Query 045016
Match_columns 204
No_of_seqs 114 out of 1085
Neff 10.2
Searched_HMMs 46136
Date Fri Mar 29 09:01:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045016.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045016hhsearch_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 4.7E-48 1E-52 293.3 18.5 196 1-199 51-246 (324)
2 KOG1471 Phosphatidylinositol t 100.0 1.3E-38 2.8E-43 250.6 15.8 198 1-199 47-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 5.6E-38 1.2E-42 223.8 7.5 152 44-195 3-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 1.5E-33 3.1E-38 200.8 15.1 143 54-197 14-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 100.0 1.6E-30 3.4E-35 184.4 12.9 146 48-195 9-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.8 2.9E-19 6.3E-24 125.9 5.6 141 49-198 3-146 (149)
7 KOG4406 CDC42 Rho GTPase-activ 98.9 1.3E-08 2.8E-13 80.1 10.1 123 55-186 89-213 (467)
8 PF03765 CRAL_TRIO_N: CRAL/TRI 98.3 7.3E-07 1.6E-11 51.5 2.6 23 1-23 33-55 (55)
9 PF14555 UBA_4: UBA-like domai 85.9 1 2.2E-05 24.2 2.5 19 3-21 19-37 (43)
10 PF11964 SpoIIAA-like: SpoIIAA 85.6 4.1 8.8E-05 26.4 5.9 77 74-158 10-87 (109)
11 KOG1534 Putative transcription 81.2 5.2 0.00011 29.9 5.2 98 83-186 74-192 (273)
12 PF03474 DMA: DMRTA motif; In 74.9 3.3 7.2E-05 21.7 2.0 18 3-20 21-38 (39)
13 PF04838 Baculo_LEF5: Baculovi 73.0 2.4 5.2E-05 29.4 1.5 68 120-188 16-99 (159)
14 PF00627 UBA: UBA/TS-N domain; 72.8 4.3 9.3E-05 20.8 2.2 17 4-20 21-37 (37)
15 TIGR02364 dha_pts dihydroxyace 67.2 30 0.00065 23.4 5.9 59 91-158 51-109 (125)
16 cd00194 UBA Ubiquitin Associat 65.8 9.3 0.0002 19.4 2.6 18 3-20 19-36 (38)
17 PF02845 CUE: CUE domain; Int 65.8 12 0.00027 19.7 3.1 21 2-22 20-40 (42)
18 smart00165 UBA Ubiquitin assoc 62.8 11 0.00025 19.0 2.6 18 3-20 19-36 (37)
19 PF14213 DUF4325: Domain of un 62.1 32 0.0007 20.7 5.6 48 103-152 19-68 (74)
20 smart00546 CUE Domain that may 60.5 13 0.00028 19.7 2.7 20 3-22 22-41 (43)
21 PF11339 DUF3141: Protein of u 55.2 1.1E+02 0.0023 26.5 8.1 60 74-145 115-174 (581)
22 PF02954 HTH_8: Bacterial regu 50.6 24 0.00053 18.5 2.7 19 2-20 10-28 (42)
23 COG0401 Uncharacterized homolo 48.2 28 0.0006 19.8 2.6 26 118-143 29-54 (56)
24 PF01740 STAS: STAS domain; I 48.1 41 0.00088 21.9 4.1 50 101-153 48-97 (117)
25 PRK14484 phosphotransferase ma 47.5 82 0.0018 21.3 5.4 47 100-157 58-104 (124)
26 PF08938 HBS1_N: HBS1 N-termin 44.4 12 0.00026 23.0 0.9 21 4-24 51-71 (79)
27 KOG1838 Alpha/beta hydrolase [ 44.4 1.9E+02 0.0041 24.1 10.1 86 57-155 122-216 (409)
28 PF03641 Lysine_decarbox: Poss 43.3 69 0.0015 21.8 4.7 62 118-182 64-132 (133)
29 PF04548 AIG1: AIG1 family; I 41.7 1.4E+02 0.0031 22.0 7.1 77 56-142 45-122 (212)
30 PF10516 SHNi-TPR: SHNi-TPR; 40.5 54 0.0012 17.0 2.9 23 10-32 14-36 (38)
31 PF13556 HTH_30: PucR C-termin 40.5 63 0.0014 18.4 3.5 26 4-29 6-34 (59)
32 PF11385 DUF3189: Protein of u 40.0 1.1E+02 0.0024 21.4 5.3 53 47-110 49-101 (148)
33 TIGR02886 spore_II_AA anti-sig 39.2 1E+02 0.0022 19.6 5.7 52 102-156 40-91 (106)
34 PRK06394 rpl13p 50S ribosomal 38.4 77 0.0017 22.2 4.3 66 100-173 28-107 (146)
35 TIGR01077 L13_A_E ribosomal pr 38.2 59 0.0013 22.6 3.6 25 149-173 72-102 (142)
36 PF08923 MAPKK1_Int: Mitogen-a 36.6 40 0.00087 22.6 2.6 55 53-108 21-75 (119)
37 PF04548 AIG1: AIG1 family; I 35.9 1.5E+02 0.0032 21.9 5.8 70 101-170 49-122 (212)
38 COG0052 RpsB Ribosomal protein 35.2 29 0.00063 26.5 1.9 66 130-198 30-103 (252)
39 smart00804 TAP_C C-terminal do 35.0 58 0.0013 19.1 2.8 21 4-24 32-52 (63)
40 PF07872 DUF1659: Protein of u 33.3 33 0.00071 18.7 1.5 31 49-80 10-41 (47)
41 PRK05703 flhF flagellar biosyn 32.8 2.2E+02 0.0048 23.8 6.9 94 101-199 300-396 (424)
42 PF07853 DUF1648: Protein of u 32.7 22 0.00047 19.6 0.7 13 185-197 19-31 (51)
43 COG1219 ClpX ATP-dependent pro 32.7 29 0.00062 27.9 1.6 19 2-20 147-165 (408)
44 cd07043 STAS_anti-anti-sigma_f 31.8 1.3E+02 0.0027 18.5 5.4 52 102-156 39-90 (99)
45 PF08828 DSX_dimer: Doublesex 31.5 64 0.0014 18.7 2.5 20 5-24 30-49 (62)
46 PF13466 STAS_2: STAS domain 30.1 1.2E+02 0.0027 17.9 5.7 51 102-155 27-77 (80)
47 cd00392 Ribosomal_L13 Ribosoma 29.7 1.4E+02 0.003 19.9 4.2 37 104-144 2-45 (114)
48 TIGR00377 ant_ant_sig anti-ant 29.4 1.5E+02 0.0033 18.7 5.0 52 100-155 42-94 (108)
49 PF02228 Gag_p19: Major core p 29.3 46 0.001 20.4 1.7 15 126-140 70-84 (92)
50 cd06844 STAS Sulphate Transpor 29.2 1.5E+02 0.0033 18.6 5.6 52 101-155 39-90 (100)
51 PRK02399 hypothetical protein; 28.5 2.2E+02 0.0048 23.7 6.0 80 75-160 313-403 (406)
52 PF08423 Rad51: Rad51; InterP 27.9 2.4E+02 0.0051 21.7 5.9 48 97-148 69-116 (256)
53 PF14148 YhdB: YhdB-like prote 27.8 1.1E+02 0.0023 18.5 3.0 26 3-28 38-68 (77)
54 PF00572 Ribosomal_L13: Riboso 26.3 1.3E+02 0.0029 20.4 3.8 24 149-172 85-113 (128)
55 PF04378 RsmJ: Ribosomal RNA s 24.4 31 0.00068 26.4 0.5 28 135-162 204-231 (245)
56 PF10829 DUF2554: Protein of u 24.2 96 0.0021 18.7 2.4 21 13-33 52-72 (76)
57 PF09967 DUF2201: VWA-like dom 23.2 2.3E+02 0.005 19.0 4.6 9 102-110 1-9 (126)
58 PTZ00068 60S ribosomal protein 23.1 1E+02 0.0022 22.9 2.9 64 99-172 28-106 (202)
59 PRK11889 flhF flagellar biosyn 23.1 4.2E+02 0.009 22.4 6.6 95 101-200 321-417 (436)
60 PRK09216 rplM 50S ribosomal pr 22.2 2.2E+02 0.0048 19.9 4.3 13 149-161 99-111 (144)
61 PF13768 VWA_3: von Willebrand 21.8 2.6E+02 0.0056 19.0 4.8 9 102-110 3-11 (155)
62 PF06972 DUF1296: Protein of u 21.8 1.5E+02 0.0032 17.2 2.7 20 3-22 25-44 (60)
63 CHL00159 rpl13 ribosomal prote 21.7 2.3E+02 0.0049 19.8 4.3 41 100-144 13-60 (143)
64 PF09740 DUF2043: Uncharacteri 21.4 31 0.00068 22.8 -0.0 8 55-62 99-106 (110)
65 PF07034 ORC3_N: Origin recogn 21.2 1.5E+02 0.0033 23.7 3.8 84 101-195 200-291 (330)
66 PF05762 VWA_CoxE: VWA domain 21.1 1E+02 0.0022 23.1 2.7 18 76-93 69-86 (222)
67 PRK06731 flhF flagellar biosyn 20.8 3.7E+02 0.0079 21.0 5.7 94 101-199 155-250 (270)
68 cd07041 STAS_RsbR_RsbS_like Su 20.4 2.4E+02 0.0052 17.9 6.2 52 102-156 42-93 (109)
69 TIGR01066 rplM_bact ribosomal 20.3 2.5E+02 0.0055 19.5 4.3 13 149-161 97-109 (140)
70 KOG2451 Aldehyde dehydrogenase 20.1 4E+02 0.0086 22.3 5.8 97 100-204 186-284 (503)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=4.7e-48 Score=293.30 Aligned_cols=196 Identities=41% Similarity=0.722 Sum_probs=187.8
Q ss_pred ChHHHHHhcCCCHHHHHHHHHHHHhHhhhccCCCCCChhhHHHHHhhCcceeeCCCCCCCcEEEEecCCCCCCCCCHHHH
Q 045016 1 MIRRFLRARDLDIEKASAMLLKYLSWRRDFVPNGLISESEIQNHLAKNILNMQGFDKKGRPILVAFASRHKPSDGTLEDF 80 (204)
Q Consensus 1 ~LlrfL~~~~~~v~~a~~~l~~~~~~R~~~~~~~~~~~~~~~~~l~~~~~~~~g~d~~g~pV~~~~~~~~~~~~~~~~~~ 80 (204)
|++|||||++|||++|.+++.++++||+.+++...+..+++..++..|.+|+.|.|++||||+|++++.+.++..+.++.
T Consensus 51 cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~G~D~~gRPVl~~~~~~~~qn~~t~~~~ 130 (324)
T KOG1470|consen 51 CLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYILGHDKDGRPVLYLRPRPHRQNTKTQKEL 130 (324)
T ss_pred HHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEecccCCCCeEEEEecCCCCCCCCCHHHH
Confidence 68999999999999999999999999999999766888889999999999999999999999999999998999999999
Q ss_pred HHHHHHHHHHHHHhCCCCCceEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhccCCC
Q 045016 81 KRFVVYCLDKICAKMPKGHEKFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVYPFID 160 (204)
Q Consensus 81 ~~~~~~~~e~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k~~l~ 160 (204)
.++++|+||.++..++.+++++++++|++|++++|++++..+.+++++++||||||++.+++|+||++..+|+++|||++
T Consensus 131 ~r~~Vy~mE~Ai~~lp~~qe~~~~L~D~~~fs~sN~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~wkiikpflD 210 (324)
T KOG1470|consen 131 ERLLVYTLENAILFLPPGQEQFVWLFDLTGFSMSNPDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPFWKIIKPFLD 210 (324)
T ss_pred HHHHHHHHHHHHHhCCCCcceEEEEEecccCcccCCCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHHHHHhhhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceEEEEcCCcchHHHhhcCCCCCCccccCCCCCCc
Q 045016 161 DNTKKKIVFVENKNLTSTLLDEIDKSQLPDIYGGKLPLV 199 (204)
Q Consensus 161 ~~~~~ki~~~~~~~~~~~L~~~i~~~~lP~~~GG~~~~~ 199 (204)
++|+.||++..+. .++.++||++++|+.+||+..+.
