Align Bifunctional aspartokinase/homoserine dehydrogenase 1, chloroplastic; AK-HD 1; AK-HSDH 1; Beta-aspartyl phosphate homoserine 1; EC 2.7.2.4; EC 1.1.1.3 (characterized)
to candidate WP_057507033.1 ABB28_RS02115 diaminopimelate decarboxylase
Query= SwissProt::Q9SA18 (911 letters) >NCBI__GCF_001431535.1:WP_057507033.1 Length = 864 Score = 176 bits (446), Expect = 6e-48 Identities = 148/476 (31%), Positives = 231/476 (48%), Gaps = 40/476 (8%) Query: 82 DSWAVHKFGGTCVGNSERIKDVAAVVVKDDSE---RKLVVVSAMSKVTDMMYDLIHRAES 138 D W V KFGGT V R + + K E R LVVVSA+S VT+ +L A+ Sbjct: 8 DRWIVLKFGGTSVSRRHRWDTIGKLAKKRAEETGSRVLVVVSALSGVTN---ELTAIADG 64 Query: 139 RDDSYLSALSGVLEKHRATAVDLLDGDELSSFLARLNDDINNLKAMLRAIYIAGHATESF 198 DS + ++ ++E+H+A DEL A L + + L+A+L A + Sbjct: 65 AADSR-ARVAALVERHQAFL------DELELPRAVLGERLAALQALLDDARAAARTLDWQ 117 Query: 199 SDFVVGHGELWSAQMLAAVVRKSGLDCTWMDARDVLVVIPTSSNQ--------VDPDFVE 250 ++ V+G GEL S+ + AA + ++GLD WMDAR L +P NQ V+ + Sbjct: 118 AE-VLGQGELLSSSIGAAYLHQNGLDMGWMDARQWLDALPPLPNQSPWSQRLSVNCQWKS 176 Query: 251 SEKRLEKWFTQNSAKIIIATGFIASTPQNIPTTLKRDGSDFSAAIMSALFRSHQLTIWTD 310 E ++ F +++I GFIA L R GSD SAA AL + ++ IWTD Sbjct: 177 DEAWAQR-FRAQPTRLLITQGFIARHADGGTAILGRGGSDTSAAYFGALLGASRVEIWTD 235 Query: 311 VDGVYSADPRKVSEAVVLKTLSYQEAWEMSYFGANVLHPRTIIPVMKYDIPIVIRNIFNL 370 V G++SA+P+ V +A +L L Y EA E++ GA VLHPR+I P +P+ I + Sbjct: 236 VPGMFSANPKDVPDARLLTRLDYYEAQEIATTGAKVLHPRSIKPCRDAGVPMAILDTERP 295 Query: 371 SAPGTMICRQIDDEDGFKLDAP-VKGFATIDNLALVNVEGTGMAGVPGTASAIFSAVKEV 429 PGT I DG P VK + + + LV++EG GM G + +F K+ Sbjct: 296 ELPGTSI-------DGSAAPVPGVKAISRRNGIVLVSMEGIGMWQQVGFLADVFGLFKKH 348 Query: 430 GANVIMISQASSEHSVCFAVPEKEVKA-VSEALNSRFRQALAGGRLSQIEIIPNCSILAA 488 G +V +I A + +V E V V AL++ Q + +++II C+ + Sbjct: 349 GLSVDLIGSAETNVTVSLDPSENLVNTDVLAALSADLSQ------ICKVKIIVPCAAITL 402 Query: 489 VGQKMASTPGVSATFFNALAKANINIRAIAQGCSEFNITVVVKREDCIRALRAVHS 544 VG+ M S + + + +++ I+Q ++ N+T V+ D L +H+ Sbjct: 403 VGRGMRSLLHKLSDVWATFGRERVHM--ISQSSNDLNLTFVIDETDADGLLPILHA 456 Lambda K H 0.319 0.134 0.385 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1505 Number of extensions: 77 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 911 Length of database: 864 Length adjustment: 43 Effective length of query: 868 Effective length of database: 821 Effective search space: 712628 Effective search space used: 712628 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (26.2 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory