++++.+.+-...+++.. .... ++..+..=|+.++||+++|+..|.+.
T Consensus 15 ~~~~~Ls~ed~~~L~~~l~~vr~~L--g~~~~~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 15 EEEDELSPEDQAQLYSCLPQVREVL--GDYVPPEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp HHHHH-TCHHHHHHCHHCCCHHHHC--CCCC--CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred cccccCCHHHHHHHHHHHHHHHHHH--cccCCCHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 3355678888877666555555532 1112 88889999999999999999988764
No 15
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=76.81 E-value=3.3 Score=27.43 Aligned_cols=23 Identities=17% Similarity=0.440 Sum_probs=20.5
Q ss_pred CCCHHHHHHHHHHHHHHhhhCCC
Q 043459 9 NIDEKEETKIRLMRALVEKQDPS 31 (243)
Q Consensus 9 ~l~~~~~~~l~~lr~~l~~~~~~ 31 (243)
+|||.|++.|+|+-+.+.+.+|.
T Consensus 2 ~LSe~E~r~L~eiEr~L~~~DP~ 24 (82)
T PF11239_consen 2 PLSEHEQRRLEEIERQLRADDPR 24 (82)
T ss_pred CCCHHHHHHHHHHHHHHHhcCcH
Confidence 69999999999999999887663
No 16
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=76.34 E-value=40 Score=29.59 Aligned_cols=85 Identities=19% Similarity=0.152 Sum_probs=61.0
Q ss_pred CCCcEEEEeCccccccccCCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecCCCCCCCc---------cHHHHHHHHHH
Q 043459 96 KGRPIATVLGARHFQNKLGGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLKGWGYSNS---------DLRAYLGALSI 166 (243)
Q Consensus 96 ~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~g~~~~~~---------~~~~~k~~~~~ 166 (243)
+..|++++-+|.... +.+..+|.++.... +. .--++|++.+|+.-..+ ....++.+++.
T Consensus 123 ~~~P~vvilpGltg~----S~~~YVr~lv~~a~---~~-----G~r~VVfN~RG~~g~~LtTpr~f~ag~t~Dl~~~v~~ 190 (409)
T KOG1838|consen 123 GTDPIVVILPGLTGG----SHESYVRHLVHEAQ---RK-----GYRVVVFNHRGLGGSKLTTPRLFTAGWTEDLREVVNH 190 (409)
T ss_pred CCCcEEEEecCCCCC----ChhHHHHHHHHHHH---hC-----CcEEEEECCCCCCCCccCCCceeecCCHHHHHHHHHH
Confidence 566999999987653 34567776665433 22 25688999999664443 46789999999
Q ss_pred HhhcccccccceEEEeCChHHHHHHHHH
Q 043459 167 LQDYYPERLGKLFIVHAPYIFMTVWKIV 194 (243)
Q Consensus 167 ~~~~yP~rl~~i~ivn~p~~~~~~~~~i 194 (243)
+...||.+ +++.+..+.-..+++|-+
T Consensus 191 i~~~~P~a--~l~avG~S~Gg~iL~nYL 216 (409)
T KOG1838|consen 191 IKKRYPQA--PLFAVGFSMGGNILTNYL 216 (409)
T ss_pred HHHhCCCC--ceEEEEecchHHHHHHHh
Confidence 99999998 777777776666666644
No 17
>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=74.96 E-value=14 Score=25.34 Aligned_cols=76 Identities=12% Similarity=0.152 Sum_probs=53.0
Q ss_pred CCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecC-CCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHH
Q 043459 114 GGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLK-GWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWK 192 (243)
Q Consensus 114 ~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~-g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~ 192 (243)
.+.+++.. +.-.++..+. ....+.+++|++ + +..++++......+.... +...+.++=+|-.+.+.+.+.+
T Consensus 11 ~t~ed~~~-~~~~~~~~~~----~~~~~~ll~d~~~~--~~~~~~~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~~~~ 82 (109)
T PF11964_consen 11 LTEEDYKE-LLPALEELIA----DHGKIRLLVDLRRD--FEGWSPEARWEDAKFGLK-HLKHFRRIAVVGDSEWIRMIAN 82 (109)
T ss_dssp E-HHHHHH-HHHHHHHHHT----TSSSEEEEEEEC-C--EEEEHHHHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHHHHH
T ss_pred eCHHHHHH-HHHHHHHHHh----cCCceEEEEEecCc--cCCCCHHHHHHHHHhchh-hhcccCEEEEEECcHHHHHHHH
Confidence 35566666 4445554443 335699999988 6 345666666666655544 8888999999999999999999
Q ss_pred HHccc
Q 043459 193 IVYPF 197 (243)
Q Consensus 193 ~ik~~ 197 (243)
++.++
T Consensus 83 ~~~~~ 87 (109)
T PF11964_consen 83 FFAAF 87 (109)
T ss_dssp HHHHH
T ss_pred HHHhc
Confidence 99886
No 18
>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=67.08 E-value=18 Score=19.59 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHH
Q 043459 15 ETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMF 58 (243)
Q Consensus 15 ~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l 58 (243)
++.|++|++. ..+.....+-|+.+++|+++|.+-|
T Consensus 3 ~~~v~~L~~m---------Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 3 EEKVQQLMEM---------GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHH---------TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHc---------CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 3455556554 1466788899999999999998754
No 19
>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=66.44 E-value=5.2 Score=29.53 Aligned_cols=49 Identities=20% Similarity=0.454 Sum_probs=41.5
Q ss_pred HHHHHHHHHhhccccccc--ceEEEeCChHHHHHHHHHcccCCh--hhhhceEE
Q 043459 159 AYLGALSILQDYYPERLG--KLFIVHAPYIFMTVWKIVYPFIDN--NTKKKIVF 208 (243)
Q Consensus 159 ~~k~~~~~~~~~yP~rl~--~i~ivn~p~~~~~~~~~ik~~l~~--~~~~ki~~ 208 (243)
..+.+++.+...||..++ .+-+.|.+-.+.++|+-+ |-++. +-++.|.+
T Consensus 16 ~y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRL 68 (159)
T PF04838_consen 16 DYKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRL 68 (159)
T ss_pred CHHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhh
Confidence 467789999999999999 889999999999999988 66777 56666665
No 20
>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=64.34 E-value=32 Score=24.77 Aligned_cols=53 Identities=23% Similarity=0.277 Sum_probs=35.4
Q ss_pred CceEEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHcccCC
Q 043459 138 QEKFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVYPFID 199 (243)
Q Consensus 138 ~~~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik~~l~ 199 (243)
..+++++.|+ |-+..+ ... .+..+. ++..+.+..+|.|.....+...+..-..
