Query 026657
Match_columns 235
No_of_seqs 106 out of 1117
Neff 9.6
Searched_HMMs 46136
Date Fri Mar 29 10:54:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026657.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026657hhsearch_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 7.6E-47 1.7E-51 304.3 17.3 212 14-232 46-258 (324)
2 KOG1471 Phosphatidylinositol t 100.0 4.4E-37 9.6E-42 256.7 18.2 215 4-220 31-260 (317)
3 PF00650 CRAL_TRIO: CRAL/TRIO 100.0 8.3E-35 1.8E-39 219.6 9.4 153 62-216 3-159 (159)
4 smart00516 SEC14 Domain in hom 100.0 8.8E-31 1.9E-35 197.4 14.7 144 72-218 14-158 (158)
5 cd00170 SEC14 Sec14p-like lipi 100.0 1.7E-28 3.7E-33 184.0 13.9 144 67-216 10-157 (157)
6 PF13716 CRAL_TRIO_2: Divergen 99.8 1.6E-19 3.5E-24 134.7 3.5 139 68-219 4-146 (149)
7 KOG4406 CDC42 Rho GTPase-activ 98.9 1.3E-08 2.8E-13 84.8 10.0 123 73-208 89-214 (467)
8 PF03765 CRAL_TRIO_N: CRAL/TRI 98.6 4.1E-08 8.8E-13 60.1 3.7 29 13-41 27-55 (55)
9 PF02845 CUE: CUE domain; Int 89.0 1.4 3E-05 24.8 4.5 34 4-40 7-40 (42)
10 smart00546 CUE Domain that may 87.3 1.8 3.8E-05 24.5 4.2 34 4-40 8-41 (43)
11 PF06972 DUF1296: Protein of u 78.2 3.5 7.5E-05 25.1 3.0 39 2-40 6-44 (60)
12 PF14555 UBA_4: UBA-like domai 76.6 4.9 0.00011 22.7 3.3 25 15-39 13-37 (43)
13 cd00194 UBA Ubiquitin Associat 62.2 17 0.00037 19.5 3.4 24 15-38 13-36 (38)
14 PF03474 DMA: DMRTA motif; In 62.0 20 0.00043 19.9 3.5 26 13-38 13-38 (39)
15 COG0052 RpsB Ribosomal protein 61.9 12 0.00027 30.0 3.8 68 150-219 29-103 (252)
16 smart00165 UBA Ubiquitin assoc 61.1 18 0.00039 19.3 3.4 24 15-38 13-36 (37)
17 PF10905 DUF2695: Protein of u 60.9 34 0.00073 20.5 4.7 37 2-38 2-39 (53)
18 PF00627 UBA: UBA/TS-N domain; 60.5 19 0.00042 19.4 3.4 24 15-38 14-37 (37)
19 COG0401 Uncharacterized homolo 54.1 16 0.00034 21.9 2.4 27 138-164 28-54 (56)
20 PF11964 SpoIIAA-like: SpoIIAA 52.7 69 0.0015 21.6 6.3 71 97-179 16-87 (109)
21 PF14213 DUF4325: Domain of un 51.4 61 0.0013 20.5 5.7 49 123-173 18-68 (74)
22 TIGR02364 dha_pts dihydroxyace 49.4 88 0.0019 22.3 6.2 53 120-181 59-111 (125)
23 smart00804 TAP_C C-terminal do 46.9 48 0.001 20.6 3.9 29 14-42 24-52 (63)
24 PF04838 Baculo_LEF5: Baculovi 46.5 16 0.00034 26.9 1.9 48 142-190 17-68 (159)
25 PF04378 RsmJ: Ribosomal RNA s 43.4 16 0.00034 29.5 1.7 29 156-184 204-232 (245)
26 KOG1838 Alpha/beta hydrolase [ 42.5 2.4E+02 0.0051 24.8 10.4 84 76-176 123-216 (409)
27 PF02954 HTH_8: Bacterial regu 41.1 48 0.001 18.4 3.1 23 16-38 6-28 (42)
28 PF11339 DUF3141: Protein of u 38.4 2.1E+02 0.0045 26.1 7.8 58 94-167 117-175 (581)
29 PF09949 DUF2183: Uncharacteri 36.9 1.4E+02 0.003 20.4 5.3 49 101-164 51-99 (100)
30 COG1219 ClpX ATP-dependent pro 35.0 22 0.00048 30.0 1.4 25 14-38 141-165 (408)
31 COG2961 ComJ Protein involved 34.3 31 0.00068 27.9 2.1 26 158-183 237-262 (279)
32 KOG1534 Putative transcription 34.2 1.3E+02 0.0029 24.0 5.4 105 101-207 75-192 (273)
33 PF08938 HBS1_N: HBS1 N-termin 32.6 26 0.00057 22.7 1.2 26 16-41 45-70 (79)
34 PF05762 VWA_CoxE: VWA domain 32.5 70 0.0015 25.2 3.9 39 121-162 58-96 (222)
35 PF03641 Lysine_decarbox: Poss 29.4 2.1E+02 0.0046 20.4 6.5 42 159-203 86-132 (133)
36 PF03943 TAP_C: TAP C-terminal 27.6 47 0.001 19.5 1.6 28 14-41 12-39 (51)
37 PF13556 HTH_30: PucR C-termin 27.2 1.4E+02 0.0031 17.8 3.8 27 21-47 5-34 (59)
38 PF01740 STAS: STAS domain; I 26.6 1.2E+02 0.0026 20.7 3.8 51 122-175 48-98 (117)
39 TIGR02934 nifT_nitrog probable 25.4 24 0.00053 22.2 0.1 36 198-233 20-55 (67)
40 PF11385 DUF3189: Protein of u 24.9 2.4E+02 0.0053 20.8 5.3 54 63-131 47-101 (148)
41 PF07034 ORC3_N: Origin recogn 23.1 2.4E+02 0.0052 23.8 5.6 85 122-217 200-292 (330)
42 PF07872 DUF1659: Protein of u 22.7 72 0.0016 18.4 1.7 28 67-94 10-38 (47)
43 TIGR01012 Sa_S2_E_A ribosomal 21.2 1.8E+02 0.004 22.6 4.2 70 151-221 28-102 (196)
44 PRK04020 rps2P 30S ribosomal p 20.9 1.7E+02 0.0037 22.9 4.0 71 151-222 34-109 (204)
45 TIGR02886 spore_II_AA anti-sig 20.5 2.7E+02 0.0059 18.5 6.4 51 123-177 40-91 (106)
46 PF04548 AIG1: AIG1 family; I 20.2 4.2E+02 0.009 20.5 7.3 70 122-191 49-122 (212)
No 1
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=7.6e-47 Score=304.32 Aligned_cols=212 Identities=29% Similarity=0.500 Sum_probs=198.9
Q ss_pred CCChHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCCCCCCCCCCccccccCCcceecCCCCCCCeEEEEeccccCCCCC
Q 026657 14 KYGDPTLMRFLIARSMDSEKAARMFVQWQKWRATMVPNGFIADSEVPDELEPRKIFLQGLTKDGLPLLVIQVRKHFPSKD 93 (235)
Q Consensus 14 ~~~d~~llRfL~~~~~~~~~a~~~l~~~~~wR~~~~~~~~~~~~~~~~~~~~~~~~~~g~d~~g~~v~~~~~~~~~~~~~ 93 (235)
.++|.+++|||||+|+|+++|.+++.+++.||+.+++...+..+++..++..|+.|+.|.|++||||+|++++.+.++..