T Consensus 211 p~t~~Kv~F~~~~---~~l~~~~d~~~l~s~~GG~~~~~ 246 (324)
T KOG1470|consen 211 PKTASKVKFVEPK---DDLSEYFDESQLPSLFGGKLLFE 246 (324)
T ss_pred hhhhceeEEecCh---hHHHhhCCccccchhhCCCcccc
Confidence 9999999999874 56999999999999999977653
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=1.3e-38 Score=250.59 Aligned_cols=198 Identities=33% Similarity=0.524 Sum_probs=163.4
Q ss_pred ChHHHHHhcCCCHHHHHHHHHHHHhHhhhccCCCCCChhhHHHHHh-hCcceeeCCCCCCCcEEEEecCCCCCCC----C
Q 045016 1 MIRRFLRARDLDIEKASAMLLKYLSWRRDFVPNGLISESEIQNHLA-KNILNMQGFDKKGRPILVAFASRHKPSD----G 75 (204)
Q Consensus 1 ~LlrfL~~~~~~v~~a~~~l~~~~~~R~~~~~~~~~~~~~~~~~l~-~~~~~~~g~d~~g~pV~~~~~~~~~~~~----~ 75 (204)
+|+||||+++||+++|.+++.+++.||+++..+...........+. ......+|.|++|+||.+.+.+..+... .
T Consensus 47 ~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~g~~~~~~l~~~~ 126 (317)
T KOG1471|consen 47 NLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDDELLKYYPQGLHGVDKEGRPVYIERLGKIDPKGLLKRT 126 (317)
T ss_pred HHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccchhhhhhccccccccCCCCCEEEEeccCCCCcccceeec
Confidence 4899999999999999999999999999988876544322222222 3456788999999999999999886432 3
Q ss_pred CHHHHHH--------HHHHHHHHHHHhCCCCCceEEEEEeCCCCCCCCc---cHHHHHHHHHHHhhchhccccceEEEeC
Q 045016 76 TLEDFKR--------FVVYCLDKICAKMPKGHEKFVYIGDLQGWGYSCS---DIRAYLACLSILQDCFPERLGKLYIVHA 144 (204)
Q Consensus 76 ~~~~~~~--------~~~~~~e~~~~~~~~~~~~~~~iiD~~g~~~~~~---~~~~~~~~~~~~~~~yP~~l~~i~ivn~ 144 (204)
...+..+ .+...+|........++.|++.|+|++|++++++ .++.+++++.+++++||++++++||||+
T Consensus 127 ~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~ 206 (317)
T KOG1471|consen 127 GSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKILQDNYPERLKRIHIINA 206 (317)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcC
Confidence 4444444 4445555444444567899999999999999987 5788999999999999999999999999
Q ss_pred ChhHHHHHHHhccCCCccccceEEEEcCCcchHHHhhcCCCCCCccccCCCCCCc
Q 045016 145 PKLFMTVWKVVYPFIDDNTKKKIVFVENKNLTSTLLDEIDKSQLPDIYGGKLPLV 199 (204)
Q Consensus 145 p~~~~~~~~~~k~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~lP~~~GG~~~~~ 199 (204)
|++++++|++++|||++++++||+++++ ++.++|.++|+++.||.+|||++.+.
T Consensus 207 P~~f~~~~~~ikpfL~~kt~~ki~~~~~-~~~~~L~k~i~~~~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 207 PTIFSALWKVVKPFLDEKTRKKIHVLHS-KDKESLLKYIPPEVLPEEYGGTCGDL 260 (317)
T ss_pred chhHHHHHHHHhccCCHHHHhhheecCC-CchhhhhhhCCHhhCccccCCCcccc
Confidence 9999999999999999999999995543 45799999999999999999999975
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=5.6e-38 Score=223.82 Aligned_cols=152 Identities=39% Similarity=0.671 Sum_probs=130.6
Q ss_pred HHhhCcceeeCCCCCCCcEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhCC--CCCceEEEEEeCCCCCCCCcc---H
Q 045016 44 HLAKNILNMQGFDKKGRPILVAFASRHKPSDGTLEDFKRFVVYCLDKICAKMP--KGHEKFVYIGDLQGWGYSCSD---I 118 (204)
Q Consensus 44 ~l~~~~~~~~g~d~~g~pV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~--~~~~~~~~iiD~~g~~~~~~~---~ 118 (204)
..+.+..+++|+|++||||++++++++++...+.+++.+++++.+|.+++.++ .+..|+++|+|++|+++++++ .
T Consensus 3 ~~~~~~~~~~g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~~ 82 (159)
T PF00650_consen 3 ILKSGPFYLHGRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPEGGQVEGIVVIIDLSGFSLSNFDWWPI 82 (159)
T ss_dssp HHTTSCEEEEEE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHHTSHHH-EEEEEE-TT--HHHHHCHHH
T ss_pred HHCCeeEEECCCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcccccceeEEEEEeCCCceEeccccchh
Confidence 45678889999999999999999999998888899999999999999987654 467999999999999999987 8
Q ss_pred HHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhccCCCccccceEEEEcCCcchHHHhhcCCCCCCccccCCC
Q 045016 119 RAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVYPFIDDNTKKKIVFVENKNLTSTLLDEIDKSQLPDIYGGK 195 (204)
Q Consensus 119 ~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~lP~~~GG~ 195 (204)
+.++.+++.++++||++++++||+|+|++++++|+++++|+++++++||+++++.++.++|.+++++++||++||||
T Consensus 83 ~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~~GG~ 159 (159)
T PF00650_consen 83 SFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVEYGGT 159 (159)
T ss_dssp HHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGGGTSS
T ss_pred hhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchhcCCC
Confidence 99999999999999999999999999999999999999999999999999998777778999999999999999997
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=1.5e-33 Score=200.80 Aligned_cols=143 Identities=43% Similarity=0.753 Sum_probs=135.3
Q ss_pred CCCCCCCcEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHh--CCCCCceEEEEEeCCCCCCCCccHHHHHHHHHHHhhc
Q 045016 54 GFDKKGRPILVAFASRHKPSDGTLEDFKRFVVYCLDKICAK--MPKGHEKFVYIGDLQGWGYSCSDIRAYLACLSILQDC 131 (204)
Q Consensus 54 g~d~~g~pV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~--~~~~~~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~ 131 (204)
|.|++||||++++++.+++...+.+++++++++.+|.+.+. .+.+..|+++|+|++|+++++++.+.++.+++.++.+
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~lk~~~~~~~~~ 93 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQREKKTGGIEGFTVIFDLKGLSMSNPDLSVLRKILKILQDH 93 (158)
T ss_pred CCCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHHHhcCCCeeeEEEEEECCCCCcccccHHHHHHHHHHHHHH
Confidence 79999999999999999988999999999999999998876 5667899999999999999999999999999999999
Q ss_pred hhccccceEEEeCChhHHHHHHHhccCCCccccceEEEEcCCcchHHHhhcCCCCCCccccCCCCC
Q 045016 132 FPERLGKLYIVHAPKLFMTVWKVVYPFIDDNTKKKIVFVENKNLTSTLLDEIDKSQLPDIYGGKLP 197 (204)
Q Consensus 132 yP~~l~~i~ivn~p~~~~~~~~~~k~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~lP~~~GG~~~ 197 (204)
||++++++||||+|++++++|+++++|+++++++||+++++ ++.++|.+++|+++||.+|||+++
T Consensus 94 yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~-~~~~~L~~~i~~~~lP~~~GG~~~ 158 (158)
T smart00516 94 YPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGN-DSKEELLEYIDPEQLPEELGGTLD 158 (158)
T ss_pred hHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCC-CCHHHHHhhCCHhhCcHhhCCCCC
Confidence 99999999999999999999999999999999999999997 445899999999999999999974
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=99.97 E-value=1.6e-30 Score=184.42 Aligned_cols=146 Identities=40% Similarity=0.663 Sum_probs=130.4
Q ss_pred CcceeeCCCCCCCcEEEEecCCCCC-CCCCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeCCCCCCCCc--cHHHHHHH
Q 045016 48 NILNMQGFDKKGRPILVAFASRHKP-SDGTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDLQGWGYSCS--DIRAYLAC 124 (204)
Q Consensus 48 ~~~~~~g~d~~g~pV~~~~~~~~~~-~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~~g~~~~~~--~~~~~~~~ 124 (204)
+..+..|.|++||||++++++..+. ...+.++++++.++.+|.+++.......|+++|+|++|.+++++ +.+.++++
T Consensus 9 ~~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~~~k~~ 88 (157)
T cd00170 9 KVGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQEDDEQVEGFVVIIDLKGLSLSHLLPDPSLLKKI 88 (157)
T ss_pred cccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhhhhhcccceEEEEECCCCChhccchhHHHHHHH
Confidence 3344555799999999999996443 33455889999999999998877666679999999999999998 78899999
Q ss_pred HHHHhhchhccccceEEEeCChhHHHHHHHhccCCCccccceEEEEcCCcchHHHhhcCCCCCCccccCCC
Q 045016 125 LSILQDCFPERLGKLYIVHAPKLFMTVWKVVYPFIDDNTKKKIVFVENKNLTSTLLDEIDKSQLPDIYGGK 195 (204)
Q Consensus 125 ~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~lP~~~GG~ 195 (204)
++.++++||++++++||||+|++++++|+++++++++++++||+++++. .++|.+++++++||.+|||+
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 9999999999999999999999999999999999999999999999874 58999999999999999996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.78 E-value=2.9e-19 Score=125.92 Aligned_cols=141 Identities=30% Similarity=0.475 Sum_probs=95.7
Q ss_pred cceeeCCCCCCCcEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeCCCCCCCCc-cHHHHHHHHHH
Q 045016 49 ILNMQGFDKKGRPILVAFASRHKPSDGTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDLQGWGYSCS-DIRAYLACLSI 127 (204)
Q Consensus 49 ~~~~~g~d~~g~pV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~~g~~~~~~-~~~~~~~~~~~ 127 (204)
+++..|+|++|+||+++..... ++..+.+.++.+++..+ ... -...++++|+|+++.+..+- +...++++.+.