T Consensus 59 ~dgVlvl~DL-Ggs~~n--~e~---a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~~g 111 (125)
T TIGR02364 59 ADGVLIFYDL-GSAVMN--AEM---AVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQVG 111 (125)
T ss_pred CCCEEEEEcC-CCcHhH--HHH---HHHHhc---cccccEEEEechhHHHHHHHHHHHHcCC
Confidence 5789999999 533322 111 222222 4556889999999999998888765433
No 21
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=62.21 E-value=17 Score=19.59 Aligned_cols=24 Identities=25% Similarity=0.299 Sum_probs=20.4
Q ss_pred CChHHHHHHHHhcCCCHHHHHHHH
Q 043459 35 VDDPTLRRFLRARDLDVEKASGMF 58 (243)
Q Consensus 35 ~~d~~llrfL~~~~~d~~~a~~~l 58 (243)
.++....+-|+.+++|+++|..-|
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 577789999999999999997654
No 22
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=62.13 E-value=7.8 Score=34.50 Aligned_cols=65 Identities=18% Similarity=0.295 Sum_probs=48.7
Q ss_pred CcccccCCCCCHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 043459 1 MSCEYMKSNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKYLKWR 65 (243)
Q Consensus 1 ~~~~~~~~~l~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~~~~R 65 (243)
.+|+|..++++++-.-.+++-++--...+|.....-+..+..=||-+.+|.++|.+.|+.....+
T Consensus 130 ~~CRFl~aHld~~g~~~~~kek~~d~~~~~~t~N~~s~elq~~LrKre~~fekse~~l~~~~~~~ 194 (614)
T KOG2333|consen 130 FKCRFLGAHLDIEGNNLIQKEKDPDGQFPPTTKNGVSKELQVDLRKREYDFEKSEEILEIIDSFE 194 (614)
T ss_pred ceeehhhcccCccccchhhhhhCcccCCCCccccccCHHHHHHHHHhhcChHHHHHHHHHHhccc
Confidence 48999999999887776644444333333444455667777779999999999999999887777
No 23
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=61.57 E-value=46 Score=26.86 Aligned_cols=112 Identities=13% Similarity=0.150 Sum_probs=63.0
Q ss_pred CHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhcCCCCCCCCCCchhhhhcCCc-e
Q 043459 11 DEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKYLKWRQTFVPNGSISLSEVPNELSQNKM-F 89 (243)
Q Consensus 11 ~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~~~~R~~~~~~~~~~~~~~~~~l~~~~~-~ 89 (243)
..+-+..++..+.|.++ ++...-.....+++||++.+||+. +|++ +.+++-.. +|.. |
T Consensus 3 i~~iq~~~~ni~~~y~~-~~nEa~vrq~lIlp~L~slGwdi~----------------nPkE-V~PEe~t~---~GraDy 61 (284)
T COG2810 3 ISTIQKIKNNINKFYNK-SRNEAAVRQHLILPFLSSLGWDID----------------NPKE-VRPEEKTE---EGRADY 61 (284)
T ss_pred hHHHHHHHHHHHHHhcc-CccHHHHHHHHHHHHHHHcCCCCC----------------Cccc-cCcccccc---cCccce
Confidence 34556777778888766 233333455668999999998874 3433 22222221 2221 2
Q ss_pred eccCCCCCCcEEEEeCccccccccCCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecC
Q 043459 90 MQGFDKKGRPIATVLGARHFQNKLGGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLK 148 (243)
Q Consensus 90 ~~g~d~~Grpv~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~ 148 (243)
. .=++|+.+.++..+.... ....++.++.-|.++...+-.-..++.+=+|+|..
T Consensus 62 a--likd~kvfafieak~ls~---~~akd~qq~~~Yav~~Gv~~~iVtnGrvWiV~d~~ 115 (284)
T COG2810 62 A--LIKDGKVFAFIEAKNLSV---NPAKDVQQLAKYAVDKGVEVGIVTNGRVWIVVDAF 115 (284)
T ss_pred E--EEecCcEEEEEeccccCc---CchHHHHHHHHHHHhcCcEEEEEeCCeEEEEEecc
Confidence 1 234566666665554332 34567888888888865543212224455666664
No 24
>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=61.32 E-value=18 Score=19.58 Aligned_cols=24 Identities=29% Similarity=0.379 Sum_probs=21.0
Q ss_pred CChHHHHHHHHhcCCCHHHHHHHH
Q 043459 35 VDDPTLRRFLRARDLDVEKASGMF 58 (243)
Q Consensus 35 ~~d~~llrfL~~~~~d~~~a~~~l 58 (243)
.+.....+-|+.+++|+++|...|
T Consensus 13 f~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 13 FSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 568889999999999999998765
No 25
>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=54.03 E-value=25 Score=24.43 Aligned_cols=52 Identities=19% Similarity=0.085 Sum_probs=36.3
Q ss_pred eEEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHH
Q 043459 140 KFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIV 194 (243)
Q Consensus 140 ~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~i 194 (243)
--.+|+||+++ ..+|...+..+.++.+..- .+-..++++|++.-+...+...
T Consensus 48 ~~~vIlD~s~v--~~iDssgi~~L~~~~~~~~-~~g~~~~l~~~~~~v~~~l~~~ 99 (117)
T PF01740_consen 48 IKNVILDMSGV--SFIDSSGIQALVDIIKELR-RRGVQLVLVGLNPDVRRILERS 99 (117)
T ss_dssp SSEEEEEETTE--SEESHHHHHHHHHHHHHHH-HTTCEEEEESHHHHHHHHHHHT
T ss_pred ceEEEEEEEeC--CcCCHHHHHHHHHHHHHHH-HCCCEEEEEECCHHHHHHHHHc
Confidence 36899999995 4567666666655555444 5677899999988776665443
No 26
>TIGR02886 spore_II_AA anti-sigma F factor antagonist. The anti-sigma F factor antagonist, also called stage II sporulation protein AA, is a protein universal among endospore-forming bacteria, all of which belong to the Firmcutes
Probab=51.56 E-value=64 Score=21.87 Aligned_cols=52 Identities=12% Similarity=0.094 Sum_probs=34.1
Q ss_pred EEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHc
Q 043459 141 FVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVY 195 (243)
Q Consensus 141 ~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik 195 (243)
-.+|+|+++++. +|.+.+..+....+. .-.+-.+++++|++.-+.-++....
T Consensus 40 ~~vilDls~v~~--iDssgi~~L~~~~~~-~~~~g~~l~l~~~~~~v~~~l~~~g 91 (106)
T TIGR02886 40 KHLILNLKNVTF--MDSSGLGVILGRYKK-IKNEGGEVIVCNVSPAVKRLFELSG 91 (106)
T ss_pred CEEEEECCCCcE--ecchHHHHHHHHHHH-HHHcCCEEEEEeCCHHHHHHHHHhC
Confidence 479999999664 454444444333332 2235678999999988877776554
No 27
>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=51.21 E-value=38 Score=18.96 Aligned_cols=24 Identities=25% Similarity=0.228 Sum_probs=20.0
Q ss_pred CChHHHHHHHHhcCCCHHHHHHHH
Q 043459 35 VDDPTLRRFLRARDLDVEKASGMF 58 (243)
Q Consensus 35 ~~d~~llrfL~~~~~d~~~a~~~l 58 (243)
.....|-.-|.+|++|+-+|.+.+
T Consensus 15 ~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 15 QKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CChHHHHHHHHHcCCcHHHHHHHh
Confidence 456678888999999999998864
No 28
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=47.64 E-value=72 Score=20.34 Aligned_cols=51 Identities=18% Similarity=0.032 Sum_probs=32.3
Q ss_pred eEEEEEecCCCCCCCccHHHHHHHHHHHhhccc--ccccceEEEeCChHHHHHHH
Q 043459 140 KFVVIGDLKGWGYSNSDLRAYLGALSILQDYYP--ERLGKLFIVHAPYIFMTVWK 192 (243)
Q Consensus 140 ~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP--~rl~~i~ivn~p~~~~~~~~ 192 (243)
|-.+++|++|+. .++.+.+-.++.-+...|| ..-.++.++|++.....+.+
T Consensus 17 ~~~V~lDF~gv~--~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I~ 69 (74)
T PF14213_consen 17 GEKVVLDFEGVE--SITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMIK 69 (74)
T ss_pred CCeEEEECCCcc--cccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHHH
Confidence 334899999974 3455555555555555555 45567888888776655544
No 29
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=45.90 E-value=81 Score=23.89 Aligned_cols=59 Identities=14% Similarity=0.220 Sum_probs=40.4
Q ss_pred ccCCCCCHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHHHH
Q 043459 5 YMKSNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKYLK 63 (243)
Q Consensus 5 ~~~~~l~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~~~ 63 (243)
|-...||+++++.+..+.+-=....+....-+-.-+..-+++.+||..++...+....+
T Consensus 52 f~~l~LTd~QR~qmr~im~~~r~~~~~~~~~~~~~m~~Li~Ad~FDeaAvra~~~kma~ 110 (162)
T PRK12751 52 FDGINLTEQQRQQMRDLMRQSHQSQPRLDLEDREAMHKLITADKFDEAAVRAQAEKMSQ 110 (162)
T ss_pred hccCCCCHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence 45678999999999888765444322222223444788999999999888777765543
No 30
>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=45.33 E-value=1.7e+02 Score=25.73 Aligned_cols=44 Identities=20% Similarity=0.221 Sum_probs=35.9
Q ss_pred HHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHH
Q 043459 17 KIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKY 61 (243)
Q Consensus 17 ~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~ 61 (243)
+++.|-+.+++. .+++......+--||.+.+.++++|.+-.+..
