Query 022593
Match_columns 294
No_of_seqs 169 out of 1524
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 04:44:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022593.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022593hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0819 Annexin [Intracellular 100.0 1.2E-86 2.6E-91 580.7 25.8 293 1-293 28-321 (321)
2 KOG0819 Annexin [Intracellular 100.0 1E-54 2.2E-59 380.0 21.0 221 61-292 16-245 (321)
3 PF00191 Annexin: Annexin; In 99.7 1.4E-17 3E-22 116.5 8.3 66 223-288 1-66 (66)
4 PF00191 Annexin: Annexin; In 99.7 2.3E-17 4.9E-22 115.5 7.5 66 148-213 1-66 (66)
5 smart00335 ANX Annexin repeats 99.5 2.7E-14 5.8E-19 95.3 6.1 53 6-58 1-53 (53)
6 smart00335 ANX Annexin repeats 99.4 2.7E-13 5.9E-18 90.4 6.0 53 236-288 1-53 (53)
7 PF14003 YlbE: YlbE-like prote 56.9 15 0.00034 25.1 3.1 37 241-278 13-49 (65)
8 KOG2875 8-oxoguanine DNA glyco 47.6 28 0.00061 31.1 4.0 109 175-290 172-286 (323)
9 PF14003 YlbE: YlbE-like prote 44.7 51 0.0011 22.6 4.1 44 171-214 17-61 (65)
10 PHA01794 hypothetical protein 34.9 1.9E+02 0.0041 22.6 6.3 52 8-59 34-98 (134)
11 PF13720 Acetyltransf_11: Udp 34.0 71 0.0015 22.9 3.8 21 18-38 27-47 (83)
12 PHA02613 48 baseplate subunit; 31.4 41 0.00089 30.4 2.5 101 5-105 114-225 (361)
13 KOG0859 Synaptobrevin/VAMP-lik 30.6 1.3E+02 0.0027 25.6 5.1 48 174-221 75-123 (217)
14 COG5173 SEC6 Exocyst complex s 30.0 1E+02 0.0022 30.5 5.0 170 14-203 298-477 (742)
15 KOG1086 Cytosolic sorting prot 29.8 3.2E+02 0.0068 26.3 8.0 108 141-266 24-140 (594)
16 PF08587 UBA_2: Ubiquitin asso 29.4 16 0.00034 23.2 -0.3 30 3-32 11-41 (46)
17 PF01992 vATP-synt_AC39: ATP s 29.0 3.5E+02 0.0076 24.3 8.5 47 223-271 173-220 (337)
18 PF11791 Aconitase_B_N: Aconit 27.6 2.2E+02 0.0049 23.0 5.9 65 163-248 38-105 (154)
19 PF13766 ECH_C: 2-enoyl-CoA Hy 25.5 2.3E+02 0.005 21.6 5.6 50 11-60 35-92 (118)
20 TIGR03031 cas_csx12 CRISPR-ass 25.1 1E+02 0.0022 30.7 4.2 50 9-58 239-288 (802)
21 PF08748 DUF1789: Domain of un 24.6 1.4E+02 0.0031 23.4 4.3 45 146-190 74-121 (128)
22 PF13062 DUF3924: Protein of u 24.6 76 0.0016 20.6 2.2 21 252-272 14-34 (62)
23 PF10788 DUF2603: Protein of u 22.6 1.1E+02 0.0023 24.4 3.2 36 179-214 65-100 (137)
24 KOG0859 Synaptobrevin/VAMP-lik 22.5 2.1E+02 0.0045 24.3 5.0 66 91-157 75-141 (217)
25 COG4800 Predicted transcriptio 22.1 2.9E+02 0.0063 22.1 5.5 44 205-248 16-66 (170)
26 PF13766 ECH_C: 2-enoyl-CoA Hy 22.1 1.2E+02 0.0027 23.2 3.5 49 166-214 35-91 (118)
27 PF15173 FAM180: FAM180 family 21.8 3.3E+02 0.0072 21.6 5.7 69 161-247 59-127 (137)
28 PF13043 DUF3903: Domain of un 21.7 85 0.0019 18.8 1.9 17 253-269 9-25 (40)
29 COG5118 BDP1 Transcription ini 21.7 1.3E+02 0.0027 28.2 3.9 54 148-201 371-424 (507)
30 TIGR03164 UHCUDC OHCU decarbox 20.1 1.5E+02 0.0033 24.0 3.8 25 177-201 94-118 (157)
No 1
>KOG0819 consensus Annexin [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.2e-86 Score=580.66 Aligned_cols=293 Identities=46% Similarity=0.700 Sum_probs=290.5
Q ss_pred CCCcccCChHHHHHHhcCCCHHHHHHHHHHHHHhhcccHHHHHhhhcchhHHHHHHHHcCCChHHHHHHHHHHHhcCCCC
Q 022593 1 MFAGWGTNEALIISVLAHRNAAQRKLIREIYNETYGEDLLKALDKELSSDFERSVLLWTLTPAERDAYLANEATKRFTLS 80 (294)
Q Consensus 1 a~kg~gtde~~li~il~~rs~~q~~~i~~~Y~~~~g~~L~~~l~~e~~g~~~~~l~~~~~~~~~~da~~l~~A~~g~gtd 80 (294)
|||||||||+.||+||++||++||+.|+.+|+..||++|.++|++|+||+|++++++|+.+|+++||..|++||+|.|||
T Consensus 28 A~kG~Gtde~aII~iL~~Rsn~QRq~I~~ayk~~ygkDLi~~Lk~ELsG~Fe~~i~al~~~p~~~DA~~l~~amkg~gtd 107 (321)
T KOG0819|consen 28 AMKGFGTDEQAIIDILTHRSNAQRQLIRAAYKTMYGKDLIKDLKSELSGDFERAIVALMKPPAEYDAKELKKAMKGLGTD 107 (321)
T ss_pred HHhcCCCCHHHHHHHHHccCHHHHHHHHHHHHHHHhHHHHHHHHHHhCccHHHHHHHHcCCHHHhHHHHHHHHHhccCcc
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhhccCCHHHHHHHHHHHHhccCCCHHHHHHhccccchHhhHHhhhccccccccccchhhHHHHHHHHHHcccC-
Q 022593 81 NWVLMEIACTRSSRDLFAAKQAYHARYKKSLEEDVAYHTSGDFRKLLVPLVSTFRYDGGDVNMMLARTEAKILRDKISD- 159 (294)
Q Consensus 81 e~~li~il~~rs~~~~~~I~~~Y~~~y~~~L~~~i~~~~sg~~~~ll~~ll~~~r~e~~~vd~~~~~~da~~L~~A~~~- 159 (294)
+.+||||+|+|||.|+++|+++|+..|+++|++||.+++||+|+++|+.|+.+.|+|+..||..+++.||+.|++|+++
T Consensus 108 e~vlIEIlcTRT~~el~~i~~aY~~~y~~sLEeDI~s~TSG~frklLv~L~~~~R~e~~~vd~~la~~dA~~L~~Age~k 187 (321)
T KOG0819|consen 108 EKVLIEILCTRTNEELRAIRQAYQELYKKSLEEDIASDTSGDFRKLLVSLVQGNRDEGDRVDDALAKQDAQDLYEAGEKK 187 (321)
T ss_pred hhhheeeeccCCHHHHHHHHHHHHHHHcccHHHHhhhccCchHHHHHHHHHhcCCccCCCcCHHHHHHHHHHHHHHhhhh
Confidence 9999999999999999999999999999999999999999999999999999999998999999999999999999998
Q ss_pred CCCChhHHHHHHhcCCHHHHHHHHHHHHHHhCCCHHHhhhhCCCchHHHHHHHHHHhcCCChHHHHHHHHHHhccCCCCc
Q 022593 160 KDYAHEELIRILTTRSKAQINATLNHYNDTFGNAINKDLKADPNDEYLKLLRAAIKCLTYPEKHFAKVLRLAINGLGTDE 239 (294)
Q Consensus 160 ~gtde~~li~Il~~rs~~~l~~i~~~Y~~~~g~~L~~~I~~~~sg~~~~~ll~~l~~~~~~~~~~A~~L~~A~~g~gtd~ 239 (294)
+|||+..++.||++||..||+++++.|++.+|+++++.|+++++|+|+++|++++.|.+|||.|||+.||.||+|.|||+
T Consensus 188 ~gtde~~~~~Il~tRs~~qL~~vf~~y~~~~g~diek~I~~e~~gd~~~~llaiv~c~~n~~~yFA~~L~~amkg~GTdd 267 (321)
T KOG0819|consen 188 WGTDEDKFIRILTTRSKAQLRLVFEEYQRISGKDIEKSIKEEFSGDFEKLLLAIVKCIRNPPAYFAERLRKAMKGLGTDD 267 (321)
T ss_pred ccCcHHHHHHHHHhCCHHHHHHHHHHHHHhcchhHHHHHhhccCchHHHHHHHHHHHHcCHHHHHHHHHHHHHhccCCCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHhcCHHHHHHHHHHHHHhcCccHHHHHhhcCcHHHHHHHHHhhcCCC
