Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF3202 HP15_3144 NAD-dependent aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Marino:GFF3202 Length = 533 Score = 340 bits (873), Expect = 5e-98 Identities = 190/475 (40%), Positives = 272/475 (57%), Gaps = 14/475 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 ++I G++V + G+ F+NI P T + + A +IDLA+ AA KA W K + E Sbjct: 48 NYIGGEWVAPVKGQYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAAPA-WGKTSPTE 106 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +L K+ D I E+L+V E+ D GK + + DIP AA +F +F+ +R Sbjct: 107 RSNILLKIADRIEANLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGHM 166 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 ++D + Y P+GV+G I PWN P+L+ WKL P LAAGN V+KPAE TP + V Sbjct: 167 GEIDHNTVAYHFHEPLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASILV 226 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 L EI D +P GV+N+V+G+G AG AL + I+FTG T G I+ AA+ + Sbjct: 227 LMEIIGDL-LPPGVLNIVNGYG-IEAGQALATSKRIAKIAFTGSTPVGSHILKCAAENII 284 Query: 253 RLSYELGGKNPNVIFAD------SNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306 + ELGGK+PN+ F+D +D+ +E + +F NQGEVC C SR V+ +E Sbjct: 285 PSTVELGGKSPNIYFSDVMKAEPEFIDKCVE-GLVLAFFNQGEVCTCPSRALVQEDMFEE 343 Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKR---P 363 F++K V +TK + G+P D +VGA S E ++++ Y+ + EEG +LTGG R Sbjct: 344 FMQKVVQRTKSIKRGNPLDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHLD 403 Query: 364 EGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423 E G++++PT+ G RV +EEIFGPVV V F TEEE L NDT +GL A VW Sbjct: 404 EEFNNGFYIQPTLFKG-DNKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAGVW 462 Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478 T D A+R+ I+AG VW+N + FGG K+SG+GRE + E Y + Sbjct: 463 TRDTNLAYRMGRNIQAGRVWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQ 517 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: 657 Number of extensions: 27 Number of successful extensions: 6 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: 533 Length adjustment: 34 Effective length of query: 452 Effective length of database: 499 Effective search space: 225548 Effective search space used: 225548 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 Apr 09 2024. 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