T Consensus 46 ~~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~~~~~~~~~Ev~~e~~tGK~yi~G~D~~gRPVl~~~~~~~~qn~~ 125 (324)
T KOG1470|consen 46 WCSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFGPEEVIEADEVAAELETGKAYILGHDKDGRPVLYLRPRPHRQNTK 125 (324)
T ss_pred cCcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcCCccccCHHHHHHHhhcCcEEEecccCCCCeEEEEecCCCCCCCC
Confidence 68999999999999999999999999999999999886547777799999999999999999999999999999999888
Q ss_pred hHH-HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCCCCCcCCcchHHHHHHHHHHHhccccccceeEEEeCChhHHHH
Q 026657 94 PLQ-FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLRQISYKNVDVRGMITGFQFLQAYYPERLAKLYILHMPGFFVSV 172 (235)
Q Consensus 94 ~~~-~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~k~~~~~l~~~yP~~l~~i~ivn~p~~~~~~ 172 (235)
+.+ +.|+++++||.++.. .+.+.+++++++|++|+|++|++++..+.++.++|+|||+||+..+++|+||+|..+
T Consensus 126 t~~~~~r~~Vy~mE~Ai~~----lp~~qe~~~~L~D~~~fs~sN~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~ 201 (324)
T KOG1470|consen 126 TQKELERLLVYTLENAILF----LPPGQEQFVWLFDLTGFSMSNPDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPF 201 (324)
T ss_pred CHHHHHHHHHHHHHHHHHh----CCCCcceEEEEEecccCcccCCCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHH
Confidence 888 999999999999999 778889999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhccChhhhcceEEecCchhHHHHHhhCCCCCCCcccCCCcCceeccccccccccc
Q 026657 173 WRMVSRCLERATLEKIVIVTNEEEMKNFVKDIGEEVLPEEYGGRAKLVAVQDVTLPQLED 232 (235)
Q Consensus 173 ~~~vk~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~~~~~~~~~~~~~~~~~ 232 (235)
|+++|+|+++.|++||+|+.+ .+.++++||+++||..+||+..+..-++.+|+.+-+
T Consensus 202 wkiikpflDp~t~~Kv~F~~~---~~~l~~~~d~~~l~s~~GG~~~~~y~~e~~~~~~~~ 258 (324)
T KOG1470|consen 202 WKIIKPFLDPKTASKVKFVEP---KDDLSEYFDESQLPSLFGGKLLFEYTHEEYWPQMKE 258 (324)
T ss_pred HHHhhhccChhhhceeEEecC---hhHHHhhCCccccchhhCCCcccccCCcchhhhhhh
Confidence 999999999999999999997 467999999999999999999988777777775543
No 2
>KOG1471 consensus Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism]
Probab=100.00 E-value=4.4e-37 Score=256.66 Aligned_cols=215 Identities=28% Similarity=0.433 Sum_probs=171.6
Q ss_pred hhhhhCCCCC--CCChHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCCCCCCCCCCccccccC-CcceecCCCCCCCeE
Q 026657 4 SVQKLGSSTG--KYGDPTLMRFLIARSMDSEKAARMFVQWQKWRATMVPNGFIADSEVPDELEP-RKIFLQGLTKDGLPL 80 (235)
Q Consensus 4 ~l~~~~~~~~--~~~d~~llRfL~~~~~~~~~a~~~l~~~~~wR~~~~~~~~~~~~~~~~~~~~-~~~~~~g~d~~g~~v 80 (235)
|+... |+++ ..||..|+|||||++||+++|++++.+++.||..++.+..+...+....+.. .....+|.|+.|+|+
T Consensus 31 ~~~~~-~~l~~~~~~d~~LlRfLra~~f~ve~a~~~l~~~l~~r~~~~~d~i~~~~~~~~~~~~~~~~~~~~~~~~g~~v 109 (317)
T KOG1471|consen 31 WLLQK-PHLPNKYDDDFNLLRFLRARKFDVEKAKQMLKRYLNWRKRNKLDEIFEDFEEDDELLKYYPQGLHGVDKEGRPV 109 (317)
T ss_pred HHhhc-cCCCCCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhCCccHhhccccchhhhhhccccccccCCCCCEE
Confidence 77777 6665 6999999999999999999999999999999999877543333122222222 235678899999999
Q ss_pred EEEeccccCCCCC----hHH-HHHHHHHHHHHHHHhhc----cCCCCCCceEEEEEeCCCCCcCCc---chHHHHHHHHH
Q 026657 81 LVIQVRKHFPSKD----PLQ-FKKFVVHLLDKTIASSF----RGSEVGNEKLTAILDLRQISYKNV---DVRGMITGFQF 148 (235)
Q Consensus 81 ~~~~~~~~~~~~~----~~~-~~~~~~~~~E~~~~~~~----~~~~~~~~~~~~i~D~~~~~~~~~---~~~~~k~~~~~ 148 (235)
++-+.+..+.... ... +.++.+.-+|....... +..+.+++|++.|+|++|++++++ .+..++.++.+
T Consensus 110 ~~~~~g~~~~~~l~~~~~~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~~~g~~~I~Dl~G~~~~~~~~~~~~~~~~~~~~ 189 (317)
T KOG1471|consen 110 YIERLGKIDPKGLLKRTGSLDYLKYHFKEFEKVFKLVLELELKTGERQISGIVTIFDLKGVSLSHLLKPAPTLLKKILKI 189 (317)
T ss_pred EEeccCCCCcccceeeccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeEEEEECCCCcchhHHHHHHHHHHHHHHH
Confidence 9999998865431 222 44444444444332222 114568999999999999999875 57889999999
Q ss_pred HHhccccccceeEEEeCChhHHHHHHHhhhccChhhhcceEEecCchhHHHHHhhCCCCCCCcccCCCcCce
Q 026657 149 LQAYYPERLAKLYILHMPGFFVSVWRMVSRCLERATLEKIVIVTNEEEMKNFVKDIGEEVLPEEYGGRAKLV 220 (235)
Q Consensus 149 l~~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~~~~~ 220 (235)
++++||++++++||||+|++|.++|+++||||+++|++||+++++ ++.++|.++|++++||.+|||++.+.
T Consensus 190 ~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~-~~~~~L~k~i~~~~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 190 LQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHS-KDKESLLKYIPPEVLPEEYGGTCGDL 260 (317)
T ss_pred HHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCC-CchhhhhhhCCHhhCccccCCCcccc
Confidence 999999999999999999999999999999999999999995543 45899999999999999999999965
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=8.3e-35 Score=219.59 Aligned_cols=153 Identities=33% Similarity=0.523 Sum_probs=129.2
Q ss_pred cccCCcceecCCCCCCCeEEEEeccccCCCCChHH-HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCCCCCcCCcc--
Q 026657 62 ELEPRKIFLQGLTKDGLPLLVIQVRKHFPSKDPLQ-FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLRQISYKNVD-- 138 (235)
Q Consensus 62 ~~~~~~~~~~g~d~~g~~v~~~~~~~~~~~~~~~~-~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~-- 138 (235)
..+.+..+++|+|++|+||++++++++++.....+ +.+++++.+|.+++++.+ +.+.+++++|+|++|+++++++
T Consensus 3 ~~~~~~~~~~g~D~~gr~v~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~~~~--~~~~~~~~~iiD~~g~~~~~~~~~ 80 (159)
T PF00650_consen 3 ILKSGPFYLHGRDKDGRPVIYIRLGRFDPKKFSPEDVIRFFVYLLERMLKRMPE--GGQVEGIVVIIDLSGFSLSNFDWW 80 (159)
T ss_dssp HHTTSCEEEEEE-TTS-EEEEEEGTT--HHTS-HHHHHHHHHHHHHHHHHTHHH--TSHHH-EEEEEE-TT--HHHHHCH
T ss_pred HHCCeeEEECCCCCCcCEEEEEEcccCCCCcCCHHHHHHHHHHHHHHHHhhhcc--cccceeEEEEEeCCCceEeccccc
Confidence 34567889999999999999999999998888877 999999999999876432 3578999999999999999887
Q ss_pred -hHHHHHHHHHHHhccccccceeEEEeCChhHHHHHHHhhhccChhhhcceEEecCchhHHHHHhhCCCCCCCcccCCC
Q 026657 139 -VRGMITGFQFLQAYYPERLAKLYILHMPGFFVSVWRMVSRCLERATLEKIVIVTNEEEMKNFVKDIGEEVLPEEYGGR 216 (235)
Q Consensus 139 -~~~~k~~~~~l~~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~ 216 (235)
.+.++.++++++.+||++++++||+|+|++++++|+++++|+++++++||+++++.++.++|.++||+++||++|||+
T Consensus 81 ~~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~~GG~ 159 (159)
T PF00650_consen 81 PISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVEYGGT 159 (159)
T ss_dssp HHHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGGGTSS
T ss_pred hhhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchhcCCC
Confidence 899999999999999999999999999999999999999999999999999998767778999999999999999997
No 4
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.97 E-value=8.8e-31 Score=197.36 Aligned_cols=144 Identities=33% Similarity=0.555 Sum_probs=133.5
Q ss_pred CCCCCCCeEEEEeccccCCCCChHH-HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCCCCCcCCcchHHHHHHHHHHH
Q 026657 72 GLTKDGLPLLVIQVRKHFPSKDPLQ-FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLRQISYKNVDVRGMITGFQFLQ 150 (235)
Q Consensus 72 g~d~~g~~v~~~~~~~~~~~~~~~~-~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~k~~~~~l~ 150 (235)
|.|++|+||+++++++++++..+.+ +.+++++.+|.+.... ..+....++++|+|++|+++++++.+.++.+++.++
T Consensus 14 g~D~~GrpV~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~--~~~~~~~~~~~i~D~~~~~~~~~~~~~lk~~~~~~~ 91 (158)
T smart00516 14 GYDKDGRPVLIFRAGRFDLKSVTLEELLRYLVYVLEKILQRE--KKTGGIEGFTVIFDLKGLSMSNPDLSVLRKILKILQ 91 (158)
T ss_pred CCCCCcCEEEEEeccccccCcCCHHHHHHHHHHHHHHHHHHH--hcCCCeeeEEEEEECCCCCcccccHHHHHHHHHHHH
Confidence 6999999999999999998888888 9999999999888751 135678999999999999999999999999999999
Q ss_pred hccccccceeEEEeCChhHHHHHHHhhhccChhhhcceEEecCchhHHHHHhhCCCCCCCcccCCCcC
Q 026657 151 AYYPERLAKLYILHMPGFFVSVWRMVSRCLERATLEKIVIVTNEEEMKNFVKDIGEEVLPEEYGGRAK 218 (235)
Q Consensus 151 ~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~~~ 218 (235)
.+||++++++||+|+|++++++|+++++|+++++++||+++++ ++.+.|.++||+++||++|||++.