T Consensus 3 ~~~~gG~d~~g~pV~~~~~~~~-~~~~~~~~ll~yl~~~l---~~~--~~~~~f~vVid~~~~~~~~~~~~~~l~~~~~~ 76 (149)
T PF13716_consen 3 FFYPGGRDREGRPVVVFIASRL-PSSDDLERLLLYLLSTL---SEE--VVDKPFSVVIDHTGFSRSSEPSLSWLKQLYKL 76 (149)
T ss_dssp E-EEEEEBTTS-EEEEEEGGG--C-TTHHHHHHHHHHHHH----TT--TTTS-EEEEEE-TT--GGG---HHHHHHTTTS
T ss_pred EEEecccCCCcCEEEEEECCcC-cchhhHHHHHHHHHHhh---hHH--hcCCCEEEEEEcCCCccccCCchHHHHHHHHH
Confidence 3456789999999999998877 44444444444444444 222 23467999999999888654 78999999999
Q ss_pred HhhchhccccceEEEeCChhHHHHH-HHhccCCCccc-cceEEEEcCCcchHHHhhcCCCCCCccccCCCCCC
Q 045016 128 LQDCFPERLGKLYIVHAPKLFMTVW-KVVYPFIDDNT-KKKIVFVENKNLTSTLLDEIDKSQLPDIYGGKLPL 198 (204)
Q Consensus 128 ~~~~yP~~l~~i~ivn~p~~~~~~~-~~~k~~l~~~~-~~ki~~~~~~~~~~~L~~~i~~~~lP~~~GG~~~~ 198 (204)
+...|+.+++++||||++++++... .+.+++.+.+. .+||+.+.+ .++|.++|++++||+++||+.+.
T Consensus 77 l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s---l~~L~~~i~~~qL~~~lp~~~~~ 146 (149)
T PF13716_consen 77 LPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS---LSELSKHIDPSQLPESLPGVLQY 146 (149)
T ss_dssp S-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS---TCGGGGTSGGGG------HHH--
T ss_pred HHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC---HHHHHhhCCHHHhcccCCCEEec
Confidence 9999999999999999999999999 56666678888 899999987 48999999999999999987653
No 7
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.92 E-value=1.3e-08 Score=80.13 Aligned_cols=123 Identities=23% Similarity=0.412 Sum_probs=103.6
Q ss_pred CCCCCCcEEEEecCCCCCCC-CCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeCCCCCCCCc-cHHHHHHHHHHHhhch
Q 045016 55 FDKKGRPILVAFASRHKPSD-GTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDLQGWGYSCS-DIRAYLACLSILQDCF 132 (204)
Q Consensus 55 ~d~~g~pV~~~~~~~~~~~~-~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~~g~~~~~~-~~~~~~~~~~~~~~~y 132 (204)
+|++||+|+.+-..++.+.. .+-..+++++.+.+|..++. .++.++-..|+...+- ...++.+...-+..+|
T Consensus 89 ~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~Ve~------DYt~vYfh~gl~s~nkp~l~~l~~aYke~Dr~~ 162 (467)
T KOG4406|consen 89 KDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVEN------DYTLVYFHHGLPSDNKPYLQLLFDAYKELDRNF 162 (467)
T ss_pred ccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHhc------cceeeehhcCCcccccchHHHHHHHHHHHHHHH
Confidence 69999999999888876433 23334889999999998885 2888888899887776 4677778888888889
Q ss_pred hccccceEEEeCChhHHHHHHHhccCCCccccceEEEEcCCcchHHHhhcCCCC
Q 045016 133 PERLGKLYIVHAPKLFMTVWKVVYPFIDDNTKKKIVFVENKNLTSTLLDEIDKS 186 (204)
Q Consensus 133 P~~l~~i~ivn~p~~~~~~~~~~k~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~ 186 (204)
-..++.+|+|++-|+..++|+++||+++.+..+||+.+.. .++|.+++.-+
T Consensus 163 ~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n~---lseL~~~l~l~ 213 (467)
T KOG4406|consen 163 KKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFNS---LSELFEALKLN 213 (467)
T ss_pred hhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEeeh---HHHHHHhhhhh
Confidence 9999999999999999999999999999999999999976 58999887644
No 8
>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=98.26 E-value=7.3e-07 Score=51.53 Aligned_cols=23 Identities=57% Similarity=0.775 Sum_probs=20.4
Q ss_pred ChHHHHHhcCCCHHHHHHHHHHH
Q 045016 1 MIRRFLRARDLDIEKASAMLLKY 23 (204)
Q Consensus 1 ~LlrfL~~~~~~v~~a~~~l~~~ 23 (204)
+|+|||||++|||++|.++|.++
T Consensus 33 ~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 33 FLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp HHHHHHHHTTT-HHHHHHHHHHH
T ss_pred HHHHHHHHccCCHHHHHHHHHhC
Confidence 58999999999999999999875
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=85.91 E-value=1 Score=24.16 Aligned_cols=19 Identities=26% Similarity=0.455 Sum_probs=15.2
Q ss_pred HHHHHhcCCCHHHHHHHHH
Q 045016 3 RRFLRARDLDIEKASAMLL 21 (204)
Q Consensus 3 lrfL~~~~~~v~~a~~~l~ 21 (204)
..||.+++||++.|...+-
T Consensus 19 ~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 19 IQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp HHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 4789999999999988753
No 10
>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=85.55 E-value=4.1 Score=26.37 Aligned_cols=77 Identities=17% Similarity=0.202 Sum_probs=53.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeCC-CCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHH
Q 045016 74 DGTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDLQ-GWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVW 152 (204)
Q Consensus 74 ~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~~-g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~ 152 (204)
..+.+++.. +.-.++..+. ....+.+++|++ + +..+++.......+.... ....++++=+|-.+.+...+.
T Consensus 10 ~~t~ed~~~-~~~~~~~~~~----~~~~~~ll~d~~~~--~~~~~~~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~~~ 81 (109)
T PF11964_consen 10 KLTEEDYKE-LLPALEELIA----DHGKIRLLVDLRRD--FEGWSPEARWEDAKFGLK-HLKHFRRIAVVGDSEWIRMIA 81 (109)
T ss_dssp EE-HHHHHH-HHHHHHHHHT----TSSSEEEEEEEC-C--EEEEHHHHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHHHH
T ss_pred eeCHHHHHH-HHHHHHHHHh----cCCceEEEEEecCc--cCCCCHHHHHHHHHhchh-hhcccCEEEEEECcHHHHHHH
Confidence 345677766 5555555444 346789999988 6 344556666666655545 888889999999999999988
Q ss_pred HHhccC
Q 045016 153 KVVYPF 158 (204)
Q Consensus 153 ~~~k~~ 158 (204)
+++..+
T Consensus 82 ~~~~~~ 87 (109)
T PF11964_consen 82 NFFAAF 87 (109)
T ss_dssp HHHHHH
T ss_pred HHHHhc
Confidence 888886
No 11
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=81.16 E-value=5.2 Score=29.94 Aligned_cols=98 Identities=13% Similarity=0.173 Sum_probs=58.6
Q ss_pred HHHHHHHHHHHhC------CCCCceEEEEEeCCCCCCCCc----cHHHHHHHHHHHhhchhccccceEEEeCChhH----
Q 045016 83 FVVYCLDKICAKM------PKGHEKFVYIGDLQGWGYSCS----DIRAYLACLSILQDCFPERLGKLYIVHAPKLF---- 148 (204)
Q Consensus 83 ~~~~~~e~~~~~~------~~~~~~~~~iiD~~g~~~~~~----~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~---- 148 (204)
.++|++|+.+... .+..++-.+|+||-| ++ -...++++++-++. .--++..+|++.++.+.
T Consensus 74 gLv~cmEyl~~NldwL~~~~Gd~eddylifDcPG----QIELytH~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~K 148 (273)
T KOG1534|consen 74 GLVYCMEYLLENLDWLEEEIGDVEDDYLIFDCPG----QIELYTHLPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTK 148 (273)
T ss_pred cchhHHHHHHHHHHHHHhhccCccCCEEEEeCCC----eeEEeecChhHHHHHHHHhc-ccCceeEEEEeccchhhhHHH
Confidence 4577888766543 244577899999988 43 25677777777766 44566778877776543
Q ss_pred --HHHH----HHhccCCCc-cccceEEEEcCCcchHHHhhcCCCC
Q 045016 149 --MTVW----KVVYPFIDD-NTKKKIVFVENKNLTSTLLDEIDKS 186 (204)
Q Consensus 149 --~~~~----~~~k~~l~~-~~~~ki~~~~~~~~~~~L~~~i~~~ 186 (204)
+... .++.--+|. .+..|.-++++ ..+++|.++++++
T Consensus 149 fiSG~lsAlsAMi~lE~P~INvlsKMDLlk~-~~k~~l~~Fl~~d 192 (273)
T KOG1534|consen 149 FISGCLSALSAMISLEVPHINVLSKMDLLKD-KNKKELERFLNPD 192 (273)
T ss_pred HHHHHHHHHHHHHHhcCcchhhhhHHHHhhh-hhHHHHHHhcCCc
Confidence 3333 333322332 13344444443 2256788888776
No 12
>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=74.86 E-value=3.3 Score=21.73 Aligned_cols=18 Identities=17% Similarity=0.163 Sum_probs=15.0
Q ss_pred HHHHHhcCCCHHHHHHHH
Q 045016 3 RRFLRARDLDIEKASAML 20 (204)
Q Consensus 3 lrfL~~~~~~v~~a~~~l 20 (204)
-.-|++|++||-+|.+.+
T Consensus 21 e~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 21 ELILQRCNGDVVQAIEQF 38 (39)
T ss_pred HHHHHHcCCcHHHHHHHh
Confidence 356899999999998865
No 13
>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=72.95 E-value=2.4 Score=29.39 Aligned_cols=68 Identities=22% Similarity=0.451 Sum_probs=48.7
Q ss_pred HHHHHHHHHhhchhcccc--ceEEEeCChhHHHHHHHhccCCCc--cccceEEEE----------cCC--cchHHHhhcC
Q 045016 120 AYLACLSILQDCFPERLG--KLYIVHAPKLFMTVWKVVYPFIDD--NTKKKIVFV----------ENK--NLTSTLLDEI 183 (204)
Q Consensus 120 ~~~~~~~~~~~~yP~~l~--~i~ivn~p~~~~~~~~~~k~~l~~--~~~~ki~~~----------~~~--~~~~~L~~~i 183 (204)
..+.+++.+..+||..++ -+-++|++-.+.++|+-+ |-++. +-|+.|++- +.. ...++|.+.+
T Consensus 16 ~y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRLs~dcI~kL~~nT~NdfKLY~Elf~~i 94 (159)
T PF04838_consen 16 DYKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRLSEDCIEKLFVNTINDFKLYEELFDMI 94 (159)
T ss_pred CHHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhhhHHHHHHHHHhcCchHHHHHHHHHHH
Confidence 456788999999999999 788999999999999887 55555 455556651 111 2235777777
Q ss_pred CCCCC
Q 045016 184 DKSQL 188 (204)
Q Consensus 184 ~~~~l 188 (204)
+.+.+
T Consensus 95 ~~~~~ 99 (159)
T PF04838_consen 95 DDNKL 99 (159)
T ss_pred HccCC
Confidence 65533
No 14
>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=72.75 E-value=4.3 Score=20.80 Aligned_cols=17 Identities=35% Similarity=0.403 Sum_probs=11.5
Q ss_pred HHHHhcCCCHHHHHHHH
Q 045016 4 RFLRARDLDIEKASAML 20 (204)
Q Consensus 4 rfL~~~~~~v~~a~~~l 20 (204)
+=|+.+++|+++|.+-|
T Consensus 21 ~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 21 EALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHTTTSHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHhC
Confidence 45677777887777643
No 15
>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=67.23 E-value=30 Score=23.42 Aligned_cols=59 Identities=19% Similarity=0.140 Sum_probs=37.1
Q ss_pred HHHhCCCCCceEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhccC
Q 045016 91 ICAKMPKGHEKFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVYPF 158 (204)
Q Consensus 91 ~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k~~ 158 (204)
++++.....++++++.|+ |-+..+ ... .+..+. ++..+.+..+|.|-...++...+..-
T Consensus 51 ai~~~~~~~dgVlvl~DL-Ggs~~n--~e~---a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~ 109 (125)
T TIGR02364 51 AIEKADNEADGVLIFYDL-GSAVMN--AEM---AVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQ 109 (125)
T ss_pred HHHHhcCCCCCEEEEEcC-CCcHhH--HHH---HHHHhc---cccccEEEEechhHHHHHHHHHHHHc
Confidence 344443335899999999 633322 112 222222 45568899999999988887776544
No 16
>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=65.85 E-value=9.3 Score=19.44 Aligned_cols=18 Identities=39% Similarity=0.578 Sum_probs=13.9
Q ss_pred HHHHHhcCCCHHHHHHHH
Q 045016 3 RRFLRARDLDIEKASAML 20 (204)
Q Consensus 3 lrfL~~~~~~v~~a~~~l 20 (204)
.+-|+.+++|+++|...|
T Consensus 19 ~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 19 RKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHHhCCCHHHHHHHH
Confidence 456788888988887665
No 17
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=65.77 E-value=12 Score=19.69 Aligned_cols=21 Identities=38% Similarity=0.472 Sum_probs=16.9
Q ss_pred hHHHHHhcCCCHHHHHHHHHH
Q 045016 2 IRRFLRARDLDIEKASAMLLK 22 (204)
Q Consensus 2 LlrfL~~~~~~v~~a~~~l~~ 22 (204)
+..=|.++++|++.|...|.+
T Consensus 20 I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 20 IEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHc
Confidence 345578999999999998864
No 18
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=62.80 E-value=11 Score=18.99 Aligned_cols=18 Identities=33% Similarity=0.471 Sum_probs=12.2
Q ss_pred HHHHHhcCCCHHHHHHHH
Q 045016 3 RRFLRARDLDIEKASAML 20 (204)
Q Consensus 3 lrfL~~~~~~v~~a~~~l 20 (204)
.+-|+.+++|+++|..-|
T Consensus 19 ~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 19 LKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHhCCCHHHHHHHH
Confidence 456777777877776543
No 19
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=62.13 E-value=32 Score=20.66 Aligned_cols=48 Identities=15% Similarity=0.059 Sum_probs=30.9
Q ss_pred EEEEeCCCCCCCCccHHHHHHHHHHHhhchh--ccccceEEEeCChhHHHHH
Q 045016 103 VYIGDLQGWGYSCSDIRAYLACLSILQDCFP--ERLGKLYIVHAPKLFMTVW 152 (204)
Q Consensus 103 ~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP--~~l~~i~ivn~p~~~~~~~ 152 (204)
.+++|++|+ .-++.+.+-.++.-+...|| +.-+++.++|++.....+.