T Consensus 227 Cm~~l~~~l~~~-~hL~h~gR~ql~lFLk~iGl~~~e~l~~~~~~ 270 (390)
T cd07322 227 CMRQLHEALRKN-HHLKHGGRLQLGLFLKGIGLSLEEALKFWRSE 270 (390)
T ss_pred HHHHHHHHHhcC-CCCCchhHHHHHHHHHhCCCCHHHHHHHHHHh
Confidence 567777777774 67777888889999999999999999985544
No 31
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=45.14 E-value=1.2e+02 Score=23.01 Aligned_cols=59 Identities=14% Similarity=0.245 Sum_probs=39.8
Q ss_pred ccCCCCCHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHHHH
Q 043459 5 YMKSNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKYLK 63 (243)
Q Consensus 5 ~~~~~l~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~~~ 63 (243)
|-.-.||+++++.++.|++.=....+.....+-.-+...+.+-+||-.++...+.+..+
T Consensus 46 F~gLdLTdaQRqQmRdLm~~~r~~~~~~~~~er~amh~LI~ad~FDEaavra~a~kma~ 104 (166)
T PRK10363 46 FDGISLTEHQRQQMRDLMQQARHEQPPVNVSEMETMHRLVTAENFDENAVRAQAEKMAQ 104 (166)
T ss_pred ccCCCCCHHHHHHHHHHHHHHHhcccccCHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence 45678999999999999976554323222223334567888889998877776655543
No 32
>PRK02399 hypothetical protein; Provisional
Probab=44.06 E-value=2.2e+02 Score=25.12 Aligned_cols=80 Identities=15% Similarity=0.146 Sum_probs=60.3
Q ss_pred CCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecCCCCCCC------ccHHHHHHHHHHHhhcccccccceEE-----Ee
Q 043459 114 GGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLKGWGYSN------SDLRAYLGALSILQDYYPERLGKLFI-----VH 182 (243)
Q Consensus 114 ~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~g~~~~~------~~~~~~k~~~~~~~~~yP~rl~~i~i-----vn 182 (243)
.+.+|..+.--++.|++-. ....+.+++-.+|+|.-. .|+..-..+++.+++..+..+. ++ ||
T Consensus 313 Tt~eE~~~~g~~ia~kLn~----a~gpv~vllP~~G~S~~D~~G~~f~Dpead~alf~~l~~~l~~~~~--v~~~~~hIN 386 (406)
T PRK02399 313 TTPEENRQIGRWIAEKLNR----AKGPVAFLIPLGGVSALDRPGQPFHDPEADAAFFDALEETVTETRR--LIEVPAHIN 386 (406)
T ss_pred cCHHHHHHHHHHHHHHHhc----CCCCeEEEEeCCCCccccCCCCCccChhHHHHHHHHHHHhCCCCce--EEECCCCCC
Confidence 4778888877777777522 234699999999999866 3778888888999888877654 44 79
Q ss_pred CChHHHHHHHHHcccCC
Q 043459 183 APYIFMTVWKIVYPFID 199 (243)
Q Consensus 183 ~p~~~~~~~~~ik~~l~ 199 (243)
-|.|...+...+..++.
T Consensus 387 D~~FA~a~~~~l~~~~~ 403 (406)
T PRK02399 387 DPEFAEAAVEAFEELMA 403 (406)
T ss_pred CHHHHHHHHHHHHHHHh
Confidence 99999888877655543
No 33
>KOG2267 consensus Eukaryotic-type DNA primase, large subunit [Replication, recombination and repair]
Probab=44.04 E-value=44 Score=29.06 Aligned_cols=78 Identities=14% Similarity=0.257 Sum_probs=50.9
Q ss_pred HHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhcCCCCCCCCCCchhhhhcCCceeccCCC
Q 043459 16 TKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKYLKWRQTFVPNGSISLSEVPNELSQNKMFMQGFDK 95 (243)
Q Consensus 16 ~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~~~~R~~~~~~~~~~~~~~~~~l~~~~~~~~g~d~ 95 (243)
-+.++|-+.|..+ .|+.......+--||.+.+.++++|.+. ||.++.. . ++.+.+..+.. +-+-|....
T Consensus 289 pCmk~lhe~LrkN-hHLry~gR~qygLFLKgiGLS~deal~f------wr~sFtk-~-~t~dkFdKEY~--YnIRh~YGl 357 (475)
T KOG2267|consen 289 PCMKQLHERLRKN-HHLRYGGRQQYGLFLKGIGLSVDEALAF------WRGSFTK-K-MTRDKFDKEYR--YNIRHNYGL 357 (475)
T ss_pred HHHHHHHHHHhhc-ccccccchhhhhhhhhccCcCHHHHHHH------HHHHHhc-c-CChhHhchhhc--eeheecccc
Confidence 3788888999885 7788888888999999999999999998 5655421 1 22233322221 112344556
Q ss_pred CCCcEEEEe
Q 043459 96 KGRPIATVL 104 (243)
Q Consensus 96 ~Grpv~~~~ 104 (243)
+|+++-|..
T Consensus 358 EGkR~nyt~ 366 (475)
T KOG2267|consen 358 EGKRANYTP 366 (475)
T ss_pred ccccccCCc
Confidence 666655543
No 34
>cd07043 STAS_anti-anti-sigma_factors Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation. Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a feedback mechanism the anti-anti-sigma factor can be inactivated via phosphorylation by the anti-sigma factor. Well studied examples from Bacillus subtilis are SpoIIAA (regulating sigmaF and sigmaC which play an important role in sporulation) and RsbV (regulating sigmaB involved in the general stress response). The STAS domain is also found in the C- terminal region of sulphate transporters and stressosomes.