T Consensus 92 ~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~-~~~~~L~~~i~~~~lP~~~GG~~~ 158 (158)
T smart00516 92 DHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGN-DSKEELLEYIDPEQLPEELGGTLD 158 (158)
T ss_pred HHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCC-CCHHHHHhhCCHhhCcHhhCCCCC
Confidence 9999999999999999999999999999999999999999996 446899999999999999999974
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=1.7e-28 Score=183.97 Aligned_cols=144 Identities=32% Similarity=0.547 Sum_probs=127.4
Q ss_pred cceecCCCCCCCeEEEEeccccCCC-CChHH-HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCCCCCcCCc--chHHH
Q 026657 67 KIFLQGLTKDGLPLLVIQVRKHFPS-KDPLQ-FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLRQISYKNV--DVRGM 142 (235)
Q Consensus 67 ~~~~~g~d~~g~~v~~~~~~~~~~~-~~~~~-~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~~~~~~~--~~~~~ 142 (235)
..+..|.|++|+||++++++..+.. ..+.+ +.+++++.+|.++.. ......|+++|+|++|++++++ +.+.+
T Consensus 10 ~~~~~~~D~~gr~V~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~----~~~~~~~~~~i~D~~~~~~~~~~~~~~~~ 85 (157)
T cd00170 10 VGYLGGRDKEGRPVLIIRAGNKDLSKSLDSEELLRYLVYTLEKLLQE----DDEQVEGFVVIIDLKGLSLSHLLPDPSLL 85 (157)
T ss_pred ccccCCCCCCcCEEEEEecCCcchhhcCCHHHHHHHHHHHHHHHHhh----hhhcccceEEEEECCCCChhccchhHHHH
Confidence 3344557999999999999865443 33436 999999999999887 3344479999999999999987 88899
Q ss_pred HHHHHHHHhccccccceeEEEeCChhHHHHHHHhhhccChhhhcceEEecCchhHHHHHhhCCCCCCCcccCCC
Q 026657 143 ITGFQFLQAYYPERLAKLYILHMPGFFVSVWRMVSRCLERATLEKIVIVTNEEEMKNFVKDIGEEVLPEEYGGR 216 (235)
Q Consensus 143 k~~~~~l~~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~ 216 (235)
++++++++.+||++++++||+|+|+++.++|+++++|+++++++||+++++. .++|.+++++++||.+|||+
T Consensus 86 k~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~--~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 86 KKILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSD--KEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred HHHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCC--HHHHHhhCChhhCcHhhCCC
Confidence 9999999999999999999999999999999999999999999999999874 58999999999999999996
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=99.77 E-value=1.6e-19 Score=134.71 Aligned_cols=139 Identities=21% Similarity=0.396 Sum_probs=97.3
Q ss_pred ceecCCCCCCCeEEEEeccccCCCCChHH-HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCCCCCcCC-cchHHHHHH
Q 026657 68 IFLQGLTKDGLPLLVIQVRKHFPSKDPLQ-FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLRQISYKN-VDVRGMITG 145 (235)
Q Consensus 68 ~~~~g~d~~g~~v~~~~~~~~~~~~~~~~-~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~~~~~~-~~~~~~k~~ 145 (235)
++..|+|++|+||+++...+. ++..+.+ ++.|++..++.. ....++++|+|+++++..+ .++.+++++
T Consensus 4 ~~~gG~d~~g~pV~~~~~~~~-~~~~~~~~ll~yl~~~l~~~---------~~~~~f~vVid~~~~~~~~~~~~~~l~~~ 73 (149)
T PF13716_consen 4 FYPGGRDREGRPVVVFIASRL-PSSDDLERLLLYLLSTLSEE---------VVDKPFSVVIDHTGFSRSSEPSLSWLKQL 73 (149)
T ss_dssp -EEEEEBTTS-EEEEEEGGG--C-TTHHHHHHHHHHHHH-TT---------TTTS-EEEEEE-TT--GGG---HHHHHHT
T ss_pred EEecccCCCcCEEEEEECCcC-cchhhHHHHHHHHHHhhhHH---------hcCCCEEEEEEcCCCccccCCchHHHHHH
Confidence 356789999999999998777 5555666 666666665211 1224699999999998855 579999999
Q ss_pred HHHHHhccccccceeEEEeCChhHHHHH-HHhhhccChhh-hcceEEecCchhHHHHHhhCCCCCCCcccCCCcCc
Q 026657 146 FQFLQAYYPERLAKLYILHMPGFFVSVW-RMVSRCLERAT-LEKIVIVTNEEEMKNFVKDIGEEVLPEEYGGRAKL 219 (235)
Q Consensus 146 ~~~l~~~yP~~l~~i~ivn~p~~~~~~~-~~vk~~l~~~~-~~ki~~~~~~~~~~~L~~~i~~~~LP~~~GG~~~~ 219 (235)
.+.+...|+.+++++||+|++++++... .+.+++.+.+. ..|++++.+ .++|.++||+++||+++||+.++
T Consensus 74 ~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s---l~~L~~~i~~~qL~~~lp~~~~~ 146 (149)
T PF13716_consen 74 YKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS---LSELSKHIDPSQLPESLPGVLQY 146 (149)
T ss_dssp TTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS---TCGGGGTSGGGG------HHH--
T ss_pred HHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC---HHHHHhhCCHHHhcccCCCEEec
Confidence 9999999999999999999999999999 55566778888 899999997 78999999999999999988764
No 7
>KOG4406 consensus CDC42 Rho GTPase-activating protein [Signal transduction mechanisms; Cytoskeleton]
Probab=98.90 E-value=1.3e-08 Score=84.79 Aligned_cols=123 Identities=15% Similarity=0.271 Sum_probs=103.7
Q ss_pred CCCCCCeEEEEeccccCCCCC-hHH-HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCCCCCcCCc-chHHHHHHHHHH
Q 026657 73 LTKDGLPLLVIQVRKHFPSKD-PLQ-FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLRQISYKNV-DVRGMITGFQFL 149 (235)
Q Consensus 73 ~d~~g~~v~~~~~~~~~~~~~-~~~-~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~~~~~~~-~~~~~k~~~~~l 149 (235)
.|+.|+.|+.+.+.++-..+. +-. ++++.++.+|+.+++ -+++++-..|....+- .+.++..-..-+
T Consensus 89 ~D~~gr~iivv~a~rlp~~~eld~~~li~~~v~~id~~Ve~----------DYt~vYfh~gl~s~nkp~l~~l~~aYke~ 158 (467)
T KOG4406|consen 89 KDKQGRKIIVVYACRLPSSSELDDIRLISYLVYTIDKYVEN----------DYTLVYFHHGLPSDNKPYLQLLFDAYKEL 158 (467)
T ss_pred ccccCCeeEEEEEecCCchhhhhhHHHHHHHHHHHHHHHhc----------cceeeehhcCCcccccchHHHHHHHHHHH
Confidence 599999999999877765443 333 899999999999987 2888887888777654 477777777777
Q ss_pred HhccccccceeEEEeCChhHHHHHHHhhhccChhhhcceEEecCchhHHHHHhhCCCCC
Q 026657 150 QAYYPERLAKLYILHMPGFFVSVWRMVSRCLERATLEKIVIVTNEEEMKNFVKDIGEEV 208 (235)
Q Consensus 150 ~~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~~~~~~ki~~~~~~~~~~~L~~~i~~~~ 208 (235)
..+|-..++.+|+|++.|+++.+|++.||++|.+..+||+.++. .++|.+++.-++
T Consensus 159 Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n~---lseL~~~l~l~r 214 (467)
T KOG4406|consen 159 DRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFNS---LSELFEALKLNR 214 (467)
T ss_pred HHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEeeh---HHHHHHhhhhhh
Confidence 88899999999999999999999999999999999999999987 789999986443
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=98.62 E-value=4.1e-08 Score=60.14 Aligned_cols=29 Identities=41% Similarity=0.507 Sum_probs=25.2
Q ss_pred CCCChHHHHHHHHhcCCCHHHHHHHHHHH
Q 026657 13 GKYGDPTLMRFLIARSMDSEKAARMFVQW 41 (235)
Q Consensus 13 ~~~~d~~llRfL~~~~~~~~~a~~~l~~~ 41 (235)
...+|.+|+|||||++||+++|.++|.++
T Consensus 27 ~~~~d~~llRFLRARkf~v~~A~~mL~~t 55 (55)
T PF03765_consen 27 EDHDDNFLLRFLRARKFDVEKAFKMLKKT 55 (55)
T ss_dssp SS-SHHHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHccCCHHHHHHHHHhC
Confidence 47899999999999999999999999875
No 9