T Consensus 19 ~V~lDF~gv--~~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I 68 (74)
T PF14213_consen 19 KVVLDFEGV--ESITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMI 68 (74)
T ss_pred eEEEECCCc--ccccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHH
Confidence 488999996 44555666655554544555 4556777888776665443
No 20
>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=60.46 E-value=13 Score=19.65 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=16.3
Q ss_pred HHHHHhcCCCHHHHHHHHHH
Q 045016 3 RRFLRARDLDIEKASAMLLK 22 (204)
Q Consensus 3 lrfL~~~~~~v~~a~~~l~~ 22 (204)
-+-|+++++|++.|...|.+
T Consensus 22 ~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 22 KAVLEANNGNVEATINNLLE 41 (43)
T ss_pred HHHHHHcCCCHHHHHHHHHc
Confidence 45688899999999988753
No 21
>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=55.23 E-value=1.1e+02 Score=26.52 Aligned_cols=60 Identities=28% Similarity=0.396 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCC
Q 045016 74 DGTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAP 145 (204)
Q Consensus 74 ~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p 145 (204)
..+.++++++....+|.....-+... ..++|=+|+| .+ .+.++...+|+.++.+.+--+|
T Consensus 115 gQTl~DV~~ae~~Fv~~V~~~hp~~~-kp~liGnCQg--------GW---a~~mlAA~~Pd~~gplvlaGaP 174 (581)
T PF11339_consen 115 GQTLEDVMRAEAAFVEEVAERHPDAP-KPNLIGNCQG--------GW---AAMMLAALRPDLVGPLVLAGAP 174 (581)
T ss_pred CCcHHHHHHHHHHHHHHHHHhCCCCC-CceEEeccHH--------HH---HHHHHHhcCcCccCceeecCCC
Confidence 35677787777777776555433332 6677777765 11 2334566778877777776665
No 22
>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=50.61 E-value=24 Score=18.53 Aligned_cols=19 Identities=32% Similarity=0.415 Sum_probs=14.8
Q ss_pred hHHHHHhcCCCHHHHHHHH
Q 045016 2 IRRFLRARDLDIEKASAML 20 (204)
Q Consensus 2 LlrfL~~~~~~v~~a~~~l 20 (204)
|..-|..++||+.+|++.|
T Consensus 10 i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 10 IRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 4456888999999999987
No 23
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=48.16 E-value=28 Score=19.81 Aligned_cols=26 Identities=19% Similarity=0.290 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhhchhccccceEEEe
Q 045016 118 IRAYLACLSILQDCFPERLGKLYIVH 143 (204)
Q Consensus 118 ~~~~~~~~~~~~~~yP~~l~~i~ivn 143 (204)
.+.+.+++-.+-.++|+.++.+|||-
T Consensus 29 ~df~iNiLLtlLg~~PGiiHA~yvi~ 54 (56)
T COG0401 29 KDFLINILLTLLGYIPGIIHALYVIL 54 (56)
T ss_pred HHHHHHHHHHHHHhhhhhHhheEEEE
Confidence 56666777777779999999999973
No 24
>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=48.15 E-value=41 Score=21.88 Aligned_cols=50 Identities=20% Similarity=0.097 Sum_probs=32.9
Q ss_pred eEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHH
Q 045016 101 KFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWK 153 (204)
Q Consensus 101 ~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~ 153 (204)
--.+|+||+++ ..++.+.+..+.++.+..- .+-..++++|.+....-.+.
T Consensus 48 ~~~vIlD~s~v--~~iDssgi~~L~~~~~~~~-~~g~~~~l~~~~~~v~~~l~ 97 (117)
T PF01740_consen 48 IKNVILDMSGV--SFIDSSGIQALVDIIKELR-RRGVQLVLVGLNPDVRRILE 97 (117)
T ss_dssp SSEEEEEETTE--SEESHHHHHHHHHHHHHHH-HTTCEEEEESHHHHHHHHHH
T ss_pred ceEEEEEEEeC--CcCCHHHHHHHHHHHHHHH-HCCCEEEEEECCHHHHHHHH
Confidence 36899999994 5566555554544443333 57778999998876655543
No 25
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=47.53 E-value=82 Score=21.34 Aligned_cols=47 Identities=19% Similarity=0.165 Sum_probs=29.5
Q ss_pred ceEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhcc
Q 045016 100 EKFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVYP 157 (204)
Q Consensus 100 ~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k~ 157 (204)
+|++++.|+ |- +.++......+ + .+- ++++++++|-.=..+...+..
T Consensus 58 dGVlVltDL-Gs--sp~n~~~a~e~---~----~~~-~~v~~~daPlVEGa~~Aav~~ 104 (124)
T PRK14484 58 DGVLIFFDL-GS--AEMNAEMAIEM---L----DGE-KKIIIIDAPIVEGAFTAAVLL 104 (124)
T ss_pred CCeEEEEeC-CC--hHHHHHHHHHh---c----CCC-CcEEEECCcHHHHHHHHHHHH
Confidence 899999999 63 33333332222 2 222 899999999776665555543
No 26
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=44.44 E-value=12 Score=23.05 Aligned_cols=21 Identities=33% Similarity=0.311 Sum_probs=15.9
Q ss_pred HHHHhcCCCHHHHHHHHHHHH
Q 045016 4 RFLRARDLDIEKASAMLLKYL 24 (204)
Q Consensus 4 rfL~~~~~~v~~a~~~l~~~~ 24 (204)
-=|+.++|||++|...|.+..
T Consensus 51 eal~~~~fDvekAl~~Ll~~~ 71 (79)
T PF08938_consen 51 EALWHYYFDVEKALDYLLSKF 71 (79)
T ss_dssp HHHHHTTT-CCHHHHHHHHCC
T ss_pred HHHHHHcCCHHHHHHHHHHhc
Confidence 347889999999999887643
No 27
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=44.36 E-value=1.9e+02 Score=24.14 Aligned_cols=86 Identities=16% Similarity=0.106 Sum_probs=56.9
Q ss_pred CCCCcEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeCCCCCCCCc---------cHHHHHHHHHH
Q 045016 57 KKGRPILVAFASRHKPSDGTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDLQGWGYSCS---------DIRAYLACLSI 127 (204)
Q Consensus 57 ~~g~pV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~~g~~~~~~---------~~~~~~~~~~~ 127 (204)
.+..|++++-.|-... +.+..++.++... .++ .--++|+..+|+.-..+ ...-++.+++.
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 DGTDPIVVILPGLTGG---SHESYVRHLVHEA---QRK-----GYRVVVFNHRGLGGSKLTTPRLFTAGWTEDLREVVNH 190 (409)
T ss_pred CCCCcEEEEecCCCCC---ChhHHHHHHHHHH---HhC-----CcEEEEECCCCCCCCccCCCceeecCCHHHHHHHHHH
Confidence 3556888887776543 3345555544332 232 35689999999765554 36789999999
Q ss_pred HhhchhccccceEEEeCChhHHHHHHHh
Q 045016 128 LQDCFPERLGKLYIVHAPKLFMTVWKVV 155 (204)
Q Consensus 128 ~~~~yP~~l~~i~ivn~p~~~~~~~~~~ 155 (204)
+...||.+ +++.|-.+.-..++++-+
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 667776655555555443
No 28
>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=43.28 E-value=69 Score=21.77 Aligned_cols=62 Identities=13% Similarity=0.155 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHhhchhcc-cc-ceEEEeCChhHHHHHHHh-----ccCCCccccceEEEEcCCcchHHHhhc
Q 045016 118 IRAYLACLSILQDCFPER-LG-KLYIVHAPKLFMTVWKVV-----YPFIDDNTKKKIVFVENKNLTSTLLDE 182 (204)
Q Consensus 118 ~~~~~~~~~~~~~~yP~~-l~-~i~ivn~p~~~~~~~~~~-----k~~l~~~~~~ki~~~~~~~~~~~L~~~ 182 (204)
...+-.+...+.-.+=+. -+ .+.++|..-+++-++..+ ..+++++..+.+.+..+. +++.++
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 455555555555333332 33 699999887777777766 567888888889988764 565543
No 29
>PF04548 AIG1: AIG1 family; InterPro: IPR006703 This entry represents a domain found in Arabidopsis protein AIG1 which appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 (avrRpt2-induced gene) exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2 []. The domain is also apparently found in a number of mammalian proteins, for example the rat immune-associated nucleotide 4 protein. ; GO: 0005525 GTP binding; PDB: 3LXX_A 3BB4_A 3DEF_A 3BB3_A 2J3E_A 3V70_B 3BB1_A 1H65_B 2XTP_A 3P1J_C ....
