Align 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized)
to candidate WP_015446956.1 R2APBS1_RS03885 aldehyde dehydrogenase
Query= SwissProt::P23105 (486 letters) >NCBI__GCF_000230695.2:WP_015446956.1 Length = 527 Score = 187 bits (474), Expect = 1e-51 Identities = 144/429 (33%), Positives = 207/429 (48%), Gaps = 27/429 (6%) Query: 32 IGRVHEAGRAEVDAAVRAARAALKGP-WGKMTVAERAEILHRVADGITARFGEFLEARM- 89 +G AG +V AA+ AA+AA GP W M VAER +LHRV + + R + A + Sbjct: 63 LGEFGLAGDNDVQAAMCAAQAA--GPAWRAMPVAERTRLLHRVGELLEERVYDIAAAMVL 120 Query: 90 -PGHRQAEVAGQPHRHSARRANFKVFADLLKNVANEAFEMATPD----GAGALNYGVRRP 144 G + E G+ F +AD ++ A + PD G + N V RP Sbjct: 121 EVGKNRMEALGEAQETVDF---FHHYADDFESHAG--YNHVLPDDPVTGFASHNASVMRP 175 Query: 145 KGVIGVISPWNLPLLLMTWKVGPALACGNCVVVKPSEETPLTATLLGEVMQAAGVPAGVY 204 GV VI+P+N PL L V AL GN VV+K + +TP LL + ++ AG+P GV+ Sbjct: 176 YGVWVVIAPFNFPLALAGGPVAAALVTGNTVVLKGASDTPWAGRLLADCIRDAGLPPGVF 235 Query: 205 NVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGETIMRAAAKGV--RQVSLELGGKNAGI 262 N + G G + G L +HP TFTG G +MR A G R E+GGKN I Sbjct: 236 NYLSGAGRE-IGEALAQHPLTAGITFTGSVPVGRHLMRQMAGGAYPRPCIAEMGGKNPCI 294 Query: 263 VFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDAFVARLKAGAEALKIGEPND 322 V D+D+A G +RSA+ GQ C R+YV + DA + RL A A A++IG+P Sbjct: 295 VTERADLDRAAAGIVRSAYGMGGQKCSALSRLYVHESVADALIGRLHAQATAIRIGDPRR 354 Query: 323 PEANFGPLISHKPREKVPSYYQQAVDDGATVVTGGGVPEMPA----HLAGGAWVQPTIWT 378 E GP+++ E + D GA V+ GG + + LA G +V+P + Sbjct: 355 HENWLGPVVNATAYENYQHHADALRDAGANVLCGGARIGLGSGGRTALARGYYVEPML-A 413 Query: 379 GLADDSAVVTEEIFGPCCHIRPFDSEEEAIELANSLPYGLASAIW--TENVRRAHRVAGQ 436 + + E+F P + + +EA+ LAN P GL + + + V H Sbjct: 414 EVPLQHPLWQHEMFLPILTVHRYGDRDEAMRLANDSPMGLTAGFYGGADEVSWFHE---H 470 Query: 437 IEAGIVWVN 445 IEAG+ + N Sbjct: 471 IEAGVTYAN 479 Lambda K H 0.318 0.136 0.413 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: 653 Number of extensions: 27 Number of successful extensions: 5 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: 486 Length of database: 527 Length adjustment: 34 Effective length of query: 452 Effective length of database: 493 Effective search space: 222836 Effective search space used: 222836 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 24 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