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=89.04 E-value=1.4 Score=24.83 Aligned_cols=34 Identities=18% Similarity=0.200 Sum_probs=27.8
Q ss_pred hhhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHH
Q 026657 4 SVQKLGSSTGKYGDPTLMRFLIARSMDSEKAARMFVQ 40 (235)
Q Consensus 4 ~l~~~~~~~~~~~d~~llRfL~~~~~~~~~a~~~l~~ 40 (235)
.|++. .|..+...+..-|.++++|++.|...+.+
T Consensus 7 ~L~~m---FP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 7 QLQEM---FPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHH---SSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHH---CCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 45555 47799999999999999999999998764
No 10
>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=87.25 E-value=1.8 Score=24.48 Aligned_cols=34 Identities=9% Similarity=0.164 Sum_probs=28.1
Q ss_pred hhhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHH
Q 026657 4 SVQKLGSSTGKYGDPTLMRFLIARSMDSEKAARMFVQ 40 (235)
Q Consensus 4 ~l~~~~~~~~~~~d~~llRfL~~~~~~~~~a~~~l~~ 40 (235)
-|++. .|..++..+.+.|+++++|++.|...+.+
T Consensus 8 ~L~~m---FP~l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 8 DLKDM---FPNLDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred HHHHH---CCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 34555 47899999999999999999999987753
No 11
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=78.25 E-value=3.5 Score=25.12 Aligned_cols=39 Identities=21% Similarity=0.338 Sum_probs=30.6
Q ss_pred hhhhhhhCCCCCCCChHHHHHHHHhcCCCHHHHHHHHHH
Q 026657 2 RNSVQKLGSSTGKYGDPTLMRFLIARSMDSEKAARMFVQ 40 (235)
Q Consensus 2 r~~l~~~~~~~~~~~d~~llRfL~~~~~~~~~a~~~l~~ 40 (235)
|..+|+.-......+|..+..-|+-|+.|+.+|.++|..
T Consensus 6 rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 6 RKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 444555533344679999999999999999999999876
No 12
>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=76.59 E-value=4.9 Score=22.70 Aligned_cols=25 Identities=20% Similarity=0.332 Sum_probs=20.5
Q ss_pred CChHHHHHHHHhcCCCHHHHHHHHH
Q 026657 15 YGDPTLMRFLIARSMDSEKAARMFV 39 (235)
Q Consensus 15 ~~d~~llRfL~~~~~~~~~a~~~l~ 39 (235)
.++..-..||.+++||++.|...+-
T Consensus 13 ~~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 13 ADEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp SSHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred cCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4778889999999999999988754
No 13
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=62.15 E-value=17 Score=19.51 Aligned_cols=24 Identities=17% Similarity=0.224 Sum_probs=20.5
Q ss_pred CChHHHHHHHHhcCCCHHHHHHHH
Q 026657 15 YGDPTLMRFLIARSMDSEKAARMF 38 (235)
Q Consensus 15 ~~d~~llRfL~~~~~~~~~a~~~l 38 (235)
.+.....+-|+.+++|+++|...+
T Consensus 13 f~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 13 FSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 557888999999999999998765
No 14
>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=61.97 E-value=20 Score=19.93 Aligned_cols=26 Identities=19% Similarity=0.068 Sum_probs=21.4
Q ss_pred CCCChHHHHHHHHhcCCCHHHHHHHH
Q 026657 13 GKYGDPTLMRFLIARSMDSEKAARMF 38 (235)
Q Consensus 13 ~~~~d~~llRfL~~~~~~~~~a~~~l 38 (235)
|......|-.-|++|++|+-+|.+.+
T Consensus 13 P~~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 13 PHQKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CCCChHHHHHHHHHcCCcHHHHHHHh
Confidence 45566778888999999999998865
No 15
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=61.89 E-value=12 Score=30.02 Aligned_cols=68 Identities=19% Similarity=0.302 Sum_probs=46.2
Q ss_pred HhccccccceeEEEeCChhHHHHHHHhhhccChhh--hcceEEecCch----hHHHHHhhCCCCCCCccc-CCCcCc
Q 026657 150 QAYYPERLAKLYILHMPGFFVSVWRMVSRCLERAT--LEKIVIVTNEE----EMKNFVKDIGEEVLPEEY-GGRAKL 219 (235)
Q Consensus 150 ~~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~~~~--~~ki~~~~~~~----~~~~L~~~i~~~~LP~~~-GG~~~~ 219 (235)
...|.+| +.+||||.-.....+-... .|+.... -.+|-|+++.. ...+..+..+.-.+...| ||++..
T Consensus 29 ~fIf~~R-ngihIIDL~kT~~~l~~A~-~~v~~~~~~~g~ILfVgTK~~a~~~V~~~A~r~g~~yV~~RwLgG~LTN 103 (252)
T COG0052 29 PFIFGER-NGIHIIDLQKTLERLREAY-KFLRRIAANGGKILFVGTKKQAQEPVKEFAERTGAYYVNGRWLGGMLTN 103 (252)
T ss_pred ccceeec-CCcEEEEHHHHHHHHHHHH-HHHHHHHcCCCEEEEEechHHHHHHHHHHHHHhCCceecCcccCccccC
Confidence 3568999 9999999876554433332 2444444 47899998743 234566677777888777 999874
No 16
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=61.13 E-value=18 Score=19.29 Aligned_cols=24 Identities=21% Similarity=0.306 Sum_probs=19.7
Q ss_pred CChHHHHHHHHhcCCCHHHHHHHH
Q 026657 15 YGDPTLMRFLIARSMDSEKAARMF 38 (235)
Q Consensus 15 ~~d~~llRfL~~~~~~~~~a~~~l 38 (235)
.++....+-|+.+++|+++|..-+
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 566688999999999999997643
No 17
>PF10905 DUF2695: Protein of unknown function (DUF2695); InterPro: IPR024248 This bacterial family of proteins has no known function.
Probab=60.88 E-value=34 Score=20.47 Aligned_cols=37 Identities=19% Similarity=0.125 Sum_probs=27.2
Q ss_pred hhhhhhhCCCCC-CCChHHHHHHHHhcCCCHHHHHHHH
Q 026657 2 RNSVQKLGSSTG-KYGDPTLMRFLIARSMDSEKAARMF 38 (235)
Q Consensus 2 r~~l~~~~~~~~-~~~d~~llRfL~~~~~~~~~a~~~l 38 (235)
-++|.+.++..+ +.|-....+||+.++.+.+.-...+
T Consensus 2 f~yl~~~l~~~~CdHtlr~t~~fl~~~~~~~~~vl~~l 39 (53)
T PF10905_consen 2 FDYLDEKLSAFGCDHTLRLTRQFLRQRQLDWEDVLEWL 39 (53)
T ss_pred hhHHHhHcCcCCCCCcHHHHHHHHHHcCCCHHHHHHHH
Confidence 356677766656 8899999999999998885444443
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=60.53 E-value=19 Score=19.37 Aligned_cols=24 Identities=17% Similarity=0.138 Sum_probs=17.7
Q ss_pred CChHHHHHHHHhcCCCHHHHHHHH
Q 026657 15 YGDPTLMRFLIARSMDSEKAARMF 38 (235)
Q Consensus 15 ~~d~~llRfL~~~~~~~~~a~~~l 38 (235)
.+.....+-|+.+++|+++|..-|
T Consensus 14 f~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 14 FSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp S-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCHHHHHHhC
Confidence 455577888888888999887643
No 19
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=54.14 E-value=16 Score=21.93 Aligned_cols=27 Identities=22% Similarity=0.319 Sum_probs=21.9
Q ss_pred chHHHHHHHHHHHhccccccceeEEEe
Q 026657 138 DVRGMITGFQFLQAYYPERLAKLYILH 164 (235)
Q Consensus 138 ~~~~~k~~~~~l~~~yP~~l~~i~ivn 164 (235)
+.+++-+++-.+-.++|+.++++|++-
T Consensus 28 ~~df~iNiLLtlLg~~PGiiHA~yvi~ 54 (56)
T COG0401 28 GKDFLINILLTLLGYIPGIIHALYVIL 54 (56)
T ss_pred cHHHHHHHHHHHHHhhhhhHhheEEEE
Confidence 366777777777779999999999973
No 20
>PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A.