Q 022593 240 WGLTRVVTTRAEVDMQRIKEEYHRRNTVTLEKAIAGDTSGDYERMLLALIGHGD 293 (294)
Q Consensus 240 ~~liril~~rs~~~l~~I~~~Y~~~yg~~L~~~I~~~~~G~~~~~Ll~l~~~~~ 293 (294)
++||||+++||+.||..|+.+|+++||+||.++|++++||||+++|++||+.+|
T Consensus 268 ~~LiRI~VsRsEiDl~~Ik~ef~~~Y~ksL~~~I~~dtsGdY~~~LlaL~g~~~ 321 (321)
T KOG0819|consen 268 KTLIRIVVSRSEIDLLDIKEEFQRKYGKSLYSAIKGDTSGDYKKALLALLGGDD 321 (321)
T ss_pred cceeeeeeeHHHhhHHHHHHHHHHHhCccHHHHHhhhccchHHHHHHHHhCCCC
Confidence 999999999999999999999999999999999999999999999999999875
No 2
>KOG0819 consensus Annexin [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1e-54 Score=380.03 Aligned_cols=221 Identities=29% Similarity=0.403 Sum_probs=213.7
Q ss_pred CChHHHHHHHHHHHhcCCCChHHHHHhhccCCHHHHHHHHHHHHhccCCCHHHHHHhccccchHhhHHhhhccccccccc
Q 022593 61 TPAERDAYLANEATKRFTLSNWVLMEIACTRSSRDLFAAKQAYHARYKKSLEEDVAYHTSGDFRKLLVPLVSTFRYDGGD 140 (294)
Q Consensus 61 ~~~~~da~~l~~A~~g~gtde~~li~il~~rs~~~~~~I~~~Y~~~y~~~L~~~i~~~~sg~~~~ll~~ll~~~r~e~~~ 140 (294)
+.|..||+.|++||+|+|||+.++|+||++|||.|++.|+++|+.+||++|.+++++++||+|++++++|+.+|
T Consensus 16 f~p~~DAe~L~kA~kG~Gtde~aII~iL~~Rsn~QRq~I~~ayk~~ygkDLi~~Lk~ELsG~Fe~~i~al~~~p------ 89 (321)
T KOG0819|consen 16 FDPVQDAEQLRKAMKGFGTDEQAIIDILTHRSNAQRQLIRAAYKTMYGKDLIKDLKSELSGDFERAIVALMKPP------ 89 (321)
T ss_pred CChHHHHHHHHHHHhcCCCCHHHHHHHHHccCHHHHHHHHHHHHHHHhHHHHHHHHHHhCccHHHHHHHHcCCH------
Confidence 44789999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cchhhHHHHHHHHHHcccCCCCChhHHHHHHhcCCHHHHHHHHHHHHHHhCCCHHHhhhhCCCchHHHHHHHHHHhcCCC
Q 022593 141 VNMMLARTEAKILRDKISDKDYAHEELIRILTTRSKAQINATLNHYNDTFGNAINKDLKADPNDEYLKLLRAAIKCLTYP 220 (294)
Q Consensus 141 vd~~~~~~da~~L~~A~~~~gtde~~li~Il~~rs~~~l~~i~~~Y~~~~g~~L~~~I~~~~sg~~~~~ll~~l~~~~~~ 220 (294)
+++||++|++||+|.|||+.++|+|+|+|||.|+++|+++|+..|++||+++|.+++||+|+++|+.++++.|++
T Consensus 90 -----~~~DA~~l~~amkg~gtde~vlIEIlcTRT~~el~~i~~aY~~~y~~sLEeDI~s~TSG~frklLv~L~~~~R~e 164 (321)
T KOG0819|consen 90 -----AEYDAKELKKAMKGLGTDEKVLIEILCTRTNEELRAIRQAYQELYKKSLEEDIASDTSGDFRKLLVSLVQGNRDE 164 (321)
T ss_pred -----HHhHHHHHHHHHhccCcchhhheeeeccCCHHHHHHHHHHHHHHHcccHHHHhhhccCchHHHHHHHHHhcCCcc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999974
Q ss_pred --------hHHHHHHHHHHh-ccCCCCchhHHHHHHhcCHHHHHHHHHHHHHhcCccHHHHHhhcCcHHHHHHHHHhhcC
Q 022593 221 --------EKHFAKVLRLAI-NGLGTDEWGLTRVVTTRAEVDMQRIKEEYHRRNTVTLEKAIAGDTSGDYERMLLALIGH 291 (294)
Q Consensus 221 --------~~~~A~~L~~A~-~g~gtd~~~liril~~rs~~~l~~I~~~Y~~~yg~~L~~~I~~~~~G~~~~~Ll~l~~~ 291 (294)
+..||+.|++|. +.+|||+..|++||++||..||+.++++|++.+|++++++|+++++||++.+|+++++|
T Consensus 165 ~~~vd~~la~~dA~~L~~Age~k~gtde~~~~~Il~tRs~~qL~~vf~~y~~~~g~diek~I~~e~~gd~~~~llaiv~c 244 (321)
T KOG0819|consen 165 GDRVDDALAKQDAQDLYEAGEKKWGTDEDKFIRILTTRSKAQLRLVFEEYQRISGKDIEKSIKEEFSGDFEKLLLAIVKC 244 (321)
T ss_pred CCCcCHHHHHHHHHHHHHHhhhhccCcHHHHHHHHHhCCHHHHHHHHHHHHHhcchhHHHHHhhccCchHHHHHHHHHHH
Confidence 367999999998 55689999999999999999999999999999999999999999999999999999987
Q ss_pred C
Q 022593 292 G 292 (294)
Q Consensus 292 ~ 292 (294)
-
T Consensus 245 ~ 245 (321)
T KOG0819|consen 245 I 245 (321)
T ss_pred H
Confidence 4
No 3
>PF00191 Annexin: Annexin; InterPro: IPR018502 The annexins (or lipocortins) are a family of proteins that bind to phospholipids in a calcium-dependent manner []. They are distributed ubiquitously in different tissues and cell types of higher and lower eukaryotes, including mammals, fish, birds, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Caenorhabditis elegans , Dictyostelium discoideum (Slime mold) and Neurospora crassa [, ]. Annexins are absent from yeasts and prokaryotes []. The plant annexins are somewhat distinct from those found in other taxa []. Most eukaryotic species have 1-20 annexin (ANX) genes. All annexins share a core domain made up of four similar repeats, each approximately 70 amino acids long []. Each individual annexin repeat (sometimes referred to as endonexin folds) is folded into five alpha-helices, and in turn are wound into a right-handed super-helix; they usually contain a characteristic 'type 2' motif for binding calcium ions with the sequence 'GxGT-[38 residues]-D/E'. Animal and fungal annexins also have variable amino-terminal domains. The core domains of most vertebrate annexins have been analysed by X-ray crystallography, revealing conservation of their secondary and tertiary structures despite only 45-55% amino-acid identity among individual members. The four repeats pack into a structure that resembles a flattened disc, with a slightly convex surface on which the Ca 2+ -binding loops are located and a concave surface at which the amino and carboxyl termini come into close apposition. Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. The famiy has been linked with inhibition of phospholipase activity, exocytosis and endoctyosis, signal transduction, organisation of the extracellular matrix, resistance to reactive oxygen species and DNA replication [].; GO: 0005509 calcium ion binding, 0005544 calcium-dependent phospholipid binding; PDB: 1N44_A 1BC1_A 2IE6_A 2H0M_A 1A8B_A 2H0K_A 1BCW_A 1BCZ_A 1N42_A 1BC0_A ....