Probab=41.70 E-value=1.4e+02 Score=21.97 Aligned_cols=77 Identities=25% Similarity=0.326 Sum_probs=42.5
Q ss_pred CCCCCcEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeCCCCCCCCccHHHHHHHHHHHhhchh-c
Q 045016 56 DKKGRPILVAFASRHKPSDGTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDLQGWGYSCSDIRAYLACLSILQDCFP-E 134 (204)
Q Consensus 56 d~~g~pV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP-~ 134 (204)
..+|+.|.++...-+.....+.+++.+-+..++. ...++++-+++|+.+. .++.-+...++ .+...|+ +
T Consensus 45 ~~~g~~v~VIDTPGl~d~~~~~~~~~~~i~~~l~----~~~~g~ha~llVi~~~--r~t~~~~~~l~----~l~~~FG~~ 114 (212)
T PF04548_consen 45 EVDGRQVTVIDTPGLFDSDGSDEEIIREIKRCLS----LCSPGPHAFLLVIPLG--RFTEEDREVLE----LLQEIFGEE 114 (212)
T ss_dssp EETTEEEEEEE--SSEETTEEHHHHHHHHHHHHH----HTTT-ESEEEEEEETT--B-SHHHHHHHH----HHHHHHCGG
T ss_pred eecceEEEEEeCCCCCCCcccHHHHHHHHHHHHH----hccCCCeEEEEEEecC--cchHHHHHHHH----HHHHHccHH
Confidence 5578899888775544344455655555544443 2345677888888877 34333333333 3444444 4
Q ss_pred cccceEEE
Q 045016 135 RLGKLYIV 142 (204)
Q Consensus 135 ~l~~i~iv 142 (204)
.++.+.||
T Consensus 115 ~~k~~ivv 122 (212)
T PF04548_consen 115 IWKHTIVV 122 (212)
T ss_dssp GGGGEEEE
T ss_pred HHhHhhHH
Confidence 67777776
No 30
>PF10516 SHNi-TPR: SHNi-TPR; InterPro: IPR019544 The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. This entry represents SHNi-TPR (Sim3-Hif1-NASP interrupted TPR), a sequence that is an interrupted form of TPR repeat [].
Probab=40.52 E-value=54 Score=16.99 Aligned_cols=23 Identities=22% Similarity=0.319 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHHHHhHhhhccC
Q 045016 10 DLDIEKASAMLLKYLSWRRDFVP 32 (204)
Q Consensus 10 ~~~v~~a~~~l~~~~~~R~~~~~ 32 (204)
+-+.++|.+-+++++.+|++..|
T Consensus 14 ~e~f~qA~~D~~~aL~i~~~l~~ 36 (38)
T PF10516_consen 14 NENFEQAIEDYEKALEIQEELLP 36 (38)
T ss_pred hccHHHHHHHHHHHHHHHHHhcC
Confidence 45788999999999999999654
No 31
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=40.50 E-value=63 Score=18.37 Aligned_cols=26 Identities=23% Similarity=0.257 Sum_probs=18.4
Q ss_pred HHHHhcCCCHHHHHHHH---HHHHhHhhh
Q 045016 4 RFLRARDLDIEKASAML---LKYLSWRRD 29 (204)
Q Consensus 4 rfL~~~~~~v~~a~~~l---~~~~~~R~~ 29 (204)
+.+-.+++|+.+|++++ ++++..|-+
T Consensus 6 ~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ 34 (59)
T PF13556_consen 6 RAYLENNGNISKTARALHIHRNTLRYRLK 34 (59)
T ss_dssp HHHHHTTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 33446678999999998 666777765
No 32
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=40.01 E-value=1.1e+02 Score=21.40 Aligned_cols=53 Identities=13% Similarity=0.080 Sum_probs=33.6
Q ss_pred hCcceeeCCCCCCCcEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeCCC
Q 045016 47 KNILNMQGFDKKGRPILVAFASRHKPSDGTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDLQG 110 (204)
Q Consensus 47 ~~~~~~~g~d~~g~pV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~~g 110 (204)
.|.++..|.|..|+.|..+-.+... +-+.+++.-+++. . ....+=++++|+..
T Consensus 49 ~G~l~y~G~De~gn~VY~lG~~~~~------~~~~~al~~l~~i----~-~~~~~~i~~vdt~~ 101 (148)
T PF11385_consen 49 IGRLIYMGTDEYGNEVYILGRKNNG------KIVERALKSLLEI----L-GIENEEIILVDTSP 101 (148)
T ss_pred CceEEEEEEcCCCCEEEEEecCChH------HHHHHHHHHHHHH----h-CCCCCcEEEEeccc
Confidence 4677899999999999998665543 2334444444432 1 11245578888765
No 33
>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=39.16 E-value=1e+02 Score=19.57 Aligned_cols=52 Identities=10% Similarity=0.100 Sum_probs=31.8
Q ss_pred EEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhc
Q 045016 102 FVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVY 156 (204)
Q Consensus 102 ~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k 156 (204)
-.+|+|+++++. ++.+.+..+....+. .-..-.++++++++.-..-++....
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 489999999554 443333333332222 2235678999999887776665543
No 34
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=38.42 E-value=77 Score=22.18 Aligned_cols=66 Identities=6% Similarity=-0.146 Sum_probs=35.6
Q ss_pred ceEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCCh--------hHHHHHHHhccCCCc------cccc
Q 045016 100 EKFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPK--------LFMTVWKVVYPFIDD------NTKK 165 (204)
Q Consensus 100 ~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~--------~~~~~~~~~k~~l~~------~~~~ 165 (204)
...++|++++.+.++--.. .. ...-.+|+ ..+.. .|+-. =-.+++..++..||. ...+
T Consensus 28 Gd~VVViNa~kv~~tG~K~---~~--~~~y~~~~-~~k~~--~np~~~~~~~~r~P~~il~~AV~gMLP~kn~~gr~~~~ 99 (146)
T PRK06394 28 GEEVVIVNAEKAVITGNRE---RV--IEKYKQRR-ERGSH--YNPYRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREALK 99 (146)
T ss_pred CCEEEEEechheEecCchh---hh--eeeEeCCC-CCccc--CCCCChHHhhhcCHHHHHHHHHHhcCCCCChhHHHHHh
Confidence 6688899988876553211 11 11223344 22222 44211 136788888889982 2345
Q ss_pred eEEEEcCC
Q 045016 166 KIVFVENK 173 (204)
Q Consensus 166 ki~~~~~~ 173 (204)
+.++..+.
T Consensus 100 rLkvy~G~ 107 (146)
T PRK06394 100 RLKVYVGV 107 (146)
T ss_pred CcEEecCC
Confidence 67777653
No 35
>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.
Probab=38.15 E-value=59 Score=22.63 Aligned_cols=25 Identities=4% Similarity=0.058 Sum_probs=17.2
Q ss_pred HHHHHHhccCCCcc------ccceEEEEcCC
Q 045016 149 MTVWKVVYPFIDDN------TKKKIVFVENK 173 (204)
Q Consensus 149 ~~~~~~~k~~l~~~------~~~ki~~~~~~ 173 (204)
.+++..++..||.. ..++.++..+.
T Consensus 72 ~il~~aVrGMLPk~~~~Gr~~~krLkvy~G~ 102 (142)
T TIGR01077 72 RIFRRTVRGMLPHKTARGRAALRRLKVYVGI 102 (142)
T ss_pred HHHHHHHHHhCCCCChhHHHHHhCcEEecCC
Confidence 57778888888875 23467777653
No 36
>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents Mitogen-activated protein kinase kinase 1 interacting protein, which is a small subcellular adaptor protein required for MAPK signalling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer []. ; PDB: 1VEU_A 1VET_A 1SKO_A 2ZL1_A 3CPT_A.
Probab=36.55 E-value=40 Score=22.61 Aligned_cols=55 Identities=11% Similarity=0.044 Sum_probs=29.0
Q ss_pred eCCCCCCCcEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeC
Q 045016 53 QGFDKKGRPILVAFASRHKPSDGTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDL 108 (204)
Q Consensus 53 ~g~d~~g~pV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~ 108 (204)
-=.|+||-||+-.-....+ +......++..+....|++-..--+....++..+|-
T Consensus 21 ~itDrDGvpi~~v~~~~~~-~~~~~~~~~~tf~~a~~Q~~KL~lG~nk~ii~~Y~~ 75 (119)
T PF08923_consen 21 VITDRDGVPIAKVSSDSAP-ESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDS 75 (119)
T ss_dssp EEEETTS-EEEEEE-TTS--GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESS
T ss_pred EEECCCCcEEEEecCCCCc-chhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCC
Confidence 3379999999998665553 222223455556677776443222333455555543
No 37
>PF04548 AIG1: AIG1 family; InterPro: IPR006703 This entry represents a domain found in Arabidopsis protein AIG1 which appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 (avrRpt2-induced gene) exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2 []. The domain is also apparently found in a number of mammalian proteins, for example the rat immune-associated nucleotide 4 protein. ; GO: 0005525 GTP binding; PDB: 3LXX_A 3BB4_A 3DEF_A 3BB3_A 2J3E_A 3V70_B 3BB1_A 1H65_B 2XTP_A 3P1J_C ....
Probab=35.92 E-value=1.5e+02 Score=21.87 Aligned_cols=70 Identities=16% Similarity=0.119 Sum_probs=45.9
Q ss_pred eEEEEEeCCCCCCCCcc-HHHHHHHHHHHhhchhccccceEEEeCChhH---HHHHHHhccCCCccccceEEEE
Q 045016 101 KFVYIGDLQGWGYSCSD-IRAYLACLSILQDCFPERLGKLYIVHAPKLF---MTVWKVVYPFIDDNTKKKIVFV 170 (204)
Q Consensus 101 ~~~~iiD~~g~~~~~~~-~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~---~~~~~~~k~~l~~~~~~ki~~~ 170 (204)
.-+.|+|.-|+.=+..+ -...+.+.+.+....|+.---++|++...+- ...+..+...+.++..+.+.++
T Consensus 49 ~~v~VIDTPGl~d~~~~~~~~~~~i~~~l~~~~~g~ha~llVi~~~r~t~~~~~~l~~l~~~FG~~~~k~~ivv 122 (212)
T PF04548_consen 49 RQVTVIDTPGLFDSDGSDEEIIREIKRCLSLCSPGPHAFLLVIPLGRFTEEDREVLELLQEIFGEEIWKHTIVV 122 (212)
T ss_dssp EEEEEEE--SSEETTEEHHHHHHHHHHHHHHTTT-ESEEEEEEETTB-SHHHHHHHHHHHHHHCGGGGGGEEEE
T ss_pred eEEEEEeCCCCCCCcccHHHHHHHHHHHHHhccCCCeEEEEEEecCcchHHHHHHHHHHHHHccHHHHhHhhHH
Confidence 45789999997444443 4456677777777888777777888887553 5666777777787777766555
No 38
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=35.17 E-value=29 Score=26.53 Aligned_cols=66 Identities=21% Similarity=0.302 Sum_probs=42.1
Q ss_pred hchhccccceEEEeCChhHH---HHHHHhccCCCccccceEEEEcCCcchH----HHhhcCCCCCCcccc-CCCCCC
Q 045016 130 DCFPERLGKLYIVHAPKLFM---TVWKVVYPFIDDNTKKKIVFVENKNLTS----TLLDEIDKSQLPDIY-GGKLPL 198 (204)
Q Consensus 130 ~~yP~~l~~i~ivn~p~~~~---~~~~~~k~~l~~~~~~ki~~~~~~~~~~----~L~~~i~~~~lP~~~-GG~~~~ 198 (204)
.-|.+| +.+||||...-.. ..+++++..-.. ..+|-|++...... +-++..+-..+...| ||+++.