Probab=42.48 E-value=96 Score=20.27 Aligned_cols=52 Identities=17% Similarity=0.068 Sum_probs=34.4
Q ss_pred EEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHc
Q 043459 141 FVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVY 195 (243)
Q Consensus 141 ~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik 195 (243)
-.+|+|+++++ .+|...+..+....+..- .+-..+.+.+++.-+.-++..+.
T Consensus 39 ~~viid~~~v~--~iDs~g~~~L~~l~~~~~-~~g~~v~i~~~~~~~~~~l~~~g 90 (99)
T cd07043 39 RRLVLDLSGVT--FIDSSGLGVLLGAYKRAR-AAGGRLVLVNVSPAVRRVLELTG 90 (99)
T ss_pred CEEEEECCCCC--EEcchhHHHHHHHHHHHH-HcCCeEEEEcCCHHHHHHHHHhC
Confidence 56789999954 455555555554444333 34567999999987777777654
No 35
>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=39.62 E-value=1e+02 Score=22.26 Aligned_cols=62 Identities=15% Similarity=0.155 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHhhccccc-cc-ceEEEeCChHHHHHHHHH-----cccCChhhhhceEEecCcchHHHHHhc
Q 043459 157 LRAYLGALSILQDYYPER-LG-KLFIVHAPYIFMTVWKIV-----YPFIDNNTKKKIVFVQDKKLKSTLLEE 221 (243)
Q Consensus 157 ~~~~k~~~~~~~~~yP~r-l~-~i~ivn~p~~~~~~~~~i-----k~~l~~~~~~ki~~~~~~~~~~~L~~~ 221 (243)
.+.+-.++..++-.+=+. -+ .+.++|...+.+-+++.+ .-|+++...+.+.++.+. +++.++
T Consensus 64 ~GTl~El~~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~~---~e~~~~ 132 (133)
T PF03641_consen 64 IGTLDELFEALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDDP---EEALEY 132 (133)
T ss_dssp HHHHHHHHHHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESSH---HHHHHH
T ss_pred CchHHHHHHHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCCH---HHHHhh
Confidence 556666666555333332 23 599999887777777766 458999999999998764 555543
No 36
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=39.22 E-value=37 Score=27.61 Aligned_cols=66 Identities=23% Similarity=0.283 Sum_probs=42.4
Q ss_pred hcccccccceEEEeCChHH---HHHHHHHcccCChhhhhceEEecCcch----HHHHHhcCCCCCCccc-cCCCCCC
Q 043459 169 DYYPERLGKLFIVHAPYIF---MTVWKIVYPFIDNNTKKKIVFVQDKKL----KSTLLEEIDESQIPEI-YGGQLPL 237 (243)
Q Consensus 169 ~~yP~rl~~i~ivn~p~~~---~~~~~~ik~~l~~~~~~ki~~~~~~~~----~~~L~~~i~~~~LP~~-~GG~~~~ 237 (243)
..|.+| ++||||+.-.-. +.+++.++..... ..+|.|+++..+ ..+..+..+.-.+..- +||++++
T Consensus 30 fIf~~R-ngihIIDL~kT~~~l~~A~~~v~~~~~~--~g~ILfVgTK~~a~~~V~~~A~r~g~~yV~~RwLgG~LTN 103 (252)
T COG0052 30 FIFGER-NGIHIIDLQKTLERLREAYKFLRRIAAN--GGKILFVGTKKQAQEPVKEFAERTGAYYVNGRWLGGMLTN 103 (252)
T ss_pred cceeec-CCcEEEEHHHHHHHHHHHHHHHHHHHcC--CCEEEEEechHHHHHHHHHHHHHhCCceecCcccCccccC
Confidence 468999 999999976544 3344444443321 368999987532 2345556666666554 7999987
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=37.10 E-value=2.2e+02 Score=26.20 Aligned_cols=59 Identities=27% Similarity=0.429 Sum_probs=40.9
Q ss_pred CCHHHHHHHHHHHHHHHHhhCCCCCceEEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCC
Q 043459 114 GGLEEFKRFVVYILDKICSRMPPGQEKFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAP 184 (243)
Q Consensus 114 ~~~~~~~~~~~~~~E~~~~~~~~~~~~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p 184 (243)
.+++++.++....++.+...-+... ..++|=+|.| +. ...++...+|+.++.+.+-.+|
T Consensus 116 QTl~DV~~ae~~Fv~~V~~~hp~~~-kp~liGnCQg--------GW---a~~mlAA~~Pd~~gplvlaGaP 174 (581)
T PF11339_consen 116 QTLEDVMRAEAAFVEEVAERHPDAP-KPNLIGNCQG--------GW---AAMMLAALRPDLVGPLVLAGAP 174 (581)
T ss_pred CcHHHHHHHHHHHHHHHHHhCCCCC-CceEEeccHH--------HH---HHHHHHhcCcCccCceeecCCC
Confidence 5788899888888887666543333 7788888765 22 2345667788888888776665
No 38
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=35.19 E-value=21 Score=29.16 Aligned_cols=28 Identities=7% Similarity=0.329 Sum_probs=22.5
Q ss_pred ccceEEEeCChHHHHHHHHHcccCChhh
Q 043459 175 LGKLFIVHAPYIFMTVWKIVYPFIDNNT 202 (243)
Q Consensus 175 l~~i~ivn~p~~~~~~~~~ik~~l~~~~ 202 (243)
-+.++||||||-+..-...+-|++...+
T Consensus 236 gSGMivINPPwtle~ql~~~LP~L~~~L 263 (279)
T COG2961 236 GSGMIVINPPWTLEQQLRAALPWLTTLL 263 (279)
T ss_pred ceeEEEECCCccHHHHHHHHHHHHHHHh
Confidence 3479999999999888888888776543
No 39
>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=35.16 E-value=29 Score=20.58 Aligned_cols=26 Identities=19% Similarity=0.203 Sum_probs=20.8
Q ss_pred CChHHHHHHHHhcCCCHHHHHHHHHH
Q 043459 35 VDDPTLRRFLRARDLDVEKASGMFLK 60 (243)
Q Consensus 35 ~~d~~llrfL~~~~~d~~~a~~~l~~ 60 (243)
++-.+-.++|...+||.++|.+.+..
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 56778899999999999999988664
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=34.44 E-value=1.4e+02 Score=24.56 Aligned_cols=57 Identities=16% Similarity=0.168 Sum_probs=44.9
Q ss_pred CCCCHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHHHHHhhh
Q 043459 8 SNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKYLKWRQT 67 (243)
Q Consensus 8 ~~l~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~~~~R~~ 67 (243)
.+++++..+.+++.|+.|-+. .-..||..+-+||.....+.++..+.+++.+.-++-
T Consensus 186 ~~ip~~~~~~~~~~r~~l~e~---vae~dd~L~e~yl~~~~~~~~el~~~l~~~~~~~~~ 242 (270)
T cd01886 186 TEIPEDLLEEAEEAREELIET---LAEFDDELMEKYLEGEEITEEEIKAAIRKGTIANKI 242 (270)
T ss_pred ecCCHHHHHHHHHHHHHHHHH---HhcCCHHHHHHHhCCCCCCHHHHHHHHHHHHHcCcE
Confidence 367777788888888877553 233699999999999999999999999887764433
No 41
>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=34.41 E-value=17 Score=29.62 Aligned_cols=32 Identities=9% Similarity=0.287 Sum_probs=20.6
Q ss_pred cccccceEEEeCChHHHHHHHHHcccCChhhh
Q 043459 172 PERLGKLFIVHAPYIFMTVWKIVYPFIDNNTK 203 (243)
Q Consensus 172 P~rl~~i~ivn~p~~~~~~~~~ik~~l~~~~~ 203 (243)
...-..++||||||-+....+-+-|+|.+.+.