Probab=99.73 E-value=1.4e-17 Score=116.53 Aligned_cols=66 Identities=39% Similarity=0.609 Sum_probs=63.6
Q ss_pred HHHHHHHHHhccCCCCchhHHHHHHhcCHHHHHHHHHHHHHhcCccHHHHHhhcCcHHHHHHHHHh
Q 022593 223 HFAKVLRLAINGLGTDEWGLTRVVTTRAEVDMQRIKEEYHRRNTVTLEKAIAGDTSGDYERMLLAL 288 (294)
Q Consensus 223 ~~A~~L~~A~~g~gtd~~~liril~~rs~~~l~~I~~~Y~~~yg~~L~~~I~~~~~G~~~~~Ll~l 288 (294)
+||+.|++|++|+|+|+..+++|+++||+.|+..|+++|++.||++|+++|+++++|+|+++|++|
T Consensus 1 ~DA~~l~~a~~~~g~de~~li~Il~~rs~~ql~~i~~~Y~~~~g~~L~~~i~~e~sGd~~~~Ll~l 66 (66)
T PF00191_consen 1 YDAELLHAALKGWGTDEDVLIEILCTRSPAQLRAIKQAYKKKYGKDLEEDIKKETSGDFEKLLLAL 66 (66)
T ss_dssp HHHHHHHHHHSSSSSTHHHHHHHHHHSTHHHHHHHHHHHHHHHSS-HHHHHHHHSTHHHHHHHHHH
T ss_pred CHHHHHHHHccCCCCChhHhhhHHhhhcccccceeehhhhhhhHHHHHHHHHHhCCHHHHHHHHhC
Confidence 589999999999999999999999999999999999999999999999999999999999999986
No 4
>PF00191 Annexin: Annexin; InterPro: IPR018502 The annexins (or lipocortins) are a family of proteins that bind to phospholipids in a calcium-dependent manner []. They are distributed ubiquitously in different tissues and cell types of higher and lower eukaryotes, including mammals, fish, birds, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Caenorhabditis elegans , Dictyostelium discoideum (Slime mold) and Neurospora crassa [, ]. Annexins are absent from yeasts and prokaryotes []. The plant annexins are somewhat distinct from those found in other taxa []. Most eukaryotic species have 1-20 annexin (ANX) genes. All annexins share a core domain made up of four similar repeats, each approximately 70 amino acids long []. Each individual annexin repeat (sometimes referred to as endonexin folds) is folded into five alpha-helices, and in turn are wound into a right-handed super-helix; they usually contain a characteristic 'type 2' motif for binding calcium ions with the sequence 'GxGT-[38 residues]-D/E'. Animal and fungal annexins also have variable amino-terminal domains. The core domains of most vertebrate annexins have been analysed by X-ray crystallography, revealing conservation of their secondary and tertiary structures despite only 45-55% amino-acid identity among individual members. The four repeats pack into a structure that resembles a flattened disc, with a slightly convex surface on which the Ca 2+ -binding loops are located and a concave surface at which the amino and carboxyl termini come into close apposition. Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. The famiy has been linked with inhibition of phospholipase activity, exocytosis and endoctyosis, signal transduction, organisation of the extracellular matrix, resistance to reactive oxygen species and DNA replication [].; GO: 0005509 calcium ion binding, 0005544 calcium-dependent phospholipid binding; PDB: 1N44_A 1BC1_A 2IE6_A 2H0M_A 1A8B_A 2H0K_A 1BCW_A 1BCZ_A 1N42_A 1BC0_A ....
Probab=99.71 E-value=2.3e-17 Score=115.48 Aligned_cols=66 Identities=30% Similarity=0.495 Sum_probs=63.1
Q ss_pred HHHHHHHHcccCCCCChhHHHHHHhcCCHHHHHHHHHHHHHHhCCCHHHhhhhCCCchHHHHHHHH
Q 022593 148 TEAKILRDKISDKDYAHEELIRILTTRSKAQINATLNHYNDTFGNAINKDLKADPNDEYLKLLRAA 213 (294)
Q Consensus 148 ~da~~L~~A~~~~gtde~~li~Il~~rs~~~l~~i~~~Y~~~~g~~L~~~I~~~~sg~~~~~ll~~ 213 (294)
+||+.|++|++|+|+|+..+++||++||+.|+++|+++|++.||++|+++|++++||+|+++|+++
T Consensus 1 ~DA~~l~~a~~~~g~de~~li~Il~~rs~~ql~~i~~~Y~~~~g~~L~~~i~~e~sGd~~~~Ll~l 66 (66)
T PF00191_consen 1 YDAELLHAALKGWGTDEDVLIEILCTRSPAQLRAIKQAYKKKYGKDLEEDIKKETSGDFEKLLLAL 66 (66)
T ss_dssp HHHHHHHHHHSSSSSTHHHHHHHHHHSTHHHHHHHHHHHHHHHSS-HHHHHHHHSTHHHHHHHHHH
T ss_pred CHHHHHHHHccCCCCChhHhhhHHhhhcccccceeehhhhhhhHHHHHHHHHHhCCHHHHHHHHhC
Confidence 589999999999999999999999999999999999999999999999999999999999999875
No 5
>smart00335 ANX Annexin repeats.
Probab=99.52 E-value=2.7e-14 Score=95.34 Aligned_cols=53 Identities=40% Similarity=0.661 Sum_probs=51.2
Q ss_pred cCChHHHHHHhcCCCHHHHHHHHHHHHHhhcccHHHHHhhhcchhHHHHHHHH
Q 022593 6 GTNEALIISVLAHRNAAQRKLIREIYNETYGEDLLKALDKELSSDFERSVLLW 58 (294)
Q Consensus 6 gtde~~li~il~~rs~~q~~~i~~~Y~~~~g~~L~~~l~~e~~g~~~~~l~~~ 58 (294)
||||..|++|+++||+.||++|+..|+..||++|.++|+++++|+|+++++++
T Consensus 1 gtde~~l~~il~~rs~~~~~~i~~~Y~~~~~~~L~~~i~~e~sG~~~~~l~~l 53 (53)
T smart00335 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53 (53)
T ss_pred CCCHHHHHHHHHcCCHHHHHHHHHHHHHHhCccHHHHHHHhcChHHHHHHHhC
Confidence 79999999999999999999999999999999999999999999999998764
No 6
>smart00335 ANX Annexin repeats.
