Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate BPHYT_RS07235 BPHYT_RS07235 2-hydroxymuconic semialdehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__BFirm:BPHYT_RS07235 Length = 496 Score = 708 bits (1828), Expect = 0.0 Identities = 340/481 (70%), Positives = 402/481 (83%) Query: 20 LLNYIDGNFVTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQD 79 L +Y+DG F+ +A++F N++PV+G +++ V EADA+ V+ AV AA A + W + Sbjct: 15 LRHYVDGEFIATATTFPNLSPVDGSVLAQVCEADAETVDAAVRAAAAAQRAGWRNTTPAQ 74 Query: 80 RAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDL 139 RA +HKIADGIQARF+EFVAAEVADTGRP+ QAR LDI R IANFRTF DL +T++++ Sbjct: 75 RADWLHKIADGIQARFDEFVAAEVADTGRPLEQARKLDIARGIANFRTFGDLIRTANSEF 134 Query: 140 FEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPS 199 FE +DGS +NY RKPLGVIG+ISPWNLPLLLFTWKVAPALA GN VVAKPSEE+P Sbjct: 135 FETHAADGSELINYVTRKPLGVIGIISPWNLPLLLFTWKVAPALAMGNCVVAKPSEETPG 194 Query: 200 SATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVA 259 SATLLAEVMHD G+PPGVFNL+HG G ++AGEFLT+HP ISA+TFTGES+TGSTIMK VA Sbjct: 195 SATLLAEVMHDIGLPPGVFNLVHGHGPNAAGEFLTRHPDISAITFTGESRTGSTIMKTVA 254 Query: 260 DGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFV 319 DGVKE+SFELGGKNAAVVFADAD DAA+ GVL+SSFTN+GQVCLCSERVYV RSIF+ FV Sbjct: 255 DGVKEISFELGGKNAAVVFADADFDAAVAGVLKSSFTNAGQVCLCSERVYVERSIFERFV 314 Query: 320 SGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDE 379 + LK + E L VG P MGPLIS GHR+KVLSY+RLAV+EGATVVTGG VP+F DE Sbjct: 315 AALKEKTEALRVGAPHDPETTMGPLISRGHREKVLSYFRLAVEEGATVVTGGHVPQFGDE 374 Query: 380 RDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTT 439 RDQGA+V PTIWTGL+D ARCV EEIFGPVCHI+PFD EDEVI RVNDS YGLA +IWTT Sbjct: 375 RDQGAFVMPTIWTGLADDARCVKEEIFGPVCHIAPFDTEDEVIGRVNDSAYGLAASIWTT 434 Query: 440 NLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIK 499 L+R HRV+R+I G+VWVN W++RDLRTPFGG KLSG+GREGGR S+DFYS++ NIC++ Sbjct: 435 QLARGHRVARRIETGIVWVNAWFVRDLRTPFGGAKLSGIGREGGRHSLDFYSELTNICVR 494 Query: 500 I 500 I Sbjct: 495 I 495 Lambda K H 0.318 0.135 0.405 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: 717 Number of extensions: 13 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 500 Length of database: 496 Length adjustment: 34 Effective length of query: 466 Effective length of database: 462 Effective search space: 215292 Effective search space used: 215292 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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