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 468899 9999999765443 344444433311 45789998753322 344566666666665 999885
No 39
>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=35.02 E-value=58 Score=19.10 Aligned_cols=21 Identities=19% Similarity=0.180 Sum_probs=17.3
Q ss_pred HHHHhcCCCHHHHHHHHHHHH
Q 045016 4 RFLRARDLDIEKASAMLLKYL 24 (204)
Q Consensus 4 rfL~~~~~~v~~a~~~l~~~~ 24 (204)
+.|..++||.++|.+...+-.
T Consensus 32 ~cLe~~~Wd~~~Al~~F~~lk 52 (63)
T smart00804 32 MCLEDNNWDYERALKNFTELK 52 (63)
T ss_pred HHHHHcCCCHHHHHHHHHHHH
Confidence 568889999999999887644
No 40
>PF07872 DUF1659: Protein of unknown function (DUF1659); InterPro: IPR012454 This family consists of hypothetical bacterial proteins of unknown function
Probab=33.32 E-value=33 Score=18.72 Aligned_cols=31 Identities=35% Similarity=0.555 Sum_probs=20.7
Q ss_pred cceeeCCCCCCCcEEEEec-CCCCCCCCCHHHH
Q 045016 49 ILNMQGFDKKGRPILVAFA-SRHKPSDGTLEDF 80 (204)
Q Consensus 49 ~~~~~g~d~~g~pV~~~~~-~~~~~~~~~~~~~ 80 (204)
+.+..|.|.+|.|++--+. +...++. +.+++
T Consensus 10 l~~~~G~d~~Gkpi~k~ks~~nvk~~A-tdedl 41 (47)
T PF07872_consen 10 LKYQTGVDENGKPIFKTKSFSNVKPDA-TDEDL 41 (47)
T ss_pred EEEEcccCCCCCEEEEeeehhhcCCCC-CHHHH
Confidence 3467899999999998754 4555443 33444
No 41
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=32.77 E-value=2.2e+02 Score=23.77 Aligned_cols=94 Identities=16% Similarity=0.132 Sum_probs=55.2
Q ss_pred eEEEEEeCCCCCCCCccHHHHHHHHHHHh-hchhccccceEEEeCChhHHHHHHHhccCCCccccceEEEEcC--CcchH
Q 045016 101 KFVYIGDLQGWGYSCSDIRAYLACLSILQ-DCFPERLGKLYIVHAPKLFMTVWKVVYPFIDDNTKKKIVFVEN--KNLTS 177 (204)
Q Consensus 101 ~~~~iiD~~g~~~~~~~~~~~~~~~~~~~-~~yP~~l~~i~ivn~p~~~~~~~~~~k~~l~~~~~~ki~~~~~--~~~~~ 177 (204)
.-.+|||..|.+ +.+...+..+..++. ..+| +..++|+++..-...+..++..|=.-.. ..+.+-.= .....
T Consensus 300 ~DlVlIDt~G~~--~~d~~~~~~L~~ll~~~~~~--~~~~LVl~a~~~~~~l~~~~~~f~~~~~-~~vI~TKlDet~~~G 374 (424)
T PRK05703 300 CDVILIDTAGRS--QRDKRLIEELKALIEFSGEP--IDVYLVLSATTKYEDLKDIYKHFSRLPL-DGLIFTKLDETSSLG 374 (424)
T ss_pred CCEEEEeCCCCC--CCCHHHHHHHHHHHhccCCC--CeEEEEEECCCCHHHHHHHHHHhCCCCC-CEEEEeccccccccc
Confidence 457999999954 444444444444444 3344 6778899987766666666655532222 23333211 11123
Q ss_pred HHhhcCCCCCCccccCCCCCCc
Q 045016 178 TLLDEIDKSQLPDIYGGKLPLV 199 (204)
Q Consensus 178 ~L~~~i~~~~lP~~~GG~~~~~ 199 (204)
.+...+....+|..|=|+++.+
T Consensus 375 ~i~~~~~~~~lPv~yit~Gq~V 396 (424)
T PRK05703 375 SILSLLIESGLPISYLTNGQRV 396 (424)
T ss_pred HHHHHHHHHCCCEEEEeCCCCC
Confidence 5566666677898888777743
No 42
>PF07853 DUF1648: Protein of unknown function (DUF1648); InterPro: IPR012867 This entry contains hypothetical proteins expressed by either bacterial or archaeal species. Some of these are annotated as being transmembrane proteins, and many contain a high proportion of hydrophobic residues.
Probab=32.74 E-value=22 Score=19.65 Aligned_cols=13 Identities=15% Similarity=0.327 Sum_probs=9.7
Q ss_pred CCCCccccCCCCC
Q 045016 185 KSQLPDIYGGKLP 197 (204)
Q Consensus 185 ~~~lP~~~GG~~~ 197 (204)
||++|.+||..++
T Consensus 19 P~~ip~H~~~~G~ 31 (51)
T PF07853_consen 19 PDQIPTHFNANGE 31 (51)
T ss_pred ChhhceeeCCCCC
Confidence 6678888886665
No 43
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=32.66 E-value=29 Score=27.95 Aligned_cols=19 Identities=32% Similarity=0.574 Sum_probs=16.9
Q ss_pred hHHHHHhcCCCHHHHHHHH
Q 045016 2 IRRFLRARDLDIEKASAML 20 (204)
Q Consensus 2 LlrfL~~~~~~v~~a~~~l 20 (204)
|+|-|.+++|||++|.+-+
T Consensus 147 llkLlqaadydV~rAerGI 165 (408)
T COG1219 147 LLKLLQAADYDVERAERGI 165 (408)
T ss_pred HHHHHHHcccCHHHHhCCe
Confidence 7899999999999998765
No 44
>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=31.83 E-value=1.3e+02 Score=18.48 Aligned_cols=52 Identities=17% Similarity=0.112 Sum_probs=32.1
Q ss_pred EEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhc
Q 045016 102 FVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVY 156 (204)
Q Consensus 102 ~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k 156 (204)
-.+++|+++ +..++.+.+..+....+ .+-.+-..+.+++.+.-..-++..+.
T Consensus 39 ~~viid~~~--v~~iDs~g~~~L~~l~~-~~~~~g~~v~i~~~~~~~~~~l~~~g 90 (99)
T cd07043 39 RRLVLDLSG--VTFIDSSGLGVLLGAYK-RARAAGGRLVLVNVSPAVRRVLELTG 90 (99)
T ss_pred CEEEEECCC--CCEEcchhHHHHHHHHH-HHHHcCCeEEEEcCCHHHHHHHHHhC
Confidence 477899999 44455444444444333 33344577999998876666665543
No 45
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=31.52 E-value=64 Score=18.75 Aligned_cols=20 Identities=30% Similarity=0.318 Sum_probs=14.6
Q ss_pred HHHhcCCCHHHHHHHHHHHH
Q 045016 5 FLRARDLDIEKASAMLLKYL 24 (204)
Q Consensus 5 fL~~~~~~v~~a~~~l~~~~ 24 (204)
-|...+.|+++|.++|.+..
T Consensus 30 ILK~A~~D~eeA~rrI~E~~ 49 (62)
T PF08828_consen 30 ILKYADADVEEASRRIDEAK 49 (62)
T ss_dssp HHHHTTT-HHHHHHHHHH--
T ss_pred HHHhcCCCHHHHHHHHHHHH
Confidence 46778889999999998764
No 46
>PF13466 STAS_2: STAS domain
Probab=30.11 E-value=1.2e+02 Score=17.93 Aligned_cols=51 Identities=14% Similarity=0.054 Sum_probs=33.2
Q ss_pred EEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHh
Q 045016 102 FVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVV 155 (204)
Q Consensus 102 ~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~ 155 (204)
-.+++|+++++ .++...+.-++. +.......-+.+.+.|+|..+..++.+.
T Consensus 27 ~~v~lDls~v~--~iDsagl~lL~~-~~~~~~~~g~~~~l~~~~~~~~~ll~~~ 77 (80)
T PF13466_consen 27 RPVVLDLSGVE--FIDSAGLQLLLA-AARRARARGRQLRLTGPSPALRRLLELL 77 (80)
T ss_pred CeEEEECCCCC--eecHHHHHHHHH-HHHHHHHCCCeEEEEcCCHHHHHHHHHh
Confidence 67899999944 444444443333 3444455678888999998877666554
No 47
>cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=29.70 E-value=1.4e+02 Score=19.92 Aligned_cols=37 Identities=19% Similarity=0.118 Sum_probs=21.6
Q ss_pred EEEeCCCCCCCCccHHHHHHHHHHHhh-----chhc--cccceEEEeC
Q 045016 104 YIGDLQGWGYSCSDIRAYLACLSILQD-----CFPE--RLGKLYIVHA 144 (204)
Q Consensus 104 ~iiD~~g~~~~~~~~~~~~~~~~~~~~-----~yP~--~l~~i~ivn~ 144 (204)
+|||++|..+. .....+...++. +.|. .-..|+|||+
T Consensus 2 ~viDA~~~~lG----RlAs~iA~~L~gKhKp~y~p~~d~Gd~VvViNa 45 (114)
T cd00392 2 HVIDAKGQVLG----RLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNA 45 (114)
T ss_pred EEEeCCCCchH----HHHHHHHHHHcCCCCCCcCCCccCCCEEEEEec
Confidence 58898883333 334444555543 3333 4567889997
No 48
>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=29.37 E-value=1.5e+02 Score=18.67 Aligned_cols=52 Identities=13% Similarity=0.141 Sum_probs=31.6
Q ss_pred ceEEEEEeCCCCCCCCc-cHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHh
Q 045016 100 EKFVYIGDLQGWGYSCS-DIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVV 155 (204)
Q Consensus 100 ~~~~~iiD~~g~~~~~~-~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~ 155 (204)
..-.+++|++++..-.. -...+..+.+.++ +.-..+.+++.+.-...++...
T Consensus 42 ~~~~vvidls~v~~iDssgl~~L~~~~~~~~----~~~~~~~l~~~~~~~~~~l~~~ 94 (108)
T TIGR00377 42 GPRPIVLDLEDLEFMDSSGLGVLLGRYKQVR----RVGGQLVLVSVSPRVARLLDIT 94 (108)
T ss_pred CCCeEEEECCCCeEEccccHHHHHHHHHHHH----hcCCEEEEEeCCHHHHHHHHHh
Confidence 34479999998554332 2444444444333 3446788999887776666544
No 49
>PF02228 Gag_p19: Major core protein p19; InterPro: IPR003139 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from delta-retroviruses such as Human T-lymphotropic virus 1 and Human T-cell leukemia virus 2 (HTLV-2), both members of the human oncovirus subclass of retroviruses [, ].; GO: 0005198 structural molecule activity, 0019013 viral nucleocapsid; PDB: 1JVR_A.
Probab=29.31 E-value=46 Score=20.41 Aligned_cols=15 Identities=20% Similarity=0.627 Sum_probs=9.3
Q ss_pred HHHhhchhccccceE
Q 045016 126 SILQDCFPERLGKLY 140 (204)
Q Consensus 126 ~~~~~~yP~~l~~i~ 140 (204)
..+-+.||+|+.+|.
T Consensus 70 ~lipkgypgrv~ei~ 84 (92)
T PF02228_consen 70 SLIPKGYPGRVNEII 84 (92)
T ss_dssp HHS-SS-STTHHHHH
T ss_pred HHccCCCCchHHHHH
Confidence 446788999987653
No 50
>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=29.23 E-value=1.5e+02 Score=18.60 Aligned_cols=52 Identities=8% Similarity=-0.084 Sum_probs=32.5
Q ss_pred eEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHh
Q 045016 101 KFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVV 155 (204)
Q Consensus 101 ~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~ 155 (204)
.-.+|+|+++ ...++.+.+..+.... ..+-..=..++++|++.-..-.+...