Probab=99.43 E-value=2.7e-13 Score=90.44 Aligned_cols=53 Identities=43% Similarity=0.728 Sum_probs=51.5
Q ss_pred CCCchhHHHHHHhcCHHHHHHHHHHHHHhcCccHHHHHhhcCcHHHHHHHHHh
Q 022593 236 GTDEWGLTRVVTTRAEVDMQRIKEEYHRRNTVTLEKAIAGDTSGDYERMLLAL 288 (294)
Q Consensus 236 gtd~~~liril~~rs~~~l~~I~~~Y~~~yg~~L~~~I~~~~~G~~~~~Ll~l 288 (294)
|||+..|++|+++|++.|+..|+++|++.||++|.++|+++++|+|+++|++|
T Consensus 1 gtde~~l~~il~~rs~~~~~~i~~~Y~~~~~~~L~~~i~~e~sG~~~~~l~~l 53 (53)
T smart00335 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53 (53)
T ss_pred CCCHHHHHHHHHcCCHHHHHHHHHHHHHHhCccHHHHHHHhcChHHHHHHHhC
Confidence 69999999999999999999999999999999999999999999999999875
No 7
>PF14003 YlbE: YlbE-like protein
Probab=56.87 E-value=15 Score=25.08 Aligned_cols=37 Identities=11% Similarity=0.156 Sum_probs=31.8
Q ss_pred hHHHHHHhcCHHHHHHHHHHHHHhcCccHHHHHhhcCc
Q 022593 241 GLTRVVTTRAEVDMQRIKEEYHRRNTVTLEKAIAGDTS 278 (294)
Q Consensus 241 ~liril~~rs~~~l~~I~~~Y~~~yg~~L~~~I~~~~~ 278 (294)
.|-|+|+ |.+.++...-.++...||+++-+.|.+-..
T Consensus 13 ~WYR~Ls-R~P~~l~~fe~~a~~~y~kT~p~rVek~~n 49 (65)
T PF14003_consen 13 IWYRILS-RNPEELEAFEKEAKHFYKKTIPHRVEKFSN 49 (65)
T ss_pred HHHHHHc-cCHHHHHHHHHHHHHHHhccccHHHHHHHh
Confidence 4667777 899999999999999999999999987543
No 8
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=47.60 E-value=28 Score=31.09 Aligned_cols=109 Identities=16% Similarity=0.213 Sum_probs=72.3
Q ss_pred CHHHHHHHHHHHHHHhCCCHHHhhhhCCCchHHHHHHHHHHhcCCChHHHHHHHHHHhccCCCCchhHHHHHHh------
Q 022593 175 SKAQINATLNHYNDTFGNAINKDLKADPNDEYLKLLRAAIKCLTYPEKHFAKVLRLAINGLGTDEWGLTRVVTT------ 248 (294)
Q Consensus 175 s~~~l~~i~~~Y~~~~g~~L~~~I~~~~sg~~~~~ll~~l~~~~~~~~~~A~~L~~A~~g~gtd~~~liril~~------ 248 (294)
.++|+++..=-|+.+|=..-...|-++-.| ++++..++..+-.+|+.--..+.|.|+.....|=++..
T Consensus 172 ~Ea~LR~~gfGYRAkYI~~ta~~l~~~~g~------~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~V 245 (323)
T KOG2875|consen 172 VEAELRKLGFGYRAKYISATARALQEKQGG------LAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAV 245 (323)
T ss_pred hHHHHHHcCcchhHHHHHHHHHHHHHhccc------chHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcc
Confidence 577888888888888854444555555444 56777777766677776666678888887776656553
Q ss_pred cCHHHHHHHHHHHHHhcCccHHHHHhhcCcHHHHHHHHHhhc
Q 022593 249 RAEVDMQRIKEEYHRRNTVTLEKAIAGDTSGDYERMLLALIG 290 (294)
Q Consensus 249 rs~~~l~~I~~~Y~~~yg~~L~~~I~~~~~G~~~~~Ll~l~~ 290 (294)
..+.|+.+|.+-| ...|.+=.+.+.....|....++..+++
T Consensus 246 PVDvHi~ria~~y-~l~~~~g~k~l~~ki~~ev~~~f~~~~G 286 (323)
T KOG2875|consen 246 PVDVHIWRIAQDY-ILPGLSGAKELTPKINGEVSNFFRSLWG 286 (323)
T ss_pred cchhhHHHHhhcc-cCCCccccccCCcchhHHHHHHHHHHhc
Confidence 3457888898888 3444443333455566666666666655
No 9
>PF14003 YlbE: YlbE-like protein
Probab=44.74 E-value=51 Score=22.59 Aligned_cols=44 Identities=9% Similarity=0.194 Sum_probs=32.5
Q ss_pred HhcCCHHHHHHHHHHHHHHhCCCHHHhhhhCCCc-hHHHHHHHHH
Q 022593 171 LTTRSKAQINATLNHYNDTFGNAINKDLKADPND-EYLKLLRAAI 214 (294)
Q Consensus 171 l~~rs~~~l~~i~~~Y~~~~g~~L~~~I~~~~sg-~~~~~ll~~l 214 (294)
..+|.|.++.+.-.++...|++.+-+.|.+-.++ .+-..++.+.
T Consensus 17 ~LsR~P~~l~~fe~~a~~~y~kT~p~rVek~~n~lqMa~MM~~M~ 61 (65)
T PF14003_consen 17 ILSRNPEELEAFEKEAKHFYKKTIPHRVEKFSNQLQMASMMMEMF 61 (65)
T ss_pred HHccCHHHHHHHHHHHHHHHhccccHHHHHHHhHHHHHHHHHHHH
Confidence 3469999999999999999999999999874333 1333444443
No 10
>PHA01794 hypothetical protein
Probab=34.93 E-value=1.9e+02 Score=22.65 Aligned_cols=52 Identities=19% Similarity=0.220 Sum_probs=30.4
Q ss_pred ChHHHHHHhcC-----CCHHHHHHHHHHHHH------hhcccHHHHHhhhc--chhHHHHHHHHc
Q 022593 8 NEALIISVLAH-----RNAAQRKLIREIYNE------TYGEDLLKALDKEL--SSDFERSVLLWT 59 (294)
Q Consensus 8 de~~li~il~~-----rs~~q~~~i~~~Y~~------~~g~~L~~~l~~e~--~g~~~~~l~~~~ 59 (294)
|+.+|+.++-- .++.....=...|-+ -.-..|.+.|+.|+ ||-|+..+.-|.
T Consensus 34 dd~Alvdllrl~~~~~lted~~~~aI~d~v~~~~~Ee~~~e~lF~eleqEm~~SGFF~~ki~kyi 98 (134)
T PHA01794 34 DESAIVDLVRLSAKKALTEDEILDAIADFVETFEDEEGTTEGLFAELEKEMVDSGFFRAKIKKYI 98 (134)
T ss_pred chHHHHHHHHHHhccccChhhHHHHHHHHHHHhhhhcchHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 56667766654 344443322222221 12357888898888 888888776554
No 11
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=33.95 E-value=71 Score=22.87 Aligned_cols=21 Identities=10% Similarity=0.156 Sum_probs=16.8
Q ss_pred CCCHHHHHHHHHHHHHhhccc
Q 022593 18 HRNAAQRKLIREIYNETYGED 38 (294)
Q Consensus 18 ~rs~~q~~~i~~~Y~~~~g~~ 38 (294)
+.|++++..|+++|+..|...
