Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate BPHYT_RS07235 BPHYT_RS07235 2-hydroxymuconic semialdehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__BFirm:BPHYT_RS07235 Length = 496 Score = 328 bits (842), Expect = 2e-94 Identities = 191/482 (39%), Positives = 262/482 (54%), Gaps = 21/482 (4%) Query: 7 INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAF-AEWGQTTPKVRAE 65 ++GE ++ P +P G VL ++ EA AE VDAAVRAA AA A W TTP RA+ Sbjct: 19 VDGEFIA-TATTFPNLSPVDGSVLAQVCEADAETVDAAVRAAAAAQRAGWRNTTPAQRAD 77 Query: 66 CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGE 125 L K+AD I+ F E + G+PL A +I + FR F R N E Sbjct: 78 WLHKIADGIQARFDEFVAAEVADTGRPLEQARKLDIARGIANFRTFGDLIRTANS----E 133 Query: 126 YLEGHTS-------MIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITP 178 + E H + + R PLGV+ I+PWN PL++ WK+APALA GNCVV KPSE TP Sbjct: 134 FFETHAADGSELINYVTRKPLGVIGIISPWNLPLLLFTWKVAPALAMGNCVVAKPSEETP 193 Query: 179 LTALKLAELAKDI-FPAGVINILFGRG-KTVGDPLTGHPKVRMVSLTGSIATGEHIISHT 236 +A LAE+ DI P GV N++ G G G+ LT HP + ++ TG TG I+ Sbjct: 194 GSATLLAEVMHDIGLPPGVFNLVHGHGPNAAGEFLTRHPDISAITFTGESRTGSTIMKTV 253 Query: 237 ASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTL 296 A +K ELGGK +VF DAD +A V GV + NAGQ C + R+Y ++ I++ Sbjct: 254 ADGVKEISFELGGKNAAVVFADADFDAAVAGVLKSSFTNAGQVCLCSERVYVERSIFERF 313 Query: 297 VEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGE----- 351 V L L+ GAP D T +GPL S H E+V A G V+TGG Sbjct: 314 VAALKEKTEALRVGAPHDPETTMGPLISRGHREKVLSYFRLAVEEG-ATVVTGGHVPQFG 372 Query: 352 KRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVW 411 + G + PT+ G D V++E+FGPV + PFD E++V+ NDS YGLA+S+W Sbjct: 373 DERDQGAFVMPTIWTGLADDARCVKEEIFGPVCHIAPFDTEDEVIGRVNDSAYGLAASIW 432 Query: 412 TKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVM 471 T + R HRV+ R++ G WVN F+ P GG KLSG G++ + L+ Y+ + ++ Sbjct: 433 TTQLARGHRVARRIETGIVWVNAWFVRDLRTPFGGAKLSGIGREGGRHSLDFYSELTNIC 492 Query: 472 VK 473 V+ Sbjct: 493 VR 494 Lambda K H 0.317 0.134 0.397 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: 536 Number of extensions: 27 Number of successful extensions: 4 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: 474 Length of database: 496 Length adjustment: 34 Effective length of query: 440 Effective length of database: 462 Effective search space: 203280 Effective search space used: 203280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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