T Consensus 39 ~~~vilDls~--v~~iDssgl~~L~~l~-~~~~~~g~~l~l~~~~~~v~~~l~~~ 90 (100)
T cd06844 39 GKTIVIDISA--LEFMDSSGTGVLLERS-RLAEAVGGQFVLTGISPAVRITLTES 90 (100)
T ss_pred CCEEEEECCC--CcEEcHHHHHHHHHHH-HHHHHcCCEEEEECCCHHHHHHHHHh
Confidence 3589999998 4445555444444432 33334567899999887666555443
No 51
>PRK02399 hypothetical protein; Provisional
Probab=28.49 E-value=2.2e+02 Score=23.70 Aligned_cols=80 Identities=15% Similarity=0.187 Sum_probs=56.9
Q ss_pred CCHHHHHHHHHHHHHHHHHhCCCCCceEEEEEeCCCCCCCC------ccHHHHHHHHHHHhhchhccccceEE-----Ee
Q 045016 75 GTLEDFKRFVVYCLDKICAKMPKGHEKFVYIGDLQGWGYSC------SDIRAYLACLSILQDCFPERLGKLYI-----VH 143 (204)
Q Consensus 75 ~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~iiD~~g~~~~~------~~~~~~~~~~~~~~~~yP~~l~~i~i-----vn 143 (204)
.+.+|..+.--.+.|++ ......+.+++-.+|+|... -+++.-..+++.+++..+..+. ++ ||
T Consensus 313 Tt~eE~~~~g~~ia~kL----n~a~gpv~vllP~~G~S~~D~~G~~f~Dpead~alf~~l~~~l~~~~~--v~~~~~hIN 386 (406)
T PRK02399 313 TTPEENRQIGRWIAEKL----NRAKGPVAFLIPLGGVSALDRPGQPFHDPEADAAFFDALEETVTETRR--LIEVPAHIN 386 (406)
T ss_pred cCHHHHHHHHHHHHHHH----hcCCCCeEEEEeCCCCccccCCCCCccChhHHHHHHHHHHHhCCCCce--EEECCCCCC
Confidence 46677766655666654 23346789999999988765 2677777788888888866644 55 79
Q ss_pred CChhHHHHHHHhccCCC
Q 045016 144 APKLFMTVWKVVYPFID 160 (204)
Q Consensus 144 ~p~~~~~~~~~~k~~l~ 160 (204)
.|.+...+...+..++.
T Consensus 387 D~~FA~a~~~~l~~~~~ 403 (406)
T PRK02399 387 DPEFAEAAVEAFEELMA 403 (406)
T ss_pred CHHHHHHHHHHHHHHHh
Confidence 99999888777755543
No 52
>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51. It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....
Probab=27.91 E-value=2.4e+02 Score=21.66 Aligned_cols=48 Identities=15% Similarity=0.020 Sum_probs=31.9
Q ss_pred CCCceEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhH
Q 045016 97 KGHEKFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLF 148 (204)
Q Consensus 97 ~~~~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~ 148 (204)
.+..+-++.||..| .+++.-+.++.+-......+.+.++++..+...-
T Consensus 69 ~g~~~~vvyidTe~----~f~~~Rl~~i~~~~~~~~~~~l~~I~v~~~~~~~ 116 (256)
T PF08423_consen 69 GGLGGKVVYIDTEG----TFSPERLQQIAERFGLDPEEILDNIFVIRVFDLE 116 (256)
T ss_dssp TSSSSEEEEEESSS----SS-HHHHHHHHHHTTS-HHHHHHTEEEEE-SSHH
T ss_pred ccCCCceEEEeCCC----CCCHHHHHHHhhccccccchhhhceeeeecCCHH
Confidence 45678899999998 6777777777654433344567888888877544
No 53
>PF14148 YhdB: YhdB-like protein
Probab=27.79 E-value=1.1e+02 Score=18.49 Aligned_cols=26 Identities=35% Similarity=0.567 Sum_probs=17.5
Q ss_pred HHHHHhcCCC-----HHHHHHHHHHHHhHhh
Q 045016 3 RRFLRARDLD-----IEKASAMLLKYLSWRR 28 (204)
Q Consensus 3 lrfL~~~~~~-----v~~a~~~l~~~~~~R~ 28 (204)
-+||+|++|. +++....|.+|+..-.
T Consensus 38 EhFLHAy~f~~d~~~i~k~l~~Ll~YIdHA~ 68 (77)
T PF14148_consen 38 EHFLHAYHFEKDYSVIEKRLYALLRYIDHAN 68 (77)
T ss_pred HHHHHHhhccccHHHHHHHHHHHHHHHHHHh
Confidence 4799999885 5556666666665544
No 54
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
Probab=26.25 E-value=1.3e+02 Score=20.41 Aligned_cols=24 Identities=13% Similarity=0.151 Sum_probs=15.3
Q ss_pred HHHHHHhccCCCccc-----cceEEEEcC
Q 045016 149 MTVWKVVYPFIDDNT-----KKKIVFVEN 172 (204)
Q Consensus 149 ~~~~~~~k~~l~~~~-----~~ki~~~~~ 172 (204)
.+++..++..||... .+++++..+
T Consensus 85 ~i~~~aVrgMLP~n~~g~~~l~rL~vy~g 113 (128)
T PF00572_consen 85 RILKRAVRGMLPKNKLGREALKRLKVYPG 113 (128)
T ss_dssp HHHHHHHHTTSTTSHHHHHHHTTEEEESS
T ss_pred HHHHHHHHHHCCCChhhhHHhhceEEECC
Confidence 566677777777732 345676655
No 55
>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=24.41 E-value=31 Score=26.38 Aligned_cols=28 Identities=11% Similarity=0.299 Sum_probs=17.2
Q ss_pred cccceEEEeCChhHHHHHHHhccCCCcc
Q 045016 135 RLGKLYIVHAPKLFMTVWKVVYPFIDDN 162 (204)
Q Consensus 135 ~l~~i~ivn~p~~~~~~~~~~k~~l~~~ 162 (204)
.-..++|||+||-+.....-+-+++.+.
T Consensus 204 ~GSGm~iiNPPw~l~~~l~~~l~~L~~~ 231 (245)
T PF04378_consen 204 NGSGMLIINPPWTLDEELEEILPWLAET 231 (245)
T ss_dssp -EEEEEEES--TTHHHHHHHHHHHHHHH
T ss_pred ecceEEEEcCCccHHHHHHHHHHHHHHH
Confidence 3456999999999876666655554443
No 56
>PF10829 DUF2554: Protein of unknown function (DUF2554); InterPro: IPR020117 This entry contains proteins with no known function.
Probab=24.25 E-value=96 Score=18.67 Aligned_cols=21 Identities=19% Similarity=0.389 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHhHhhhccCC
Q 045016 13 IEKASAMLLKYLSWRRDFVPN 33 (204)
Q Consensus 13 v~~a~~~l~~~~~~R~~~~~~ 33 (204)
.|++++-|+++..|.+...|+
T Consensus 52 aEEsA~~LREhh~WqksRKP~ 72 (76)
T PF10829_consen 52 AEESAEDLREHHHWQKSRKPE 72 (76)
T ss_pred HHHHHHHHHHHHHHHhccCcc
Confidence 478899999999999987775
No 57
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=23.21 E-value=2.3e+02 Score=18.99 Aligned_cols=9 Identities=33% Similarity=0.305 Sum_probs=7.4
Q ss_pred EEEEEeCCC
Q 045016 102 FVYIGDLQG 110 (204)
Q Consensus 102 ~~~iiD~~g 110 (204)
+++.+|.+|
T Consensus 1 i~vaiDtSG 9 (126)
T PF09967_consen 1 IVVAIDTSG 9 (126)
T ss_pred CEEEEECCC
Confidence 468899998
No 58
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=23.12 E-value=1e+02 Score=22.93 Aligned_cols=64 Identities=17% Similarity=0.179 Sum_probs=35.7
Q ss_pred CceEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEe---------CChhHHHHHHHhccCCCcc------c
Q 045016 99 HEKFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVH---------APKLFMTVWKVVYPFIDDN------T 163 (204)
Q Consensus 99 ~~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn---------~p~~~~~~~~~~k~~l~~~------~ 163 (204)
....++|++++.+.++-- ....- .+|-..++..-..| .| -.+++..++..||.+ .
T Consensus 28 ~Gd~VVVVNaeki~iTG~---k~~~K-----~~y~~~lk~~~~~nP~~g~~~~r~P--~~Il~raVrGMLPkk~~~Gr~a 97 (202)
T PTZ00068 28 LGQKIVVVRCEDLNISGS---LFRNK-----VKYEEFLRKRMNTNPRRGPFHHRAP--SDIFWRTVRGMLPHKTKRGAAA 97 (202)
T ss_pred CCCEEEEEecceeEeecc---hhhhe-----eeeEeeeEeeccCCCCcchhcccCH--HHHHHHHHhhhCCCCChhHHHH
Confidence 467788888888765421 11111 11111233333333 33 378889999999973 3
Q ss_pred cceEEEEcC
Q 045016 164 KKKIVFVEN 172 (204)
Q Consensus 164 ~~ki~~~~~ 172 (204)
.++.++..+
T Consensus 98 lkrLkVy~G 106 (202)
T PTZ00068 98 LKRLKVFEG 106 (202)
T ss_pred HhCCEEecC
Confidence 456777754
No 59
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=23.12 E-value=4.2e+02 Score=22.37 Aligned_cols=95 Identities=16% Similarity=0.067 Sum_probs=56.5
Q ss_pred eEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhccCCCccccceEEEEcCC--cchHH
Q 045016 101 KFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVYPFIDDNTKKKIVFVENK--NLTST 178 (204)
Q Consensus 101 ~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k~~l~~~~~~ki~~~~~~--~~~~~ 178 (204)
--+++||..|.+..+ ...+..+..+++..-|. ..++++++..--+.+..+++.|-.- -...+.+-.=+ .....
T Consensus 321 ~DvVLIDTaGRs~kd--~~lm~EL~~~lk~~~Pd--evlLVLsATtk~~d~~~i~~~F~~~-~idglI~TKLDET~k~G~ 395 (436)
T PRK11889 321 VDYILIDTAGKNYRA--SETVEEMIETMGQVEPD--YICLTLSASMKSKDMIEIITNFKDI-HIDGIVFTKFDETASSGE 395 (436)
T ss_pred CCEEEEeCccccCcC--HHHHHHHHHHHhhcCCC--eEEEEECCccChHHHHHHHHHhcCC-CCCEEEEEcccCCCCccH
Confidence 358999999965543 44455555555555565 3467788876667777777777442 22444443211 11134
Q ss_pred HhhcCCCCCCccccCCCCCCcc
Q 045016 179 LLDEIDKSQLPDIYGGKLPLVP 200 (204)
Q Consensus 179 L~~~i~~~~lP~~~GG~~~~~~ 200 (204)
+........+|-.|=|+++.+|
T Consensus 396 iLni~~~~~lPIsyit~GQ~VP 417 (436)
T PRK11889 396 LLKIPAVSSAPIVLMTDGQDVK 417 (436)
T ss_pred HHHHHHHHCcCEEEEeCCCCCC
Confidence 4445555678888877777443
No 60
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=22.19 E-value=2.2e+02 Score=19.87 Aligned_cols=13 Identities=15% Similarity=0.113 Sum_probs=8.2
Q ss_pred HHHHHHhccCCCc
Q 045016 149 MTVWKVVYPFIDD 161 (204)
Q Consensus 149 ~~~~~~~k~~l~~ 161 (204)
.+++..++..||.