T Consensus 27 Gfs~~~i~~l~~ayr~l~~~~ 47 (83)
T PF13720_consen 27 GFSKEEISALRRAYRILFRSG 47 (83)
T ss_dssp TS-HHHHHHHHHHHHHHHTSS
T ss_pred CCCHHHHHHHHHHHHHHHhCC
Confidence 358999999999999999543
No 12
>PHA02613 48 baseplate subunit; Provisional
Probab=31.41 E-value=41 Score=30.42 Aligned_cols=101 Identities=14% Similarity=0.015 Sum_probs=60.5
Q ss_pred ccCChHHHHHHhcCCCHHHHHHHHHHHHHhhcccHHH-----------HHhhhcchhHHHHHHHHcCCChHHHHHHHHHH
Q 022593 5 WGTNEALIISVLAHRNAAQRKLIREIYNETYGEDLLK-----------ALDKELSSDFERSVLLWTLTPAERDAYLANEA 73 (294)
Q Consensus 5 ~gtde~~li~il~~rs~~q~~~i~~~Y~~~~g~~L~~-----------~l~~e~~g~~~~~l~~~~~~~~~~da~~l~~A 73 (294)
.+.+-++|.+||..||...-..+.+.|++.-..-+.+ ......-|-++.+....+-+.-|.--..-+.+
T Consensus 114 ~~~~~~pianILlPRs~sDvd~~sHrfnDv~dSlitkGggt~tg~LS~~aS~av~GalESit~GimAD~~Eqiy~~~rsm 193 (361)
T PHA02613 114 TTFDKEPIANILLPRSKSDVDTNSHRFNDVGESLITKGGGTATGALSNMASTAVFGALESITGGIMADRGEQIYTTARSM 193 (361)
T ss_pred cccchhhhhhhhccCccccccccccccccchhhHhhcCCCccchhHHHHHHHHHHHhhhhhcccccccccchhhHhhHHH
Confidence 3457789999999999999999998888754322221 11122223333333333444333322222223
Q ss_pred HhcCCCChHHHHHhhccCCHHHHHHHHHHHHh
Q 022593 74 TKRFTLSNWVLMEIACTRSSRDLFAAKQAYHA 105 (294)
Q Consensus 74 ~~g~gtde~~li~il~~rs~~~~~~I~~~Y~~ 105 (294)
..|.-..-.....-|.-||-.++.+|-+.|+-
T Consensus 194 y~GadnRTK~y~w~ltprs~~DL~eiikIY~~ 225 (361)
T PHA02613 194 YAGADNRTKVYTWTLTPRSREDLMEIIKIYEL 225 (361)
T ss_pred hcCccccceeEEEecccccHHHHHHHHHHHHH
Confidence 34432223456677899999999999999985
No 13
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.61 E-value=1.3e+02 Score=25.58 Aligned_cols=48 Identities=17% Similarity=0.376 Sum_probs=38.1
Q ss_pred CCHHHHHHHHHHHHHHhCCCHHHhhhhCCCchHHHHHHHHHH-hcCCCh
Q 022593 174 RSKAQINATLNHYNDTFGNAINKDLKADPNDEYLKLLRAAIK-CLTYPE 221 (294)
Q Consensus 174 rs~~~l~~i~~~Y~~~~g~~L~~~I~~~~sg~~~~~ll~~l~-~~~~~~ 221 (294)
++-.-|..|++.|.+.||.....++...++.+|...|..=+. +..+|.
T Consensus 75 ipfaFLe~Ik~~F~k~YG~~a~ta~AysmN~EFs~vL~qqm~y~s~~p~ 123 (217)
T KOG0859|consen 75 IPFAFLERIKEDFKKRYGGGAHTAVAYSMNKEFSSVLKQQMQYCSEHPE 123 (217)
T ss_pred ccHHHHHHHHHHHHHHhccchhHHHHhHhHHHHHHHHHHHHHHHHcCcc
Confidence 456678999999999999999999988888888887765554 455554
No 14
>COG5173 SEC6 Exocyst complex subunit SEC6 [Intracellular trafficking and secretion]
Probab=29.98 E-value=1e+02 Score=30.46 Aligned_cols=170 Identities=14% Similarity=0.162 Sum_probs=81.3
Q ss_pred HHhcCCCHHHHHHHHHHHHHhhcccHHHHHhhhcchhHHHHHHHH-------cCCChHHHHHHHHHHHhc-CCCChHHHH
Q 022593 14 SVLAHRNAAQRKLIREIYNETYGEDLLKALDKELSSDFERSVLLW-------TLTPAERDAYLANEATKR-FTLSNWVLM 85 (294)
Q Consensus 14 ~il~~rs~~q~~~i~~~Y~~~~g~~L~~~l~~e~~g~~~~~l~~~-------~~~~~~~da~~l~~A~~g-~gtde~~li 85 (294)
+.++...|.+ -.|...|.+.|.+.|.+.+-.+.+-....+.... ..+..+.++--..++++| .+.++..
T Consensus 298 e~i~~~~pp~-~NI~~~y~~~YqecL~~L~td~v~~~~~a~~iL~ii~f~~~y~~t~e~~f~f~~dev~~~l~d~e~g-- 374 (742)
T COG5173 298 ENISLSFPPF-DNILTLYHNNYQECLLKLFTDEVTERLDAGEILAIIEFVGNYYNTIESKFNFIADEVGGRLLDNETG-- 374 (742)
T ss_pred HHccccCCch-HHHHHHHHHHHHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHHHhCCccHHHhcccccCCcch--
Confidence 3344443333 3577888888888888777666655444333221 122334444444555554 2223321
Q ss_pred HhhccCCHHHHHHHHHHHHhccCCCHHHHHHhccccchHhhHHhhhccccccccc-cchhhHHHHHHHHHHcccC-CCCC
Q 022593 86 EIACTRSSRDLFAAKQAYHARYKKSLEEDVAYHTSGDFRKLLVPLVSTFRYDGGD-VNMMLARTEAKILRDKISD-KDYA 163 (294)
Q Consensus 86 ~il~~rs~~~~~~I~~~Y~~~y~~~L~~~i~~~~sg~~~~ll~~ll~~~r~e~~~-vd~~~~~~da~~L~~A~~~-~gtd 163 (294)
.+-+.|......-+.+.+.+-+.-.+.+++-.=-.+.|++++. +-+. ...--+.+.+-++- .+|+
T Consensus 375 ------------~L~~~Yt~l~~~Kl~EWv~nl~~~evd~F~~R~~ep~~Dsdg~l~l~G-t~~~fQmitqQ~e~ia~tn 441 (742)
T COG5173 375 ------------ELLEKYTKLAQEKLKEWVMNLTRIEVDKFYARNEEPSRDSDGKLVLPG-TVSLFQMITQQLEPIAFTN 441 (742)
T ss_pred ------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcCCCcCccCcc-HHHHHHHHHHHhhhhhcCC
Confidence 1223355554445555555544444555442222223332211 1111 11112222222222 3466
Q ss_pred hhHHHHHHhcCCHHHHHHHHHHHHHHhCCCHHHhhhhCCC
Q 022593 164 HEELIRILTTRSKAQINATLNHYNDTFGNAINKDLKADPN 203 (294)
Q Consensus 164 e~~li~Il~~rs~~~l~~i~~~Y~~~~g~~L~~~I~~~~s 203 (294)
..-++-|+. +|+-.+-..|++.+...+.+.|.+.++
T Consensus 442 ~sdvvgiV~----~~i~~~~tk~q~~wks~l~ee~~kq~~ 477 (742)
T COG5173 442 RSDVVGIVF----AHITRTITKYQEIWKSNLVEEMDKQFK 477 (742)
T ss_pred ccchhhhhH----HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 554444443 366677777787777777777776543
No 15
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.83 E-value=3.2e+02 Score=26.30 Aligned_cols=108 Identities=11% Similarity=0.149 Sum_probs=59.8
Q ss_pred cchhhHHHHHHHHHHcccCCCCChhHHHHHHhc--CCHHHHHHHHHHHH-----HHhCCCHHHhhhhCCCchHHHHHHHH
Q 022593 141 VNMMLARTEAKILRDKISDKDYAHEELIRILTT--RSKAQINATLNHYN-----DTFGNAINKDLKADPNDEYLKLLRAA 213 (294)
Q Consensus 141 vd~~~~~~da~~L~~A~~~~gtde~~li~Il~~--rs~~~l~~i~~~Y~-----~~~g~~L~~~I~~~~sg~~~~~ll~~ 213 (294)
-|....+..+..+++-..| ....+++|++ .||.+|.++..--- +..|.-+.+.+ |-|+ +|..+
T Consensus 24 edw~ai~~fceqinkdp~g----p~lAv~LlaHKiqSPqe~EAl~altvLe~cmkncGekfH~ev-----gkfr-FLNEL 93 (594)
T KOG1086|consen 24 EDWKAIDGFCEQINKDPEG----PLLAVRLLAHKIQSPQEWEALQALTVLEYCMKNCGEKFHEEV-----GKFR-FLNEL 93 (594)
T ss_pred HHHHHHHHHHHHHhcCCCC----chhHHHHHHhhcCChhHHHHHHHHHHHHHHHHhhhHHHHHHH-----HHHH-HHHHH
Confidence 3445566667777776665 2234567765 58999998865321 12233222222 3333 45555
Q ss_pred HHhcCCChHHHHHHHHHHhccCCCCchhHHHHHHhc--CHHHHHHHHHHHHHhcC
Q 022593 214 IKCLTYPEKHFAKVLRLAINGLGTDEWGLTRVVTTR--AEVDMQRIKEEYHRRNT 266 (294)
Q Consensus 214 l~~~~~~~~~~A~~L~~A~~g~gtd~~~liril~~r--s~~~l~~I~~~Y~~~yg 266 (294)
++.. .+.|...+--+++++ .+|.++.+. |-.+-.+|+++|+..-.