T Consensus 202 gm~GSGm~iiNPPw~l~~~l~~~l~~L~~~L~ 233 (245)
T PF04378_consen 202 GMNGSGMLIINPPWTLDEELEEILPWLAETLA 233 (245)
T ss_dssp S--EEEEEEES--TTHHHHHHHHHHHHHHHSS
T ss_pred ceecceEEEEcCCccHHHHHHHHHHHHHHHhC
Confidence 33445799999999998877777776655443
No 42
>TIGR00377 ant_ant_sig anti-anti-sigma factor. This superfamily includes small (105-125 residue) proteins related to SpoIIAA of Bacillus subtilis, an anti-anti-sigma factor. SpoIIAA can bind to and inhibit the anti-sigma F factor SpoIIAB. Also, it can be phosphorylated by SpoIIAB on a Ser residue at position 59 of the seed alignment. A similar arrangement is inferred for RsbV, an anti-anti-sigma factor for sigma B. This Ser is fairly well conserved within a motif resembling MXS[STA]G[VIL]X[VIL][VILF] among homologous known or predicted anti-anti-sigma factors. Regions similar to SpoIIAA and apparently homologous, but differing considerably near the phosphorlated Ser of SpoIIAA, appear in a single copy in several longer proteins.
Probab=33.23 E-value=1.4e+02 Score=20.06 Aligned_cols=52 Identities=19% Similarity=0.229 Sum_probs=32.4
Q ss_pred eEEEEEecCCCCCCCc-cHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHc
Q 043459 140 KFVVIGDLKGWGYSNS-DLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVY 195 (243)
Q Consensus 140 ~~~iI~D~~g~~~~~~-~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik 195 (243)
.-.+++|+++++.-+. -+..+..+.+.++ ..-..+.+++.+.-+.-++....
T Consensus 43 ~~~vvidls~v~~iDssgl~~L~~~~~~~~----~~~~~~~l~~~~~~~~~~l~~~~ 95 (108)
T TIGR00377 43 PRPIVLDLEDLEFMDSSGLGVLLGRYKQVR----RVGGQLVLVSVSPRVARLLDITG 95 (108)
T ss_pred CCeEEEECCCCeEEccccHHHHHHHHHHHH----hcCCEEEEEeCCHHHHHHHHHhC
Confidence 4569999998664332 2344444443333 34467999998887777766554
No 43
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=33.20 E-value=71 Score=20.28 Aligned_cols=28 Identities=36% Similarity=0.500 Sum_probs=20.0
Q ss_pred HHHHHHHhhhC-CCCCCCChHHHHHHHHh
Q 043459 19 RLMRALVEKQD-PSSKEVDDPTLRRFLRA 46 (243)
Q Consensus 19 ~~lr~~l~~~~-~~~~~~~d~~llrfL~~ 46 (243)
.++..|+.+.. +.....+|..|..||.+
T Consensus 33 ~el~a~lrke~~~~y~~c~D~~L~~FL~G 61 (68)
T PF07308_consen 33 AELSAWLRKEDEKGYKECSDQLLRNFLNG 61 (68)
T ss_pred HHHHHHHCCCCCccccccChHHHHHHHHH
Confidence 45667777742 44557899999999875
No 44
>cd06844 STAS Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation.
Probab=31.51 E-value=1.6e+02 Score=19.65 Aligned_cols=53 Identities=8% Similarity=-0.145 Sum_probs=34.4
Q ss_pred eEEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHc
Q 043459 140 KFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVY 195 (243)
Q Consensus 140 ~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik 195 (243)
.-.+|+|+++++ .+|...+..+..+.+. +-.+=..++++|++.-+.-++....
T Consensus 39 ~~~vilDls~v~--~iDssgl~~L~~l~~~-~~~~g~~l~l~~~~~~v~~~l~~~g 91 (100)
T cd06844 39 GKTIVIDISALE--FMDSSGTGVLLERSRL-AEAVGGQFVLTGISPAVRITLTESG 91 (100)
T ss_pred CCEEEEECCCCc--EEcHHHHHHHHHHHHH-HHHcCCEEEEECCCHHHHHHHHHhC
Confidence 358999999855 4565555555444332 2345578999999887776665443
No 45
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=30.56 E-value=1.1e+02 Score=23.14 Aligned_cols=58 Identities=10% Similarity=0.225 Sum_probs=38.2
Q ss_pred cccccCCCCCHHHHHHHHHHHHHHhhh---CCC----CCCCChHHHHHHHHhcCCCHHHHHHHHHHH
Q 043459 2 SCEYMKSNIDEKEETKIRLMRALVEKQ---DPS----SKEVDDPTLRRFLRARDLDVEKASGMFLKY 61 (243)
Q Consensus 2 ~~~~~~~~l~~~~~~~l~~lr~~l~~~---~~~----~~~~~d~~llrfL~~~~~d~~~a~~~l~~~ 61 (243)
+|+|...|-+.+... ..|.+.-... .|. ..+..-+-+.|-|.-+++|+.++..+|.-|
T Consensus 104 A~~YLaKPAdaDdi~--aAl~~~~~d~~~~~~~~pmS~~rl~WEhIqrvl~e~~~NiSeTARrL~MH 168 (182)
T COG4567 104 ACDYLAKPADADDIL--AALLRREPDEDTAPPENPMSADRLRWEHIQRVLEECEGNISETARRLNMH 168 (182)
T ss_pred hhhhcCCCCChHHHH--HHHhhcCCCcccCCCCCCCchhHhhHHHHHHHHHHhCCCHHHHHHHhhhh
Confidence 689998888765432 2222221111 111 125566779999999999999999998766
No 46
>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=30.11 E-value=92 Score=17.32 Aligned_cols=24 Identities=21% Similarity=0.246 Sum_probs=19.1
Q ss_pred ChHHHHHHHHhcCCCHHHHHHHHH
Q 043459 36 DDPTLRRFLRARDLDVEKASGMFL 59 (243)
Q Consensus 36 ~d~~llrfL~~~~~d~~~a~~~l~ 59 (243)
+..++..-|..+++|+.+|++.|.
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHC
Confidence 446788889999999999999873
No 47
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=29.23 E-value=1.4e+02 Score=22.60 Aligned_cols=44 Identities=16% Similarity=0.400 Sum_probs=26.5
Q ss_pred HHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHH-HHHHHHHHHH
Q 043459 18 IRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVE-KASGMFLKYL 62 (243)
Q Consensus 18 l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~-~a~~~l~~~~ 62 (243)
-+.++++|++.++. ++++|.-+..-|...+.++. +++.++++.+
T Consensus 106 k~~i~~lI~~Ed~~-~PlSD~~i~~~L~~~gi~isRRTVaKYR~~L 150 (160)
T PF04552_consen 106 KARIKELIEEEDKK-KPLSDQEIAELLKEEGIKISRRTVAKYREEL 150 (160)
T ss_dssp -HHHHHHHTTS-TT-S---HHHHHHHHTTTTS---HHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCC-CCCCHHHHHHHHHHcCCCccHHHHHHHHHHc
Confidence 34788888876443 34899999999999997776 4666655543
No 48
>cd07041 STAS_RsbR_RsbS_like Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the "stressosome" complex that plays an important role in the regulation of the bacterial stress activated alternative sigma factor sigma-B. During stress conditions RsbS and RsbR are phosphorylated which leads to the release of RsbT, an activator of of the RsbU phosphatase, which in turn activates RsbV which leads to the release and activation of sigma factor B. RsbS is a single domain protein (STAS domain), while RsbR-like proteins have a well-conserved C-terminal STATS domain and a variable N-terminal domain. The STAS domain is also found in the C- terminal region of sulphate transporters and anti-anti-sigma factors.