Probab=52.71 E-value=69 Score=21.55 Aligned_cols=71 Identities=13% Similarity=0.230 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCC-CCCcCCcchHHHHHHHHHHHhccccccceeEEEeCChhHHHHHHH
Q 026657 97 FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLR-QISYKNVDVRGMITGFQFLQAYYPERLAKLYILHMPGFFVSVWRM 175 (235)
Q Consensus 97 ~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~-~~~~~~~~~~~~k~~~~~l~~~yP~~l~~i~ivn~p~~~~~~~~~ 175 (235)
+.. +.-.++..+.. ...+.+++|++ ++ ..++++......+.... ....++++=+|-.+.+.+.+.++
T Consensus 16 ~~~-~~~~~~~~~~~--------~~~~~ll~d~~~~~--~~~~~~a~~~~~~~~~~-~~~~~~r~AvV~~~~~~~~~~~~ 83 (109)
T PF11964_consen 16 YKE-LLPALEELIAD--------HGKIRLLVDLRRDF--EGWSPEARWEDAKFGLK-HLKHFRRIAVVGDSEWIRMIANF 83 (109)
T ss_dssp HHH-HHHHHHHHHTT--------SSSEEEEEEEC-CE--EEEHHHHHHHHHHHHCC-CCGGEEEEEEE-SSCCCHHHHHH
T ss_pred HHH-HHHHHHHHHhc--------CCceEEEEEecCcc--CCCCHHHHHHHHHhchh-hhcccCEEEEEECcHHHHHHHHH
Confidence 555 55555544432 24688999988 64 34455666666655444 88888999999999999999999
Q ss_pred hhhc
Q 026657 176 VSRC 179 (235)
Q Consensus 176 vk~~ 179 (235)
+.++
T Consensus 84 ~~~~ 87 (109)
T PF11964_consen 84 FAAF 87 (109)
T ss_dssp HHHH
T ss_pred HHhc
Confidence 8886
No 21
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=51.43 E-value=61 Score=20.54 Aligned_cols=49 Identities=12% Similarity=0.108 Sum_probs=30.8
Q ss_pred EEEEEeCCCCCcCCcchHHHHHHHHHHHhccc--cccceeEEEeCChhHHHHH
Q 026657 123 LTAILDLRQISYKNVDVRGMITGFQFLQAYYP--ERLAKLYILHMPGFFVSVW 173 (235)
Q Consensus 123 ~~~i~D~~~~~~~~~~~~~~k~~~~~l~~~yP--~~l~~i~ivn~p~~~~~~~ 173 (235)
-.+++|+.|+. .++.+++-..+.-+...|+ +.-.++.++|++-....+.
T Consensus 18 ~~V~lDF~gv~--~~~ssFl~eafg~l~~~~~~~~~~~~l~~~~~~~~~~~~I 68 (74)
T PF14213_consen 18 EKVVLDFEGVE--SITSSFLNEAFGQLVREFGEEEIKKRLKFKNANESIKEMI 68 (74)
T ss_pred CeEEEECCCcc--cccHHHHHHHHHHHHHHcCHHHHhheeEEecCCHHHHHHH
Confidence 34889999983 3445566666655555555 3455677888776555443
No 22
>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=49.44 E-value=88 Score=22.31 Aligned_cols=53 Identities=15% Similarity=0.137 Sum_probs=35.5
Q ss_pred CceEEEEEeCCCCCcCCcchHHHHHHHHHHHhccccccceeEEEeCChhHHHHHHHhhhccC
Q 026657 120 NEKLTAILDLRQISYKNVDVRGMITGFQFLQAYYPERLAKLYILHMPGFFVSVWRMVSRCLE 181 (235)
Q Consensus 120 ~~~~~~i~D~~~~~~~~~~~~~~k~~~~~l~~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~ 181 (235)
..+++++.|+ |-+..+. + ..+..+. ++..+.+..+|.|.+..++...+..-..
T Consensus 59 ~dgVlvl~DL-Ggs~~n~--e---~a~~~l~---~~~~~~v~g~nlPlvega~~aa~~~~~g 111 (125)
T TIGR02364 59 ADGVLIFYDL-GSAVMNA--E---MAVELLE---DEDRDKVHLVDAPLVEGAFAAAVEAQVG 111 (125)
T ss_pred CCCEEEEEcC-CCcHhHH--H---HHHHHhc---cccccEEEEechhHHHHHHHHHHHHcCC
Confidence 4789999999 6333221 1 1122222 4556889999999999999888876433
No 23
>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=46.87 E-value=48 Score=20.55 Aligned_cols=29 Identities=17% Similarity=0.143 Sum_probs=25.0
Q ss_pred CCChHHHHHHHHhcCCCHHHHHHHHHHHH
Q 026657 14 KYGDPTLMRFLIARSMDSEKAARMFVQWQ 42 (235)
Q Consensus 14 ~~~d~~llRfL~~~~~~~~~a~~~l~~~~ 42 (235)
.++..+=.++|..++||.++|.+.+.+-.
T Consensus 24 gmn~~~s~~cLe~~~Wd~~~Al~~F~~lk 52 (63)
T smart00804 24 GMNAEYSQMCLEDNNWDYERALKNFTELK 52 (63)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 57778889999999999999999887753
No 24
>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=46.52 E-value=16 Score=26.89 Aligned_cols=48 Identities=17% Similarity=0.315 Sum_probs=40.3
Q ss_pred HHHHHHHHHhccccccc--eeEEEeCChhHHHHHHHhhhccCh--hhhcceEE
Q 026657 142 MITGFQFLQAYYPERLA--KLYILHMPGFFVSVWRMVSRCLER--ATLEKIVI 190 (235)
Q Consensus 142 ~k~~~~~l~~~yP~~l~--~i~ivn~p~~~~~~~~~vk~~l~~--~~~~ki~~ 190 (235)
.+.+++.+...||..++ .+.+.|+.-.|-++|+-+- -++. +-+..|+.
T Consensus 17 y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYvP-~~s~~~kERKQIRL 68 (159)
T PF04838_consen 17 YKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYVP-SVSNVEKERKQIRL 68 (159)
T ss_pred HHHHHHHHHhhcccccccCeeecCCCchhhhhhhhccC-CCchHhHHHHHhhh
Confidence 56789999999999999 8999999999999999994 5555 55666665
No 25
>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=43.37 E-value=16 Score=29.53 Aligned_cols=29 Identities=10% Similarity=0.044 Sum_probs=18.9
Q ss_pred ccceeEEEeCChhHHHHHHHhhhccChhh
Q 026657 156 RLAKLYILHMPGFFVSVWRMVSRCLERAT 184 (235)
Q Consensus 156 ~l~~i~ivn~p~~~~~~~~~vk~~l~~~~ 184 (235)
.-..++|||+||-+....+-+-++|.+..