T Consensus 94 Ikvv--sPKYlG~~tSekvKt------kiIelLfsWtv~lpe~~KikdaYqmLKk 140 (594)
T KOG1086|consen 94 IKVV--SPKYLGSRTSEKVKT------KIIELLFSWTVSLPEEPKIKDAYQMLKK 140 (594)
T ss_pred HHHh--CchhcchhhhHHHHH------HHHHHHhhheecCcccchHHHHHHHHHh
Confidence 5443 334443333333333 567777753 34777899999997643
No 16
>PF08587 UBA_2: Ubiquitin associated domain (UBA) ; InterPro: IPR013896 This is a UBA (ubiquitin associated) protein []. Ubiquitin is involved in intracellular proteolysis. ; GO: 0004674 protein serine/threonine kinase activity; PDB: 3H4J_B.
Probab=29.42 E-value=16 Score=23.23 Aligned_cols=30 Identities=20% Similarity=0.281 Sum_probs=18.3
Q ss_pred CcccCChHHHHHHhcCCCH-HHHHHHHHHHH
Q 022593 3 AGWGTNEALIISVLAHRNA-AQRKLIREIYN 32 (294)
Q Consensus 3 kg~gtde~~li~il~~rs~-~q~~~i~~~Y~ 32 (294)
+-+|-+.+.|++.|-+-.| .|-.+|+.+|.
T Consensus 11 ~tMGY~kdeI~eaL~~~~~~~~~neIkDAY~ 41 (46)
T PF08587_consen 11 KTMGYDKDEIYEALESSEPSPQSNEIKDAYL 41 (46)
T ss_dssp CTT---HHHHHHHCCSSS------SSCCHHH
T ss_pred HHhCCCHHHHHHHHHcCCCcchHHHHHHHHH
Confidence 3478899999999998766 78888888885
No 17
>PF01992 vATP-synt_AC39: ATP synthase (C/AC39) subunit; InterPro: IPR002843 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit C from the A0 complex of A-ATPases, and subunits C and D from the V0 complex of V-ATPases, all of which are involved in the translocation of protons across a membrane. There is more than one type of D subunit in V-ATPases, where the D1 subunit is ubiquitous, while the D2 subunit has limited tissue expressivity, possibly to account for differential functions, targeting or regulation of V-ATPase activity []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015991 ATP hydrolysis coupled proton transport, 0033177 proton-transporting two-sector ATPase complex, proton-transporting domain; PDB: 1R5Z_A 1V9M_A 3J0J_M.
Probab=29.01 E-value=3.5e+02 Score=24.28 Aligned_cols=47 Identities=19% Similarity=0.276 Sum_probs=27.1
Q ss_pred HHHHHHHHHhccCCCCchhHHHHHHhcCHHHHHHHHHHHHHh-cCccHHH
Q 022593 223 HFAKVLRLAINGLGTDEWGLTRVVTTRAEVDMQRIKEEYHRR-NTVTLEK 271 (294)
Q Consensus 223 ~~A~~L~~A~~g~gtd~~~liril~~rs~~~l~~I~~~Y~~~-yg~~L~~ 271 (294)
++...+..+..-.|.+...+.+++.. ..|+.+|.-.|+-+ ||.+-++
T Consensus 173 yy~~~~~~~~~~~~~~~~~l~~~~~~--~iD~~Ni~~~~R~k~~~~~~~~ 220 (337)
T PF01992_consen 173 YYEDLLKAAKKLSGSEREILRELLGM--EIDLTNIKTILRAKKYGLSPEE 220 (337)
T ss_dssp HHHHHHHHHH---TSS-HHHHHHHHH--HHHHHHHHHHHHTTTS---GGG
T ss_pred HHHHHHHHhhccccchHHHHHHHHHH--HHHHHHHHHHHHHhhcCCCHhh
Confidence 44455555553334566666677774 78999999999965 6655533
No 18
>PF11791 Aconitase_B_N: Aconitate B N-terminal domain; InterPro: IPR015933 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents the N-terminal HEAT-like domain, which is present in bacterial aconitase (AcnB), but not in AcnA or eukaryotic cAcn/IRP2 or mAcn. This domain is multi-helical, forming two curved layers in a right-handed alpha-alpha superhelix. HEAT-like domains are usually implicated in protein-protein interactions. The HEAT-like domain and the 'swivel' domain that follows it were shown to be sufficient for dimerisation and for AcnB binding to mRNA. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0003994 aconitate hydratase activity, 0006099 tricarboxylic acid cycle; PDB: 1L5J_B.