Probab=28.88 E-value=1.9e+02 Score=19.57 Aligned_cols=53 Identities=13% Similarity=-0.094 Sum_probs=35.5
Q ss_pred eEEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHc
Q 043459 140 KFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVY 195 (243)
Q Consensus 140 ~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik 195 (243)
.-.+|+|+++++. +|.+.+..+....+.. -.+-.++++++...-+.-.+....
T Consensus 41 ~~~vvlDls~v~~--iDssg~~~l~~~~~~~-~~~g~~l~l~g~~~~v~~~l~~~g 93 (109)
T cd07041 41 ARGVIIDLTGVPV--IDSAVARHLLRLARAL-RLLGARTILTGIRPEVAQTLVELG 93 (109)
T ss_pred CCEEEEECCCCch--hcHHHHHHHHHHHHHH-HHcCCeEEEEeCCHHHHHHHHHhC
Confidence 3479999999654 5555555554444433 346688999999887777666654
No 49
>cd00870 PI3Ka_III Phosphoinositide 3-kinase (PI3K) class III, accessory domain (PIK domain); PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, PI3Ks class III phosphorylate phosphoinositol (PtdIns) only. The prototypical PI3K class III, yeast Vps34, is involved in trafficking proteins from Golgi to the vacuole.
Probab=28.67 E-value=2.6e+02 Score=21.22 Aligned_cols=37 Identities=19% Similarity=0.390 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHH
Q 043459 8 SNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVE 52 (243)
Q Consensus 8 ~~l~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~ 52 (243)
.+|+++++..|-+.|..+.. +...|-.||++-+|+-.
T Consensus 24 ~~L~~~ek~llW~~R~~l~~--------~p~aL~~~L~sv~W~~~ 60 (166)
T cd00870 24 TKLTDEEKDLIWKFRFYLTN--------NKKALTKFLKSVNWSDE 60 (166)
T ss_pred CCCCHHHHHHHHHhHHHHhh--------CcHHHHHHhhhCCCCCH
Confidence 35788888888888887755 24567789998888643
No 50
>cd07042 STAS_SulP_like_sulfate_transporter Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS 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.
Probab=28.37 E-value=1.8e+02 Score=19.22 Aligned_cols=52 Identities=19% Similarity=0.059 Sum_probs=33.8
Q ss_pred EEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHc
Q 043459 141 FVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVY 195 (243)
Q Consensus 141 ~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik 195 (243)
-.+|+|+++++ .+|...+..+..+... +-.+-..+.+.|++.-+.-++....
T Consensus 42 ~~lilD~~~v~--~iDss~~~~L~~~~~~-~~~~~~~~~l~~~~~~~~~~l~~~g 93 (107)
T cd07042 42 KVVILDLSAVN--FIDSTAAEALEELVKD-LRKRGVELYLAGLNPQVRELLERAG 93 (107)
T ss_pred eEEEEECCCCc--hhhHHHHHHHHHHHHH-HHHCCCEEEEecCCHHHHHHHHHcC
Confidence 57899999954 4565555555554433 3344578899999986666655443
No 51
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=28.00 E-value=46 Score=28.47 Aligned_cols=25 Identities=36% Similarity=0.414 Sum_probs=21.5
Q ss_pred CCChHHHHHHHHhcCCCHHHHHHHH
Q 043459 34 EVDDPTLRRFLRARDLDVEKASGMF 58 (243)
Q Consensus 34 ~~~d~~llrfL~~~~~d~~~a~~~l 58 (243)
..-+..++|-|.+++||+++|.+-+
T Consensus 141 EDVENillkLlqaadydV~rAerGI 165 (408)
T COG1219 141 EDVENILLKLLQAADYDVERAERGI 165 (408)
T ss_pred hhHHHHHHHHHHHcccCHHHHhCCe
Confidence 4567789999999999999998765
No 52
>cd00872 PI3Ka_I Phosphoinositide 3-kinase (PI3K) class I, accessory domain ; PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, PI3K class I prefer phosphoinositol (4,5)-bisphosphate as a substrate. Mammalian members interact with active Ras. They form heterodimers with adapter molecules linking them to different signaling pathways.
Probab=27.75 E-value=2.8e+02 Score=21.19 Aligned_cols=45 Identities=11% Similarity=0.218 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHH
Q 043459 9 NIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKY 61 (243)
Q Consensus 9 ~l~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~ 61 (243)
+|+++++..+=+.|..+... ...|-+||++-+|+-..+++.+...
T Consensus 18 ~L~~eek~llW~~R~~~~~~--------p~aL~~~l~sv~w~~~~~v~e~~~l 62 (171)
T cd00872 18 ELTEEDKELLWKLRHECRKK--------PQALPKLLLSVKWNKRDDVAQMYQL 62 (171)
T ss_pred CCCHHHHHHHHHHHHHHhhC--------cHHHHHHHhhCCCCCHHHHHHHHHH
Confidence 57889999999999988663 4568889999988765555444333
No 53
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=27.47 E-value=1.5e+02 Score=23.83 Aligned_cols=130 Identities=15% Similarity=0.176 Sum_probs=71.2
Q ss_pred CCCCCcEEEEeCccc----------cccccCCHHHHHH--------HHHHHHHHHHhhC------CCCCceEEEEEecCC
Q 043459 94 DKKGRPIATVLGARH----------FQNKLGGLEEFKR--------FVVYILDKICSRM------PPGQEKFVVIGDLKG 149 (243)
Q Consensus 94 d~~Grpv~~~~~~~~----------~~~~~~~~~~~~~--------~~~~~~E~~~~~~------~~~~~~~~iI~D~~g 149 (243)
..-||.+-++++... +-..+.++++++- .++|.+|+.++.. .+..++--+|+||-|
T Consensus 28 e~~gRs~~vVNLDPAae~f~y~~~iDiRdlIsvdDVmEdl~~GPNGgLv~cmEyl~~NldwL~~~~Gd~eddylifDcPG 107 (273)
T KOG1534|consen 28 ETVGRSVHVVNLDPAAEHFNYPVTIDIRDLISVDDVMEDLDLGPNGGLVYCMEYLLENLDWLEEEIGDVEDDYLIFDCPG 107 (273)
T ss_pred HhhCceeEEeecCHHHHhhCCcccccHHHhccHHHHHHHhccCCCccchhHHHHHHHHHHHHHhhccCccCCEEEEeCCC
Confidence 346788877776421 1111245555553 4678888766543 244577889999988
Q ss_pred CCCCCc-cHHHHHHHHHHHhhcccccccceEEEeCChHH------HHHHHHHcccC----Ch-hhhhceEEecCcchHHH
Q 043459 150 WGYSNS-DLRAYLGALSILQDYYPERLGKLFIVHAPYIF------MTVWKIVYPFI----DN-NTKKKIVFVQDKKLKST 217 (243)
Q Consensus 150 ~~~~~~-~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~------~~~~~~ik~~l----~~-~~~~ki~~~~~~~~~~~ 217 (243)
-= .-+ -+..++++++-++. .-.++..+|++..+.++ +..+..+..++ |. .+.+|.-++++.+ +++
T Consensus 108 QI-ELytH~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~KfiSG~lsAlsAMi~lE~P~INvlsKMDLlk~~~-k~~ 184 (273)
T KOG1534|consen 108 QI-ELYTHLPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTKFISGCLSALSAMISLEVPHINVLSKMDLLKDKN-KKE 184 (273)
T ss_pred ee-EEeecChhHHHHHHHHhc-ccCceeEEEEeccchhhhHHHHHHHHHHHHHHHHHhcCcchhhhhHHHHhhhhh-HHH
Confidence 11 111 24677888877777 44566777777766554 33333322222 21 2333444443311 356
Q ss_pred HHhcCCCCC
Q 043459 218 LLEEIDESQ 226 (243)
Q Consensus 218 L~~~i~~~~ 226 (243)
|.++.+++.