T Consensus 204 ~GSGm~iiNPPw~l~~~l~~~l~~L~~~L 232 (245)
T PF04378_consen 204 NGSGMLIINPPWTLDEELEEILPWLAETL 232 (245)
T ss_dssp -EEEEEEES--TTHHHHHHHHHHHHHHHS
T ss_pred ecceEEEEcCCccHHHHHHHHHHHHHHHh
Confidence 34469999999999877777666665544
No 26
>KOG1838 consensus Alpha/beta hydrolase [General function prediction only]
Probab=42.46 E-value=2.4e+02 Score=24.78 Aligned_cols=84 Identities=11% Similarity=0.119 Sum_probs=56.2
Q ss_pred CCCeEEEEeccccCCCCChHH-HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCCCCCcCCc---------chHHHHHH
Q 026657 76 DGLPLLVIQVRKHFPSKDPLQ-FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLRQISYKNV---------DVRGMITG 145 (235)
Q Consensus 76 ~g~~v~~~~~~~~~~~~~~~~-~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~~~~~~~---------~~~~~k~~ 145 (235)
+..|++++..|--. .+.+ ++|.++. .+.++ ..-++|++-+|+.-..+ ..+.++.+
T Consensus 123 ~~~P~vvilpGltg---~S~~~YVr~lv~---~a~~~---------G~r~VVfN~RG~~g~~LtTpr~f~ag~t~Dl~~~ 187 (409)
T KOG1838|consen 123 GTDPIVVILPGLTG---GSHESYVRHLVH---EAQRK---------GYRVVVFNHRGLGGSKLTTPRLFTAGWTEDLREV 187 (409)
T ss_pred CCCcEEEEecCCCC---CChhHHHHHHHH---HHHhC---------CcEEEEECCCCCCCCccCCCceeecCCHHHHHHH
Confidence 56688888887533 2333 5665443 34444 25688899999765442 46779999
Q ss_pred HHHHHhccccccceeEEEeCChhHHHHHHHh
Q 026657 146 FQFLQAYYPERLAKLYILHMPGFFVSVWRMV 176 (235)
Q Consensus 146 ~~~l~~~yP~~l~~i~ivn~p~~~~~~~~~v 176 (235)
++.+...||.+ +++.+-.+.-..++++-+
T Consensus 188 v~~i~~~~P~a--~l~avG~S~Gg~iL~nYL 216 (409)
T KOG1838|consen 188 VNHIKKRYPQA--PLFAVGFSMGGNILTNYL 216 (409)
T ss_pred HHHHHHhCCCC--ceEEEEecchHHHHHHHh
Confidence 99999999998 777776665555555443
No 27
>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=41.11 E-value=48 Score=18.37 Aligned_cols=23 Identities=22% Similarity=0.187 Sum_probs=18.9
Q ss_pred ChHHHHHHHHhcCCCHHHHHHHH
Q 026657 16 GDPTLMRFLIARSMDSEKAARMF 38 (235)
Q Consensus 16 ~d~~llRfL~~~~~~~~~a~~~l 38 (235)
...+|..-|..+++|+.+|++.+
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH
Confidence 34678889999999999999987
No 28
>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=38.44 E-value=2.1e+02 Score=26.12 Aligned_cols=58 Identities=14% Similarity=0.112 Sum_probs=36.2
Q ss_pred hHH-HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCCCCCcCCcchHHHHHHHHHHHhccccccceeEEEeCCh
Q 026657 94 PLQ-FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLRQISYKNVDVRGMITGFQFLQAYYPERLAKLYILHMPG 167 (235)
Q Consensus 94 ~~~-~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~k~~~~~l~~~yP~~l~~i~ivn~p~ 167 (235)
+.+ +.++-...++.+..+ -+ ...+.++|=+|.+ =..+.++...+|+..+.+.+--+|.
T Consensus 117 Tl~DV~~ae~~Fv~~V~~~----hp-~~~kp~liGnCQg-----------GWa~~mlAA~~Pd~~gplvlaGaPl 175 (581)
T PF11339_consen 117 TLEDVMRAEAAFVEEVAER----HP-DAPKPNLIGNCQG-----------GWAAMMLAALRPDLVGPLVLAGAPL 175 (581)
T ss_pred cHHHHHHHHHHHHHHHHHh----CC-CCCCceEEeccHH-----------HHHHHHHHhcCcCccCceeecCCCc
Confidence 455 677777777766665 12 2226667766665 2334466777888888877766664
No 29
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=36.88 E-value=1.4e+02 Score=20.43 Aligned_cols=49 Identities=18% Similarity=0.272 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhhccCCCCCCceEEEEEeCCCCCcCCcchHHHHHHHHHHHhccccccceeEEEe
Q 026657 101 VVHLLDKTIASSFRGSEVGNEKLTAILDLRQISYKNVDVRGMITGFQFLQAYYPERLAKLYILH 164 (235)
Q Consensus 101 ~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~~~~~~~~~~~~k~~~~~l~~~yP~~l~~i~ivn 164 (235)
-...++.+++. -+..++++|=|-.. -|++ +...+...||+++.+|||=+
T Consensus 51 K~~~i~~i~~~------fP~~kfiLIGDsgq-----~Dpe----iY~~ia~~~P~~i~ai~IR~ 99 (100)
T PF09949_consen 51 KRDNIERILRD------FPERKFILIGDSGQ-----HDPE----IYAEIARRFPGRILAIYIRD 99 (100)
T ss_pred HHHHHHHHHHH------CCCCcEEEEeeCCC-----cCHH----HHHHHHHHCCCCEEEEEEEe
Confidence 34455666665 34468999999876 3443 33445678999999999854
No 30
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=34.99 E-value=22 Score=30.04 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=21.7
Q ss_pred CCChHHHHHHHHhcCCCHHHHHHHH
Q 026657 14 KYGDPTLMRFLIARSMDSEKAARMF 38 (235)
Q Consensus 14 ~~~d~~llRfL~~~~~~~~~a~~~l 38 (235)
.+-+..|+|-|.+++||+++|.+.+
T Consensus 141 EDVENillkLlqaadydV~rAerGI 165 (408)
T COG1219 141 EDVENILLKLLQAADYDVERAERGI 165 (408)
T ss_pred hhHHHHHHHHHHHcccCHHHHhCCe
Confidence 3556789999999999999999865
No 31
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=34.32 E-value=31 Score=27.92 Aligned_cols=26 Identities=12% Similarity=0.116 Sum_probs=19.7
Q ss_pred ceeEEEeCChhHHHHHHHhhhccChh
Q 026657 158 AKLYILHMPGFFVSVWRMVSRCLERA 183 (235)
Q Consensus 158 ~~i~ivn~p~~~~~~~~~vk~~l~~~ 183 (235)
..++|||+||.+..-...+-|+|...
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~ 262 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTL 262 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHH
Confidence 46999999999887777766665443
No 32
>KOG1534 consensus Putative transcription factor FET5 [Transcription]
Probab=34.21 E-value=1.3e+02 Score=23.99 Aligned_cols=105 Identities=12% Similarity=0.100 Sum_probs=56.0
Q ss_pred HHHHHHHHHHhhc--cCCCCCCceEEEEEeCCCCCcCCcchHHHHHHHHHHHhccccccceeEEEeCCh------hHHHH
Q 026657 101 VVHLLDKTIASSF--RGSEVGNEKLTAILDLRQISYKNVDVRGMITGFQFLQAYYPERLAKLYILHMPG------FFVSV 172 (235)
Q Consensus 101 ~~~~~E~~~~~~~--~~~~~~~~~~~~i~D~~~~~~~~~~~~~~k~~~~~l~~~yP~~l~~i~ivn~p~------~~~~~ 172 (235)
++++||+...... .+..+..+.=.+|+|+-|.=---.-+..++++++-++. .--++-.+|++..++ ++...
T Consensus 75 Lv~cmEyl~~NldwL~~~~Gd~eddylifDcPGQIELytH~pVm~~iv~hl~~-~~F~~c~Vylldsqf~vD~~KfiSG~ 153 (273)
T KOG1534|consen 75 LVYCMEYLLENLDWLEEEIGDVEDDYLIFDCPGQIELYTHLPVMPQIVEHLKQ-WNFNVCVVYLLDSQFLVDSTKFISGC 153 (273)
T ss_pred chhHHHHHHHHHHHHHhhccCccCCEEEEeCCCeeEEeecChhHHHHHHHHhc-ccCceeEEEEeccchhhhHHHHHHHH
Confidence 4566666655543 12234567778999998832111124557888887776 334555777776665 44444
Q ss_pred HHHhhhccChh-----hhcceEEecCchhHHHHHhhCCCC
Q 026657 173 WRMVSRCLERA-----TLEKIVIVTNEEEMKNFVKDIGEE 207 (235)
Q Consensus 173 ~~~vk~~l~~~-----~~~ki~~~~~~~~~~~L~~~i~~~ 207 (235)
+..+.+.+.-. +.+|.-.+++. -++.|.++.+++
T Consensus 154 lsAlsAMi~lE~P~INvlsKMDLlk~~-~k~~l~~Fl~~d 192 (273)
T KOG1534|consen 154 LSALSAMISLEVPHINVLSKMDLLKDK-NKKELERFLNPD 192 (273)
T ss_pred HHHHHHHHHhcCcchhhhhHHHHhhhh-hHHHHHHhcCCc
Confidence 44444433222 22344344331 134566666544
No 33
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=32.56 E-value=26 Score=22.69 Aligned_cols=26 Identities=19% Similarity=0.144 Sum_probs=21.5
Q ss_pred ChHHHHHHHHhcCCCHHHHHHHHHHH
Q 026657 16 GDPTLMRFLIARSMDSEKAARMFVQW 41 (235)
Q Consensus 16 ~d~~llRfL~~~~~~~~~a~~~l~~~ 41 (235)
++..|..-|..+.||+++|...|.+.