Probab=27.60 E-value=2.2e+02 Score=23.04 Aligned_cols=65 Identities=23% Similarity=0.174 Sum_probs=36.5
Q ss_pred ChhHHHHHHhcCCHHHHHHHHHHHHHHhCCCHHHhhhhCCCchHHHHHHHHHHhcCCC---hHHHHHHHHHHhccCCCCc
Q 022593 163 AHEELIRILTTRSKAQINATLNHYNDTFGNAINKDLKADPNDEYLKLLRAAIKCLTYP---EKHFAKVLRLAINGLGTDE 239 (294)
Q Consensus 163 de~~li~Il~~rs~~~l~~i~~~Y~~~~g~~L~~~I~~~~sg~~~~~ll~~l~~~~~~---~~~~A~~L~~A~~g~gtd~ 239 (294)
++..+.++|..|-|. |.|=..-|+.+ +|-.++.+.... ....|..|-..|.| |.|-
T Consensus 38 ~~~~lldLL~~RV~P-------------GVD~AA~VKA~-------FL~~ia~g~~~~~~Is~~~Av~LLGtM~G-GYNV 96 (154)
T PF11791_consen 38 EEAFLLDLLTNRVPP-------------GVDEAAYVKAE-------FLAAIAKGEISSPLISPAEAVELLGTMLG-GYNV 96 (154)
T ss_dssp -HHHHHHHHHHSS---------------TT-HHHHHHHH-------HHHHHHTTSS-BTTB-HHHHHHHHTTS-S-STTH
T ss_pred cHHHHHHHHHhcCCC-------------CCChHHHHHHH-------HHHHHHcCCccCCCcCHHHHHHHHhhccC-CCcH
Confidence 677889999999876 44433333321 344444443322 24567777777877 7888
Q ss_pred hhHHHHHHh
Q 022593 240 WGLTRVVTT 248 (294)
Q Consensus 240 ~~liril~~ 248 (294)
..||.++.+
T Consensus 97 ~~LI~~L~~ 105 (154)
T PF11791_consen 97 QPLIDLLKS 105 (154)
T ss_dssp HHHHHGG--
T ss_pred HHHHHHHcC
Confidence 888888853
No 19
>PF13766 ECH_C: 2-enoyl-CoA Hydratase C-terminal region; PDB: 3JU1_A 3BPT_A.
Probab=25.53 E-value=2.3e+02 Score=21.62 Aligned_cols=50 Identities=18% Similarity=0.157 Sum_probs=36.1
Q ss_pred HHHHHhcCCCHHHHHHHHHHHHHhhcccHHHHHhhhc--------chhHHHHHHHHcC
Q 022593 11 LIISVLAHRNAAQRKLIREIYNETYGEDLLKALDKEL--------SSDFERSVLLWTL 60 (294)
Q Consensus 11 ~li~il~~rs~~q~~~i~~~Y~~~~g~~L~~~l~~e~--------~g~~~~~l~~~~~ 60 (294)
..++.|.++||--+.-....++.-.+.+|.+.+..|+ .|+|.+.+.+.+.
T Consensus 35 ~~~~~l~~~SP~Sl~vt~~~l~~~~~~sl~e~l~~E~~~a~~~~~~~DF~EGVRA~LI 92 (118)
T PF13766_consen 35 KTLETLRSGSPLSLKVTFEQLRRGRNLSLAECLRMEYRLASRCMRHPDFAEGVRALLI 92 (118)
T ss_dssp HHHHHHCCS-HHHHHHHHHHHHCCTTS-HHHHHHHHHHHHHHHHCCSCHHHHHHHHTT
T ss_pred HHHHHHHHCCHHHHHHHHHHHHHhhhCCHHHHHHHHHHHHHHHhccchHHHHHHHHHh
Confidence 4567788889998888888888887888888888776 3566666665543
No 20
>TIGR03031 cas_csx12 CRISPR-associated protein, Csx12 family. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to PFAM model pfam01844, HNH endonuclease.
Probab=25.06 E-value=1e+02 Score=30.67 Aligned_cols=50 Identities=16% Similarity=0.282 Sum_probs=40.3
Q ss_pred hHHHHHHhcCCCHHHHHHHHHHHHHhhcccHHHHHhhhcchhHHHHHHHH
Q 022593 9 EALIISVLAHRNAAQRKLIREIYNETYGEDLLKALDKELSSDFERSVLLW 58 (294)
Q Consensus 9 e~~li~il~~rs~~q~~~i~~~Y~~~~g~~L~~~l~~e~~g~~~~~l~~~ 58 (294)
-..+..++++.||-|+..+++.|.+.-......+.+..+.-.|...+..|
T Consensus 239 ~~~l~nLvGnlSN~qlk~LrrYfnDk~~~k~d~wdeqkf~~~~~r~v~~w 288 (802)
T TIGR03031 239 SVCLSNLLGNLSNLQLKNLRRYFNDKIHKKPDQWDEQKFGNEFLRMLKNW 288 (802)
T ss_pred hhhHHHHhhhhhhhhHHHHHHHhccccccccccccHhHHHHHHHHHHHhc
Confidence 34688999999999999999999987766666677777776777777765
No 21
>PF08748 DUF1789: Domain of unknown function (DUF1789); InterPro: IPR014859 This entry represents a putative uncharacterised protein found in phage-related conserved hypothetical protein from Bordetella.
Probab=24.61 E-value=1.4e+02 Score=23.38 Aligned_cols=45 Identities=13% Similarity=0.272 Sum_probs=34.9
Q ss_pred HHHHHHHHHHcccCCCCCh---hHHHHHHhcCCHHHHHHHHHHHHHHh
Q 022593 146 ARTEAKILRDKISDKDYAH---EELIRILTTRSKAQINATLNHYNDTF 190 (294)
Q Consensus 146 ~~~da~~L~~A~~~~gtde---~~li~Il~~rs~~~l~~i~~~Y~~~~ 190 (294)
++.+++.+.+.+.||+.|+ ..-+..|+..-|.=..+|.++|.+.+
T Consensus 74 ~~~~ad~i~~iv~gW~ld~~fn~Enl~~L~~~yp~a~~AI~~aY~~~l 121 (128)
T PF08748_consen 74 VDLNADFILEIVAGWDLDEEFNDENLELLVDNYPGAAEAIVDAYYQAL 121 (128)
T ss_pred hhhhHHHHHHHHhccCCCCccCHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence 6778999999999998775 23355677777778889999998754
No 22
>PF13062 DUF3924: Protein of unknown function (DUF3924)
Probab=24.58 E-value=76 Score=20.58 Aligned_cols=21 Identities=14% Similarity=0.469 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHhcCccHHHH
Q 022593 252 VDMQRIKEEYHRRNTVTLEKA 272 (294)
Q Consensus 252 ~~l~~I~~~Y~~~yg~~L~~~ 272 (294)
..|..++++|+++.|.++.+.
