Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_048102475.1 MBAR_RS02735 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_000195895.1:WP_048102475.1 Length = 479 Score = 313 bits (802), Expect = 8e-90 Identities = 174/481 (36%), Positives = 268/481 (55%), Gaps = 6/481 (1%) Query: 9 IDCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKM 68 ID I+GK V + G+ FD INPAT E + V +G + +AV++A A NG W Sbjct: 2 IDMKMQINGKAVEACSGEFFDIINPATGELIDRVPKGTEDDAAIAVESASSAFNG-WAST 60 Query: 69 TANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTI 128 + +R +L ++ +RK+EL+VL + + GKP +I A+ ++ + Sbjct: 61 SPQQRARILYTAAGIVRQRKDELAVLLTREQGKPL-AEAKNEIEGFAHVLEYYCGLASSF 119 Query: 129 TNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPM 188 + + + +++P+GV I PWN+P L+M WK+ PA+ +GNT+V+KPA TP+ Sbjct: 120 HGDFVPVPQNGYAFTVKKPLGVCTAIIPWNMPALIMAWKIGPAMISGNTLVLKPASNTPL 179 Query: 189 TATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAA 248 T LA I +AG+P GV+N+V G G G +L + P V ISFTGE TGK I AA Sbjct: 180 TNLALASILSEAGLPPGVLNIVTGPG-EVVGESLVKSPKVKKISFTGEVRTGKRIAELAA 238 Query: 249 KTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFL 308 +KR++ ELGG +P ++ D+NL+ + ++ F N G+ C R++V E F+ Sbjct: 239 GGMKRVTLELGGSDPMLVCDDANLEAAVAGALRGRFYNCGQACTAVKRLFVFESVAERFI 298 Query: 309 EKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEG-GTILTGGKRPEG-- 365 +K A + L VG+ +G L + +E + + A E+ G I+ GG+ PEG Sbjct: 299 KKLEAGIRNLRVGNGLHENIDLGPLNNRRQWEYIKELVADAEEKDEGRIVAGGRVPEGSA 358 Query: 366 LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTN 425 KGYF EPT+I + R R++ EE+FGPV+ V+ +E +E+ N+T YGL AS+WT Sbjct: 359 CSKGYFFEPTLIVDVDRKSRLLNEEVFGPVLPVVRVKDLDEAIEEANNTCYGLGASIWTK 418 Query: 426 DLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIK 485 +L RA Q+ AGI+W+N PFGG ++SGIG E G + Y +L + +K Sbjct: 419 NLDRARIGCEQLNAGIIWLNQHLKVAPEVPFGGTRESGIGNENGPDALSEYLDLKTVMLK 478 Query: 486 L 486 + Sbjct: 479 I 479 Lambda K H 0.318 0.136 0.404 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: 626 Number of extensions: 33 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: 479 Length adjustment: 34 Effective length of query: 452 Effective length of database: 445 Effective search space: 201140 Effective search space used: 201140 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 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