T Consensus 45 ~e~~i~eal~~~~fDvekAl~~Ll~~ 70 (79)
T PF08938_consen 45 PEEQIKEALWHYYFDVEKALDYLLSK 70 (79)
T ss_dssp -CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred CHHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 88889999999999999999988764
No 34
>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=32.47 E-value=70 Score=25.20 Aligned_cols=39 Identities=18% Similarity=0.208 Sum_probs=23.5
Q ss_pred ceEEEEEeCCCCCcCCcchHHHHHHHHHHHhccccccceeEE
Q 026657 121 EKLTAILDLRQISYKNVDVRGMITGFQFLQAYYPERLAKLYI 162 (235)
Q Consensus 121 ~~~~~i~D~~~~~~~~~~~~~~k~~~~~l~~~yP~~l~~i~i 162 (235)
..+++++|.+| ||... ..++..++..+...++ .++-+.+
T Consensus 58 ~~lvvl~DvSG-SM~~~-s~~~l~~~~~l~~~~~-~~~~f~F 96 (222)
T PF05762_consen 58 RRLVVLCDVSG-SMAGY-SEFMLAFLYALQRQFR-RVRVFVF 96 (222)
T ss_pred ccEEEEEeCCC-ChHHH-HHHHHHHHHHHHHhCC-CEEEEEE
Confidence 47999999999 55443 2334455556666666 3333333
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=29.42 E-value=2.1e+02 Score=20.38 Aligned_cols=42 Identities=12% Similarity=0.324 Sum_probs=32.0
Q ss_pred eeEEEeCChhHHHHHHHh-----hhccChhhhcceEEecCchhHHHHHhh
Q 026657 159 KLYILHMPGFFVSVWRMV-----SRCLERATLEKIVIVTNEEEMKNFVKD 203 (235)
Q Consensus 159 ~i~ivn~p~~~~~~~~~v-----k~~l~~~~~~ki~~~~~~~~~~~L~~~ 203 (235)
.+.++|..-+.+.++..+ .-|+++...+.+.++.+ .+++.++
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~---~~e~~~~ 132 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDD---PEEALEY 132 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESS---HHHHHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCC---HHHHHhh
Confidence 699999886667777766 35888889999999987 4666554
No 36
>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=27.62 E-value=47 Score=19.54 Aligned_cols=28 Identities=18% Similarity=0.087 Sum_probs=21.0
Q ss_pred CCChHHHHHHHHhcCCCHHHHHHHHHHH
Q 026657 14 KYGDPTLMRFLIARSMDSEKAARMFVQW 41 (235)
Q Consensus 14 ~~~d~~llRfL~~~~~~~~~a~~~l~~~ 41 (235)
.++..+-.++|..++||.++|.....+.
T Consensus 12 gmn~~~s~~CL~~n~Wd~~~A~~~F~~l 39 (51)
T PF03943_consen 12 GMNLEWSQKCLEENNWDYERALQNFEEL 39 (51)
T ss_dssp SS-CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4556677899999999999999887643
No 37
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=27.25 E-value=1.4e+02 Score=17.82 Aligned_cols=27 Identities=19% Similarity=0.279 Sum_probs=18.9
Q ss_pred HHHHHhcCCCHHHHHHHH---HHHHHHHHH
Q 026657 21 MRFLIARSMDSEKAARMF---VQWQKWRAT 47 (235)
Q Consensus 21 lRfL~~~~~~~~~a~~~l---~~~~~wR~~ 47 (235)
++.+-.+++|+.+|++.+ ++++..|-+
T Consensus 5 L~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ 34 (59)
T PF13556_consen 5 LRAYLENNGNISKTARALHIHRNTLRYRLK 34 (59)
T ss_dssp HHHHHHTTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344456788999999998 667776655
No 38
>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=26.59 E-value=1.2e+02 Score=20.71 Aligned_cols=51 Identities=16% Similarity=0.255 Sum_probs=31.6
Q ss_pred eEEEEEeCCCCCcCCcchHHHHHHHHHHHhccccccceeEEEeCChhHHHHHHH
Q 026657 122 KLTAILDLRQISYKNVDVRGMITGFQFLQAYYPERLAKLYILHMPGFFVSVWRM 175 (235)
Q Consensus 122 ~~~~i~D~~~~~~~~~~~~~~k~~~~~l~~~yP~~l~~i~ivn~p~~~~~~~~~ 175 (235)
--.+|+|+++++. +|...+..+.++.+..- .+=..++++|++......+..
T Consensus 48 ~~~vIlD~s~v~~--iDssgi~~L~~~~~~~~-~~g~~~~l~~~~~~v~~~l~~ 98 (117)
T PF01740_consen 48 IKNVILDMSGVSF--IDSSGIQALVDIIKELR-RRGVQLVLVGLNPDVRRILER 98 (117)
T ss_dssp SSEEEEEETTESE--ESHHHHHHHHHHHHHHH-HTTCEEEEESHHHHHHHHHHH
T ss_pred ceEEEEEEEeCCc--CCHHHHHHHHHHHHHHH-HCCCEEEEEECCHHHHHHHHH
Confidence 3689999999754 44444444443333332 466789999988766655443
No 39
>TIGR02934 nifT_nitrog probable nitrogen fixation protein FixT. This largely uncharacterized protein family is assigned a role in nitrogen fixation by two criteria. First, its gene occurs, generally, among genes essential for expression of active nitrogenase. Second, its phylogenetic profile closely matches that of nitrogen-fixing bacteria. However, mutational studies in Klebsiella pneumoniae failed to demonstrate any phenotype for deletion or overexpression of the protein.
Probab=25.37 E-value=24 Score=22.17 Aligned_cols=36 Identities=25% Similarity=0.318 Sum_probs=21.2
Q ss_pred HHHHhhCCCCCCCcccCCCcCceecccccccccccc
Q 026657 198 KNFVKDIGEEVLPEEYGGRAKLVAVQDVTLPQLEDA 233 (235)
Q Consensus 198 ~~L~~~i~~~~LP~~~GG~~~~~~~~~~~~~~~~~~ 233 (235)
++|.+-|=.-.-|..|||....-.=-.-++||++..
T Consensus 20 KDLEE~Vv~~e~~~~WGG~v~L~NGw~l~lp~l~~~ 55 (67)
T TIGR02934 20 KDLEEVIVSVEKEELWGGWVTLANGWRLELPEIPDD 55 (67)
T ss_pred CcchhheeeeecCccccCEEEECCccEEEeCCCCCC
Confidence 566665544447888899874332222566666543
No 40
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=24.91 E-value=2.4e+02 Score=20.80 Aligned_cols=54 Identities=9% Similarity=0.153 Sum_probs=35.3
Q ss_pred ccCCcceecCCCCCCCeEEEEeccccCCCCChHH-HHHHHHHHHHHHHHhhccCCCCCCceEEEEEeCCC
Q 026657 63 LEPRKIFLQGLTKDGLPLLVIQVRKHFPSKDPLQ-FKKFVVHLLDKTIASSFRGSEVGNEKLTAILDLRQ 131 (235)
Q Consensus 63 ~~~~~~~~~g~d~~g~~v~~~~~~~~~~~~~~~~-~~~~~~~~~E~~~~~~~~~~~~~~~~~~~i~D~~~ 131 (235)
...|.++..|.|+.|+.|+.+-.+.. .+ +.+++-.+++..-.+ ..=++++|.+.