T Consensus 185 l~~Fl~~d~ 193 (273)
T KOG1534|consen 185 LERFLNPDE 193 (273)
T ss_pred HHHhcCCch
Confidence 777776654
No 54
>PF13466 STAS_2: STAS domain
Probab=26.07 E-value=1.8e+02 Score=18.36 Aligned_cols=51 Identities=16% Similarity=0.087 Sum_probs=34.3
Q ss_pred EEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHH
Q 043459 141 FVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIV 194 (243)
Q Consensus 141 ~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~i 194 (243)
-.+++|+++++. +|...+.-++. +.......-..+.+.|+|.-+..++.+.
T Consensus 27 ~~v~lDls~v~~--iDsagl~lL~~-~~~~~~~~g~~~~l~~~~~~~~~ll~~~ 77 (80)
T PF13466_consen 27 RPVVLDLSGVEF--IDSAGLQLLLA-AARRARARGRQLRLTGPSPALRRLLELL 77 (80)
T ss_pred CeEEEECCCCCe--ecHHHHHHHHH-HHHHHHHCCCeEEEEcCCHHHHHHHHHh
Confidence 678999999654 44444433333 3334445668899999999888777654
No 55
>cd08816 CARD_RIG-I_1 Caspase activation and recruitment domain found in RIG-I, first repeat. Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), first repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction doma
Probab=25.94 E-value=2.1e+02 Score=19.14 Aligned_cols=53 Identities=25% Similarity=0.447 Sum_probs=33.4
Q ss_pred CHHHHHHHHHHHHHHhhhC-CC------CCCCChHHHHHHHHhcCCCHHHHHHHHHHHHH
Q 043459 11 DEKEETKIRLMRALVEKQD-PS------SKEVDDPTLRRFLRARDLDVEKASGMFLKYLK 63 (243)
Q Consensus 11 ~~~~~~~l~~lr~~l~~~~-~~------~~~~~d~~llrfL~~~~~d~~~a~~~l~~~~~ 63 (243)
++++++.|..+++.|++.. |. .....|+...+-+.-.+-.+..|.+.+-.++.
T Consensus 1 ~~~~k~nL~af~~yi~ktl~P~yIl~~m~~~~~~e~v~~I~aEe~kg~~~AaqlfL~~l~ 60 (89)
T cd08816 1 TAAEKRNLQRFRDYIKKILRPSYILGFMTTWLEDEEVERILSEEEKGVTSAAQLFLDYVL 60 (89)
T ss_pred CHHHHHHHHHHHHHHHHhhchHHHHHHHHHhcCHHHHHHHHHHhccChHHHHHHHHHHHH
Confidence 4789999999999999962 21 12445555555555555556666666555443
No 56
>PF05762 VWA_CoxE: VWA domain containing CoxE-like protein; InterPro: IPR008912 This group of proteins contains a VWA type domain and the function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon in several bacteria [].
Probab=25.85 E-value=1.3e+02 Score=23.95 Aligned_cols=14 Identities=14% Similarity=0.439 Sum_probs=5.8
Q ss_pred CHHHHHHHHHHHHH
Q 043459 115 GLEEFKRFVVYILD 128 (243)
Q Consensus 115 ~~~~~~~~~~~~~E 128 (243)
+...+..+++.++-
T Consensus 69 SM~~~s~~~l~~~~ 82 (222)
T PF05762_consen 69 SMAGYSEFMLAFLY 82 (222)
T ss_pred ChHHHHHHHHHHHH
Confidence 44444444443333
No 57
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=23.77 E-value=2.8e+02 Score=19.91 Aligned_cols=49 Identities=20% Similarity=0.214 Sum_probs=31.1
Q ss_pred ceEEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeCChHHHHHHHHHcccC
Q 043459 139 EKFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHAPYIFMTVWKIVYPFI 198 (243)
Q Consensus 139 ~~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~p~~~~~~~~~ik~~l 198 (243)
.|+.++.|+ |-+..+ .... ++.+ .+- .+++++++|..=..+...+....
T Consensus 58 dGVlVltDL-Gssp~n--~~~a---~e~~----~~~-~~v~~~daPlVEGa~~Aav~~~~ 106 (124)
T PRK14484 58 DGVLIFFDL-GSAEMN--AEMA---IEML----DGE-KKIIIIDAPIVEGAFTAAVLLSA 106 (124)
T ss_pred CCeEEEEeC-CChHHH--HHHH---HHhc----CCC-CcEEEECCcHHHHHHHHHHHHcC
Confidence 799999999 533322 2221 2222 222 89999999987777776665543
No 58
>PRK10455 periplasmic protein; Reviewed
Probab=22.28 E-value=3.4e+02 Score=20.45 Aligned_cols=54 Identities=15% Similarity=0.186 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHH
Q 043459 7 KSNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLK 60 (243)
Q Consensus 7 ~~~l~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~ 60 (243)
.-.||+++++.+..+.+--......+....-.-+..-+.+-.||-.++.+.+.+
T Consensus 54 ~L~LT~~Qrqqir~im~~~r~~~~~~~~~~r~~l~~li~ad~FDeaavra~~~k 107 (161)
T PRK10455 54 GLNLTDAQKQQIRDIMKAQRDQMKRPPLEERRAMHDIIASDTFDKAKAEAQITK 107 (161)
T ss_pred hCCCCHHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHccCccCHHHHHHHHHH
Confidence 457899999999988765444211121122334556677888998777665553
No 59
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=20.79 E-value=3.4e+02 Score=19.71 Aligned_cols=46 Identities=15% Similarity=0.185 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHHH
Q 043459 14 EETKIRLMRALVEKQDPSSKEVDDPTLRRFLRARDLDVEKASGMFLKY 61 (243)
Q Consensus 14 ~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~~~d~~~a~~~l~~~ 61 (243)
+++.|++=++-|+. |....-...--..||++++..-++..+.+.+.