T Consensus 14 ekl~llkqayqkktgatises 34 (62)
T PF13062_consen 14 EKLDLLKQAYQKKTGATISES 34 (62)
T ss_pred HHHHHHHHHHHhhcCCccchh
Confidence 467789999999999887654
No 23
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=22.55 E-value=1.1e+02 Score=24.39 Aligned_cols=36 Identities=17% Similarity=0.257 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhCCCHHHhhhhCCCchHHHHHHHHH
Q 022593 179 INATLNHYNDTFGNAINKDLKADPNDEYLKLLRAAI 214 (294)
Q Consensus 179 l~~i~~~Y~~~~g~~L~~~I~~~~sg~~~~~ll~~l 214 (294)
+..++.+++++|-.-|+++|-+.+.=||.++..-++
T Consensus 65 i~~~k~~~~E~f~lkLEk~I~q~~PIDF~Dvw~VAm 100 (137)
T PF10788_consen 65 IESLKNAQKENFELKLEKDILQQMPIDFEDVWAVAM 100 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHH
Confidence 467889999999999999999999999988765444
No 24
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.46 E-value=2.1e+02 Score=24.31 Aligned_cols=66 Identities=14% Similarity=0.177 Sum_probs=41.0
Q ss_pred CCHHHHHHHHHHHHhccCCCHHHHHHhccccchHhhHHhhhccccccccccch-hhHHHHHHHHHHcc
Q 022593 91 RSSRDLFAAKQAYHARYKKSLEEDVAYHTSGDFRKLLVPLVSTFRYDGGDVNM-MLARTEAKILRDKI 157 (294)
Q Consensus 91 rs~~~~~~I~~~Y~~~y~~~L~~~i~~~~sg~~~~ll~~ll~~~r~e~~~vd~-~~~~~da~~L~~A~ 157 (294)
++-.-++.|++.|.+.||.....++.......|.+.|..-+..--+++. +|. ..+...+.+++..|
T Consensus 75 ipfaFLe~Ik~~F~k~YG~~a~ta~AysmN~EFs~vL~qqm~y~s~~p~-id~lskvkaqv~evk~vM 141 (217)
T KOG0859|consen 75 IPFAFLERIKEDFKKRYGGGAHTAVAYSMNKEFSSVLKQQMQYCSEHPE-ISKLAKVKAQVTEVKGVM 141 (217)
T ss_pred ccHHHHHHHHHHHHHHhccchhHHHHhHhHHHHHHHHHHHHHHHHcCcc-hhHHHHHHHHHHHHHHHH
Confidence 3447899999999999999988887777766776665544433212111 332 33444455554443
No 25
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=22.15 E-value=2.9e+02 Score=22.07 Aligned_cols=44 Identities=25% Similarity=0.283 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHhcCCChHHHHH-------HHHHHhccCCCCchhHHHHHHh
Q 022593 205 EYLKLLRAAIKCLTYPEKHFAK-------VLRLAINGLGTDEWGLTRVVTT 248 (294)
Q Consensus 205 ~~~~~ll~~l~~~~~~~~~~A~-------~L~~A~~g~gtd~~~liril~~ 248 (294)
+|...|-.++.-.--.+..||+ -||+-++|...+-++|+||+.+
T Consensus 16 ~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G~dpr~~tl~~I~kt 66 (170)
T COG4800 16 DFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKGSDPRYDTLTRIFKT 66 (170)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHhCCCccHHHHHHHHHH
Confidence 3555555555442223344443 6888888887888999999886
No 26
>PF13766 ECH_C: 2-enoyl-CoA Hydratase C-terminal region; PDB: 3JU1_A 3BPT_A.
Probab=22.09 E-value=1.2e+02 Score=23.17 Aligned_cols=49 Identities=12% Similarity=0.222 Sum_probs=35.4
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHHHhCCCHHHhhhhCC--------CchHHHHHHHHH
Q 022593 166 ELIRILTTRSKAQINATLNHYNDTFGNAINKDLKADP--------NDEYLKLLRAAI 214 (294)
Q Consensus 166 ~li~Il~~rs~~~l~~i~~~Y~~~~g~~L~~~I~~~~--------sg~~~~~ll~~l 214 (294)
...+.|.++||-=+.-....+++-.+.+|.+++..|+ .|+|.+.+.+++
T Consensus 35 ~~~~~l~~~SP~Sl~vt~~~l~~~~~~sl~e~l~~E~~~a~~~~~~~DF~EGVRA~L 91 (118)
T PF13766_consen 35 KTLETLRSGSPLSLKVTFEQLRRGRNLSLAECLRMEYRLASRCMRHPDFAEGVRALL 91 (118)
T ss_dssp HHHHHHCCS-HHHHHHHHHHHHCCTTS-HHHHHHHHHHHHHHHHCCSCHHHHHHHHT
T ss_pred HHHHHHHHCCHHHHHHHHHHHHHhhhCCHHHHHHHHHHHHHHHhccchHHHHHHHHH
Confidence 3456778899999999999999888899999988763 456666655544
No 27
>PF15173 FAM180: FAM180 family
Probab=21.77 E-value=3.3e+02 Score=21.56 Aligned_cols=69 Identities=12% Similarity=0.111 Sum_probs=47.0
Q ss_pred CCChhHHHHHHhcCCHHHHHHHHHHHHHHhCCCHHHhhhhCCCchHHHHHHHHHHhcCCChHHHHHHHHHHhccCCCCch
Q 022593 161 DYAHEELIRILTTRSKAQINATLNHYNDTFGNAINKDLKADPNDEYLKLLRAAIKCLTYPEKHFAKVLRLAINGLGTDEW 240 (294)
Q Consensus 161 gtde~~li~Il~~rs~~~l~~i~~~Y~~~~g~~L~~~I~~~~sg~~~~~ll~~l~~~~~~~~~~A~~L~~A~~g~gtd~~ 240 (294)
+.+-..+++-+.-++..+++.....+...-| .|. .-||+..+++++.| |.+++.+..| ...+
T Consensus 59 ~~~l~~ic~~viPk~l~di~rl~~~ls~~~g-~L~-------~~DFErtlLTlvy~--------ayr~~~s~~~--~qr~ 120 (137)
T PF15173_consen 59 ARRLEVICQDVIPKSLPDIRRLSAQLSQHRG-PLS-------PEDFERTLLTLVYT--------AYRLANSSEG--HQRD 120 (137)
T ss_pred hhHHHHHHHHHCCCcHHHHHHHHHHHHhCCC-CCC-------HHHHHHHHHHHHHH--------HHHHHHhhhH--HHHH
Confidence 4566777777888999999999888876665 221 24799999999855 5666666544 3444
Q ss_pred hHHHHHH
Q 022593 241 GLTRVVT 247 (294)
Q Consensus 241 ~liril~ 247 (294)
.|.+.++
T Consensus 121 ~Wa~~f~ 127 (137)
T PF15173_consen 121 RWAQSFV 127 (137)
T ss_pred HHHHHHH
Confidence 5555444
No 28
>PF13043 DUF3903: Domain of unknown function (DUF3903)
Probab=21.72 E-value=85 Score=18.78 Aligned_cols=17 Identities=35% Similarity=0.532 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHhcCccH
Q 022593 253 DMQRIKEEYHRRNTVTL 269 (294)
Q Consensus 253 ~l~~I~~~Y~~~yg~~L 269 (294)
-++.|+.+-++.||++|
T Consensus 9 ai~kvr~eckrrfgktl 25 (40)
T PF13043_consen 9 AIQKVRAECKRRFGKTL 25 (40)
T ss_pred HHHHHHHHHHHHhchhh
Confidence 35688899999999986
No 29
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=21.67 E-value=1.3e+02 Score=28.18 Aligned_cols=54 Identities=17% Similarity=0.167 Sum_probs=36.9
Q ss_pred HHHHHHHHcccCCCCChhHHHHHHhcCCHHHHHHHHHHHHHHhCCCHHHhhhhC
Q 022593 148 TEAKILRDKISDKDYAHEELIRILTTRSKAQINATLNHYNDTFGNAINKDLKAD 201 (294)
Q Consensus 148 ~da~~L~~A~~~~gtde~~li~Il~~rs~~~l~~i~~~Y~~~~g~~L~~~I~~~ 201 (294)
.+....|+|+.-||||...+-.+|-.|+..|+.+=+..=.+.-.--+.++++..
T Consensus 371 ~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~nP~rIn~aL~~k 424 (507)
T COG5118 371 KEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKVNPERINEALNEK 424 (507)
T ss_pred HHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhhCHHHHHHHHhcc
Confidence 567778999999999999999999999988765433332222233344455543
No 30
>TIGR03164 UHCUDC OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model.
Probab=20.13 E-value=1.5e+02 Score=24.04 Aligned_cols=25 Identities=24% Similarity=0.327 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHhCCCHHHhhhhC
Q 022593 177 AQINATLNHYNDTFGNAINKDLKAD 201 (294)
Q Consensus 177 ~~l~~i~~~Y~~~~g~~L~~~I~~~ 201 (294)
.++..++..|+++||..+.-.++..
T Consensus 94 ~~L~~lN~~Y~~kFGfpFvi~v~g~ 118 (157)
T TIGR03164 94 ARFTRLNNAYRARFGFPFIMAVKGK 118 (157)
T ss_pred HHHHHHHHHHHHHCCCeeEEeeCCC
Confidence 4788999999999999998887754
Done!