T Consensus 47 ~d~G~l~y~G~De~gn~VY~lG~~~~------~~~~~~al~~l~~i~~~~---------~~~i~~vdt~~ 101 (148)
T PF11385_consen 47 EDIGRLIYMGTDEYGNEVYILGRKNN------GKIVERALKSLLEILGIE---------NEEIILVDTSP 101 (148)
T ss_pred CcCceEEEEEEcCCCCEEEEEecCCh------HHHHHHHHHHHHHHhCCC---------CCcEEEEeccc
Confidence 34578899999999999999876532 23 556555555422111 34577788765
No 41
>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=23.05 E-value=2.4e+02 Score=23.80 Aligned_cols=85 Identities=20% Similarity=0.340 Sum_probs=53.4
Q ss_pred eEEEEE-eCCCCCcCCcchHHHHHHHHHHHhccccccceeEEEeCChhHHHHHHHhhhccChhhhcce-----EEecCch
Q 026657 122 KLTAIL-DLRQISYKNVDVRGMITGFQFLQAYYPERLAKLYILHMPGFFVSVWRMVSRCLERATLEKI-----VIVTNEE 195 (235)
Q Consensus 122 ~~~~i~-D~~~~~~~~~~~~~~k~~~~~l~~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~~~~~~ki-----~~~~~~~ 195 (235)
.+++|+ |+.. ++...+..++.++.. |-.++.-++|+...+...+ +...||..+..++ ...++.+
T Consensus 200 ~lVIi~eD~Es-----F~~~VL~dlI~ils~-~~~~lP~vli~GiaTs~~~----~~~~Lp~~~~~~L~~~~F~~~~~~~ 269 (330)
T PF07034_consen 200 PLVIIFEDFES-----FDSQVLQDLILILSS-YLDRLPFVLIFGIATSVEA----FHSRLPRSTLSLLRIKKFQLQSSSE 269 (330)
T ss_pred CEEEEEccccc-----CCHHHHHHHHHHHHh-ccCCcCEEEEEecCCChHH----HHhhCCHHHHhhcCceEEEeCChHH
Confidence 444444 5555 667788888888865 4468888999987655543 5556666665544 4445555
Q ss_pred hHHHHHhhC--CCCCCCcccCCCc
Q 026657 196 EMKNFVKDI--GEEVLPEEYGGRA 217 (235)
Q Consensus 196 ~~~~L~~~i--~~~~LP~~~GG~~ 217 (235)
..+.+.+-+ +++ .|-.+||+.
T Consensus 270 ~l~~v~~~~l~~~~-~~~~l~~~~ 292 (330)
T PF07034_consen 270 ILERVLEKVLLSPD-FPFKLGPRV 292 (330)
T ss_pred HHHHHHHHHhcCCC-CCceECHHH
Confidence 556665433 444 566777754
No 42
>PF07872 DUF1659: Protein of unknown function (DUF1659); InterPro: IPR012454 This family consists of hypothetical bacterial proteins of unknown function
Probab=22.72 E-value=72 Score=18.37 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=19.0
Q ss_pred cceecCCCCCCCeEEEEe-ccccCCCCCh
Q 026657 67 KIFLQGLTKDGLPLLVIQ-VRKHFPSKDP 94 (235)
Q Consensus 67 ~~~~~g~d~~g~~v~~~~-~~~~~~~~~~ 94 (235)
..|..|.|.+|.|++--+ .+...++..+
T Consensus 10 l~~~~G~d~~Gkpi~k~ks~~nvk~~Atd 38 (47)
T PF07872_consen 10 LKYQTGVDENGKPIFKTKSFSNVKPDATD 38 (47)
T ss_pred EEEEcccCCCCCEEEEeeehhhcCCCCCH
Confidence 346779999999998775 3444444433
No 43
>TIGR01012 Sa_S2_E_A ribosomal protein Sa(cytosolic)/S2(archaeal). TIGR01011 describes the related protein of organelles and bacteria.
Probab=21.23 E-value=1.8e+02 Score=22.61 Aligned_cols=70 Identities=20% Similarity=0.172 Sum_probs=36.2
Q ss_pred hccccccceeEEEeCChhHHHHHHHhhhccChhhhcceEEecCchh----HHHHHhhCCCCCCCc-ccCCCcCcee
Q 026657 151 AYYPERLAKLYILHMPGFFVSVWRMVSRCLERATLEKIVIVTNEEE----MKNFVKDIGEEVLPE-EYGGRAKLVA 221 (235)
Q Consensus 151 ~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~~~~~~ki~~~~~~~~----~~~L~~~i~~~~LP~-~~GG~~~~~~ 221 (235)
..|..|-+.+||+|.-.....+-...+ |+......+|-|+++... ..+..+..+...+-. ..||++....
T Consensus 28 yI~~~r~~gi~IIdL~kT~~~L~~A~~-~i~~i~~~~ILfVgtk~~~~~~V~~~A~~~g~~~v~~RWlgGtLTN~~ 102 (196)
T TIGR01012 28 FIYKVRSDGLYVLDLRKTDERLRVAAK-FLVRIEPEDILVVSARIYGQKPVLKFAKVTGARAIAGRFTPGTFTNPM 102 (196)
T ss_pred ceeeecCCCCEEEcHHHHHHHHHHHHH-HHHHhhCCeEEEEecCHHHHHHHHHHHHHhCCceECCeeCCCCCCCcc
Confidence 345666667888886554433332222 222222667888876322 123334444444444 4488887543
No 44
>PRK04020 rps2P 30S ribosomal protein S2; Provisional
Probab=20.93 E-value=1.7e+02 Score=22.93 Aligned_cols=71 Identities=20% Similarity=0.310 Sum_probs=38.1
Q ss_pred hccccccceeEEEeCChhHHHHHHHhhhccChhhhcceEEecCchh----HHHHHhhCCCCCCCccc-CCCcCceec
Q 026657 151 AYYPERLAKLYILHMPGFFVSVWRMVSRCLERATLEKIVIVTNEEE----MKNFVKDIGEEVLPEEY-GGRAKLVAV 222 (235)
Q Consensus 151 ~~yP~~l~~i~ivn~p~~~~~~~~~vk~~l~~~~~~ki~~~~~~~~----~~~L~~~i~~~~LP~~~-GG~~~~~~~ 222 (235)
..|..|-+.++|+|.-.....+-...+ ++......+|-|+++... .....+.++...+-..| ||++....+
T Consensus 34 yIyg~r~~gi~IIdL~kT~~~L~~A~~-~i~~~~~~~ILfVgTk~~~~~~v~k~A~~~g~~~v~~RWlgG~LTN~~~ 109 (204)
T PRK04020 34 FIYRVRPDGLYVLDVRKTDERIRIAAK-FLSRYEPEKILVVSSRQYGQKPVQKFAEVVGAKAITGRFIPGTLTNPSL 109 (204)
T ss_pred cEeeecCCCCEEEcHHHHHHHHHHHHH-HHHHhcCCeEEEEeCCHHHHHHHHHHHHHhCCeeecCccCCCcCcCcch
Confidence 446666677888887554433332222 222234567888876322 22333445555555544 888875544
No 45
>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=20.52 E-value=2.7e+02 Score=18.47 Aligned_cols=51 Identities=6% Similarity=0.255 Sum_probs=33.9
Q ss_pred EEEEEeCCCCCcCCc-chHHHHHHHHHHHhccccccceeEEEeCChhHHHHHHHhh
Q 026657 123 LTAILDLRQISYKNV-DVRGMITGFQFLQAYYPERLAKLYILHMPGFFVSVWRMVS 177 (235)
Q Consensus 123 ~~~i~D~~~~~~~~~-~~~~~k~~~~~l~~~yP~~l~~i~ivn~p~~~~~~~~~vk 177 (235)
-.+++|++++++-.. -+..+..+.+.++ ..=.+++++|++.-+..++....
T Consensus 40 ~~vilDls~v~~iDssgi~~L~~~~~~~~----~~g~~l~l~~~~~~v~~~l~~~g 91 (106)
T TIGR02886 40 KHLILNLKNVTFMDSSGLGVILGRYKKIK----NEGGEVIVCNVSPAVKRLFELSG 91 (106)
T ss_pred CEEEEECCCCcEecchHHHHHHHHHHHHH----HcCCEEEEEeCCHHHHHHHHHhC
Confidence 479999999877433 3444555444443 24578999999877776665543
No 46
>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=20.17 E-value=4.2e+02 Score=20.48 Aligned_cols=70 Identities=13% Similarity=0.138 Sum_probs=44.9
Q ss_pred eEEEEEeCCCCCcCCc-chHHHHHHHHHHHhccccccceeEEEeCChh---HHHHHHHhhhccChhhhcceEEe
Q 026657 122 KLTAILDLRQISYKNV-DVRGMITGFQFLQAYYPERLAKLYILHMPGF---FVSVWRMVSRCLERATLEKIVIV 191 (235)
Q Consensus 122 ~~~~i~D~~~~~~~~~-~~~~~k~~~~~l~~~yP~~l~~i~ivn~p~~---~~~~~~~vk~~l~~~~~~ki~~~ 191 (235)
.-+.|+|.-|+.=... +-+..+.+.+.+..+.|+.=.-+++++...+ -..++..++..+++...+.+.++
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 4577999999754443 3455667777777777765445566666543 35677778888888877777666
Done!