T Consensus 2 Re~li~~A~~FL~~--p~V~~sp~~~k~~FL~sKGLt~~EI~~al~~a 47 (136)
T PF04695_consen 2 REDLIEQAVKFLQD--PKVRNSPLEKKIAFLESKGLTEEEIDEALGRA 47 (136)
T ss_dssp HHHHHHHHHHHHCT--TTCCCS-HHHHHHHHHHCT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCC--cccccCCHHHHHHHHHcCCCCHHHHHHHHHhc
Confidence 34556666666655 67777788889999999999888888777654
No 60
>COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.59 E-value=1.9e+02 Score=25.72 Aligned_cols=60 Identities=17% Similarity=0.213 Sum_probs=43.3
Q ss_pred ccCCCCCHHHHHHHHHHHHHHhhhCCCCCCCChHHHHHHHHhc----CCCHHHHHHHHHHHHHHhhhcCCCC
Q 043459 5 YMKSNIDEKEETKIRLMRALVEKQDPSSKEVDDPTLRRFLRAR----DLDVEKASGMFLKYLKWRQTFVPNG 72 (243)
Q Consensus 5 ~~~~~l~~~~~~~l~~lr~~l~~~~~~~~~~~d~~llrfL~~~----~~d~~~a~~~l~~~~~~R~~~~~~~ 72 (243)
.|++-.++++.++...+|+++.. +.+...+.=+-++ +=++++|.+.+-.-.+|-++ .+++
T Consensus 361 vm~~i~~~~h~~~a~~~r~lls~-------y~e~edLi~iGaY~~G~D~~~D~Ai~~~p~i~~fL~Q-~~~e 424 (441)
T COG1157 361 VMPQIVSEEHRKAARRLRQLLSR-------YEENEDLIRIGAYQKGSDPELDKAIKLYPKIEQFLKQ-GIDE 424 (441)
T ss_pred HhhhcCCHHHHHHHHHHHHHHHH-------HHHHHHHHHhcCccCCCCHHHHHHHHhhHHHHHHHcC-Cccc
Confidence 45667799999999999999987 3344433333333 34688999999888888887 4554
No 61
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=20.56 E-value=4.5e+02 Score=24.62 Aligned_cols=95 Identities=18% Similarity=0.239 Sum_probs=55.5
Q ss_pred CCCHHHHHHHHHHHHHHhhhCCC-------------CC----CCC-hHHHHHH---HHhcC-CCHHHHHHHHHHHHHHhh
Q 043459 9 NIDEKEETKIRLMRALVEKQDPS-------------SK----EVD-DPTLRRF---LRARD-LDVEKASGMFLKYLKWRQ 66 (243)
Q Consensus 9 ~l~~~~~~~l~~lr~~l~~~~~~-------------~~----~~~-d~~llrf---L~~~~-~d~~~a~~~l~~~~~~R~ 66 (243)
+|++.+.+.+.+.++.|.+..-. .| ..+ ..++.-+ |...+ -+..+.. .+....+.|.
T Consensus 488 ~Ls~~e~~~l~~~~~~L~~lGf~~e~fg~~si~I~~vP~~l~~~~~~~~l~ell~~l~~~~~~~~~~~~-~~las~ACr~ 566 (617)
T PRK00095 488 ELSEDEADRLEEHKELLARLGLELEPFGPNSFAVREVPALLGQQELEELIRDLLDELAEEGDSDTLKER-ELLATMACHG 566 (617)
T ss_pred eeCHHHHHHHHHHHHHHHhCCcEEEEcCCCEEEEEecChhhcccCHHHHHHHHHHHHHhcCCcchHHHH-HHHHHHHHHH
Confidence 57899999999999999885210 11 122 2333333 33322 2333333 5667777777
Q ss_pred hcCCCCCCCCCCchhhhhcCC-ceeccCCCCCCcEEEEe
Q 043459 67 TFVPNGSISLSEVPNELSQNK-MFMQGFDKKGRPIATVL 104 (243)
Q Consensus 67 ~~~~~~~~~~~~~~~~l~~~~-~~~~g~d~~Grpv~~~~ 104 (243)
+....+.++..++...++.-. +-.+..++.|||+++--
T Consensus 567 AIk~g~~Ls~~E~~~Ll~~L~~~~~P~~CPHGRPt~i~l 605 (617)
T PRK00095 567 AIRAGRRLTLEEMNALLRQLEATENPGTCPHGRPTYIEL 605 (617)
T ss_pred hhhccCCCCHHHHHHHHHHHHhcccccCCCCCCeeEEEC
Confidence 765444466666665554422 23456788999998863
No 62
>PF05704 Caps_synth: Capsular polysaccharide synthesis protein; InterPro: IPR008441 This entry consists of several capsular polysaccharide proteins. Capsular polysaccharide (CPS) is a major virulence factor in Streptococcus pneumoniae. This family is often transcribed with putative glycosyl transferases to give rise to bifunctional proteins [].
Probab=20.27 E-value=64 Score=26.74 Aligned_cols=40 Identities=13% Similarity=0.201 Sum_probs=25.8
Q ss_pred ceEEEEEecCCCCCCCccHHHHHHHHHHHhhcccccccceEEEeC
Q 043459 139 EKFVVIGDLKGWGYSNSDLRAYLGALSILQDYYPERLGKLFIVHA 183 (243)
Q Consensus 139 ~~~~iI~D~~g~~~~~~~~~~~k~~~~~~~~~yP~rl~~i~ivn~ 183 (243)
...+.++=..| ..++ +..++..+..+..+.|+. .|++++.
T Consensus 45 ~k~IW~~W~QG--~e~a-P~~Vk~ci~s~~k~~~~~--~Vi~lt~ 84 (276)
T PF05704_consen 45 EKIIWVCWWQG--EENA-PEIVKKCINSWRKNAPDY--EVILLTE 84 (276)
T ss_pred CCcEEEEECCC--cccc-CHHHHHHHHHHHHHCCCC--eEEEECh
Confidence 44566665555 2334 677888888888888764 5667764
No 63
>PF10400 Vir_act_alpha_C: Virulence activator alpha C-term; InterPro: IPR018309 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response []. This entry represents the C-terminal domain.; PDB: 1YG2_A.
Probab=20.14 E-value=2.4e+02 Score=18.28 Aligned_cols=33 Identities=18% Similarity=0.218 Sum_probs=24.3
Q ss_pred CChHHHHHHHHhcCCCHHHHHHHHHHHHHHhhh
Q 043459 35 VDDPTLRRFLRARDLDVEKASGMFLKYLKWRQT 67 (243)
Q Consensus 35 ~~d~~llrfL~~~~~d~~~a~~~l~~~~~~R~~ 67 (243)
.-|.+|+|-.-+...+.+.+...++.+.+..++
T Consensus 3 ~Rde~LlKlff~~~~~~~~~~~~l~~~~~~~~~ 35 (90)
T PF10400_consen 3 IRDEFLLKLFFGGHLDPEEAIELLEERREQHEE 35 (90)
T ss_dssp ---HHHHHHHGGGTS-HHHHHHHHHHHHHHHHH
T ss_pred chhHHHHHHHhcccCCHHHHHHHHHHHHHHHHH
Confidence 568889999988889999999999887665554
No 64
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=20.12 E-value=52 Score=23.13 Aligned_cols=12 Identities=42% Similarity=0.758 Sum_probs=9.1
Q ss_pred eecc----CCCCCCcE
Q 043459 89 FMQG----FDKKGRPI 100 (243)
Q Consensus 89 ~~~g----~d~~Grpv 100 (243)
.+|| +|..|+||
T Consensus 91 PfHG~IIpRD~~G~Pi 106 (110)
T PF09740_consen 91 PFHGKIIPRDDEGNPI 106 (110)
T ss_pred CCCCcccCCCCCCCCC
Confidence 4566 88889886
Done!