Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Dino:3607686 Length = 506 Score = 367 bits (941), Expect = e-106 Identities = 199/481 (41%), Positives = 286/481 (59%), Gaps = 14/481 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +FI GKFVP ++G+ FDN+ P T E +G +A AA+++LA+ AA A + W K + E Sbjct: 21 NFIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAAKDA-WGKTSVTE 79 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R ++ K+ D I E + ++ E+ D GKP + DIP A +F +F+ +R Sbjct: 80 RANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQEGSM 139 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +++D+ + Y P+GV+G I PWN +L+ WKLAPA+AAGN +V+KPAE TP V Sbjct: 140 SEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQTPAAIMV 199 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 L E+ D +P GV+N+V+G+G GAAL + I+FTG T TG+ IM +A L Sbjct: 200 LVELISDL-LPAGVLNIVNGYG-GEVGAALATSDRIAKIAFTGSTATGRKIMEAATVNLI 257 Query: 253 RLSYELGGKNPNVIFA------DSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306 ++ ELGGK+PN+ F D+ LD+ +E + +F NQGEVC C SR + YE Sbjct: 258 PVTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAF-NQGEVCTCPSRALIHEDIYEE 316 Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK---RP 363 F+ + +A+ K +V GDP +T VGA S E +++ Y ++ VEEG +LTGGK Sbjct: 317 FIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGKVADVS 376 Query: 364 EGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423 + L+ G+++EPTI+ G + RV +EEIFGPVV+V F TEEE LE NDT YGL A VW Sbjct: 377 DDLKDGFYIEPTILKGHNK-MRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAGVW 435 Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483 + D +R ++AG VWVN + FGG KQSGIGRE + Y + N+ Sbjct: 436 SRDQNTCYRFGRGVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNML 495 Query: 484 I 484 + Sbjct: 496 V 496 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: 602 Number of extensions: 28 Number of successful extensions: 7 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: 506 Length adjustment: 34 Effective length of query: 452 Effective length of database: 472 Effective search space: 213344 Effective search space used: 213344 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