T Consensus 99 ~il~~aVrgMLPk 111 (144)
T PRK09216 99 RVIEKAVKGMLPK 111 (144)
T ss_pred HHHHHHHHhcCCC
Confidence 4566666666665
No 61
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=21.82 E-value=2.6e+02 Score=19.02 Aligned_cols=9 Identities=33% Similarity=0.464 Sum_probs=5.2
Q ss_pred EEEEEeCCC
Q 045016 102 FVYIGDLQG 110 (204)
Q Consensus 102 ~~~iiD~~g 110 (204)
+++|+|.++
T Consensus 3 vvilvD~S~ 11 (155)
T PF13768_consen 3 VVILVDTSG 11 (155)
T ss_pred EEEEEeCCC
Confidence 456666555
No 62
>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=21.79 E-value=1.5e+02 Score=17.25 Aligned_cols=20 Identities=25% Similarity=0.343 Sum_probs=16.1
Q ss_pred HHHHHhcCCCHHHHHHHHHH
Q 045016 3 RRFLRARDLDIEKASAMLLK 22 (204)
Q Consensus 3 lrfL~~~~~~v~~a~~~l~~ 22 (204)
..-|+-|+.|..+|.++|..
T Consensus 25 ya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 25 YAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred HHHHHHhCCCHHHHHHHHHh
Confidence 34578899999999998865
No 63
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=21.71 E-value=2.3e+02 Score=19.78 Aligned_cols=41 Identities=17% Similarity=0.174 Sum_probs=21.1
Q ss_pred ceEEEEEeCCCCCCCCccHHHHHHHHHHHh-----hchh--ccccceEEEeC
Q 045016 100 EKFVYIGDLQGWGYSCSDIRAYLACLSILQ-----DCFP--ERLGKLYIVHA 144 (204)
Q Consensus 100 ~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~-----~~yP--~~l~~i~ivn~ 144 (204)
..--+|||++|..+..+ ...+...+. .+-| +.-..|+|||+
T Consensus 13 ~r~W~viDA~~~~lGRl----As~iA~~L~GKhKp~ytP~~d~Gd~VVViNa 60 (143)
T CHL00159 13 NRKWYIIDAKDQTLGRL----ATKIASLLRGKNKPSYHPSVDTGDYVIVINA 60 (143)
T ss_pred CCCEEEEeCCCCchHHH----HHHHHHHHhccCCCCcCCCcCCCCEEEEEec
Confidence 33467788888444333 333444443 1122 24556777786
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=21.37 E-value=31 Score=22.79 Aligned_cols=8 Identities=50% Similarity=0.904 Sum_probs=6.0
Q ss_pred CCCCCCcE
Q 045016 55 FDKKGRPI 62 (204)
Q Consensus 55 ~d~~g~pV 62 (204)
+|..|+|+
T Consensus 99 RD~~G~Pi 106 (110)
T PF09740_consen 99 RDDEGNPI 106 (110)
T ss_pred CCCCCCCC
Confidence 67778775
No 65
>PF07034 ORC3_N: Origin recognition complex (ORC) subunit 3 N-terminus; InterPro: IPR020795 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex
Probab=21.25 E-value=1.5e+02 Score=23.72 Aligned_cols=84 Identities=15% Similarity=0.183 Sum_probs=52.3
Q ss_pred eEEEEE-eCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhccCCCccccce-----EEEEcCCc
Q 045016 101 KFVYIG-DLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVYPFIDDNTKKK-----IVFVENKN 174 (204)
Q Consensus 101 ~~~~ii-D~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k~~l~~~~~~k-----i~~~~~~~ 174 (204)
.+++|+ |+. .++...+.+++.++..+ -.++--++|+...... ..+...+|..+..+ +.+.++..
T Consensus 200 ~lVIi~eD~E-----sF~~~VL~dlI~ils~~-~~~lP~vli~GiaTs~----~~~~~~Lp~~~~~~L~~~~F~~~~~~~ 269 (330)
T PF07034_consen 200 PLVIIFEDFE-----SFDSQVLQDLILILSSY-LDRLPFVLIFGIATSV----EAFHSRLPRSTLSLLRIKKFQLQSSSE 269 (330)
T ss_pred CEEEEEcccc-----cCCHHHHHHHHHHHHhc-cCCcCEEEEEecCCCh----HHHHhhCCHHHHhhcCceEEEeCChHH
Confidence 556655 433 47788999999988654 4578888888875444 34555666665543 44445544
Q ss_pred chHHHhh--cCCCCCCccccCCC
Q 045016 175 LTSTLLD--EIDKSQLPDIYGGK 195 (204)
Q Consensus 175 ~~~~L~~--~i~~~~lP~~~GG~ 195 (204)
..+.+.+ +++++ .|-.+||.
T Consensus 270 ~l~~v~~~~l~~~~-~~~~l~~~ 291 (330)
T PF07034_consen 270 ILERVLEKVLLSPD-FPFKLGPR 291 (330)
T ss_pred HHHHHHHHHhcCCC-CCceECHH
Confidence 4455543 23555 67777775
No 66
>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=21.13 E-value=1e+02 Score=23.06 Aligned_cols=18 Identities=11% Similarity=0.335 Sum_probs=8.3
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 045016 76 TLEDFKRFVVYCLDKICA 93 (204)
Q Consensus 76 ~~~~~~~~~~~~~e~~~~ 93 (204)
+...+..+++..+-.+..
T Consensus 69 SM~~~s~~~l~~~~~l~~ 86 (222)
T PF05762_consen 69 SMAGYSEFMLAFLYALQR 86 (222)
T ss_pred ChHHHHHHHHHHHHHHHH
Confidence 445555554444443333
No 67
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=20.80 E-value=3.7e+02 Score=20.95 Aligned_cols=94 Identities=16% Similarity=0.074 Sum_probs=51.9
Q ss_pred eEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhccCCCccccceEEEEcCC--cchHH
Q 045016 101 KFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVYPFIDDNTKKKIVFVENK--NLTST 178 (204)
Q Consensus 101 ~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k~~l~~~~~~ki~~~~~~--~~~~~ 178 (204)
--.+|+|..|.+..+ ...+..+.+++...=|. ..++|+++..--+-+...++.|-+ --...+.+-.=+ .-...
T Consensus 155 ~D~ViIDt~Gr~~~~--~~~l~el~~~~~~~~~~--~~~LVl~a~~~~~d~~~~~~~f~~-~~~~~~I~TKlDet~~~G~ 229 (270)
T PRK06731 155 VDYILIDTAGKNYRA--SETVEEMIETMGQVEPD--YICLTLSASMKSKDMIEIITNFKD-IHIDGIVFTKFDETASSGE 229 (270)
T ss_pred CCEEEEECCCCCcCC--HHHHHHHHHHHhhhCCC--eEEEEEcCccCHHHHHHHHHHhCC-CCCCEEEEEeecCCCCccH
Confidence 468999999965433 33444444444433343 357788887766677777777744 222344433110 00123
Q ss_pred HhhcCCCCCCccccCCCCCCc
Q 045016 179 LLDEIDKSQLPDIYGGKLPLV 199 (204)
Q Consensus 179 L~~~i~~~~lP~~~GG~~~~~ 199 (204)
+........+|-.|=|+++.+
T Consensus 230 ~l~~~~~~~~Pi~~it~Gq~v 250 (270)
T PRK06731 230 LLKIPAVSSAPIVLMTDGQDV 250 (270)
T ss_pred HHHHHHHHCcCEEEEeCCCCC
Confidence 444444556777776666643
No 68
>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=20.44 E-value=2.4e+02 Score=17.86 Aligned_cols=52 Identities=12% Similarity=-0.084 Sum_probs=32.8
Q ss_pred EEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhc
Q 045016 102 FVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVY 156 (204)
Q Consensus 102 ~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k 156 (204)
-.+|+|++++. .++.+.+..+....+ ..-.+-.++++++...-+...+....
T Consensus 42 ~~vvlDls~v~--~iDssg~~~l~~~~~-~~~~~g~~l~l~g~~~~v~~~l~~~g 93 (109)
T cd07041 42 RGVIIDLTGVP--VIDSAVARHLLRLAR-ALRLLGARTILTGIRPEVAQTLVELG 93 (109)
T ss_pred CEEEEECCCCc--hhcHHHHHHHHHHHH-HHHHcCCeEEEEeCCHHHHHHHHHhC
Confidence 47999999954 445454444444333 22356688999998876666555543
No 69
>TIGR01066 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.
Probab=20.29 E-value=2.5e+02 Score=19.47 Aligned_cols=13 Identities=8% Similarity=0.013 Sum_probs=6.8
Q ss_pred HHHHHHhccCCCc
Q 045016 149 MTVWKVVYPFIDD 161 (204)
Q Consensus 149 ~~~~~~~k~~l~~ 161 (204)
.+++..++..||+
T Consensus 97 ~ii~~aVrGMLPk 109 (140)
T TIGR01066 97 RVLEHAVKGMLPK 109 (140)
T ss_pred HHHHHHHHhcCCC
Confidence 3455555555553
No 70
>KOG2451 consensus Aldehyde dehydrogenase [Energy production and conversion]
Probab=20.13 E-value=4e+02 Score=22.25 Aligned_cols=97 Identities=12% Similarity=0.152 Sum_probs=58.9
Q ss_pred ceEEEEEeCCCCCCCCccHHHHHHHHHHHhhchhccccceEEEeCChhHHHHHHHhccCCCccccceEEEEcCCcchHHH
Q 045016 100 EKFVYIGDLQGWGYSCSDIRAYLACLSILQDCFPERLGKLYIVHAPKLFMTVWKVVYPFIDDNTKKKIVFVENKNLTSTL 179 (204)
Q Consensus 100 ~~~~~iiD~~g~~~~~~~~~~~~~~~~~~~~~yP~~l~~i~ivn~p~~~~~~~~~~k~~l~~~~~~ki~~~~~~~~~~~L 179 (204)
.|+++|+--+. .-+++.+.-.-...+..+|.=+-.+..-|.+.-- .+-+.+...-..+||.|.++.+-=+-|
T Consensus 186 aGCTvVvkPs~----~TPlsaLala~lA~~AGiP~Gv~NVit~~~~~a~----eig~~lctsp~VrkisFTGST~VGKiL 257 (503)
T KOG2451|consen 186 AGCTVVVKPSE----DTPLSALALAKLAEEAGIPAGVLNVITADASNAA----EIGKELCTSPDVRKISFTGSTNVGKIL 257 (503)
T ss_pred cCceEEEccCC----CCchHHHHHHHHHHHcCCCCcceEEEecCCCChH----HHHHHhhcCCceeeEEeeccchHHHHH
Confidence 67888876554 2234444333334567899877666665432211 233344445556799999986543334
Q ss_pred hhcC--CCCCCccccCCCCCCccCCCC
Q 045016 180 LDEI--DKSQLPDIYGGKLPLVPIQDC 204 (204)
Q Consensus 180 ~~~i--~~~~lP~~~GG~~~~~~~~~~ 204 (204)
...- .-..+.-|+||+.+++-++|+
T Consensus 258 ~~qsastvKkvslELGGNAPfIVFdda 284 (503)
T KOG2451|consen 258 MAQSASTVKKVSLELGGNAPFIVFDDA 284 (503)
T ss_pred HHhhhhhhhheehhhcCCCceEEecCc
Confidence 4332 235678899999999988874
Done!