Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_002117405.1:WP_085772038.1 Length = 506 Score = 372 bits (954), Expect = e-107 Identities = 205/481 (42%), Positives = 296/481 (61%), Gaps = 14/481 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +FI G++V L G+ FDNI+P T + VA G AA+++LA+ AA KA + W K A E Sbjct: 21 NFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKAKDA-WGKTPAAE 79 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +L K+ + + L+++E++D GKP + + DIP A +F +F+ +R Sbjct: 80 RANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQEGSL 139 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +++D + Y P+GV+G I PWN P+L+ WKL+PALAAGN VV+KPAE TPM+ Sbjct: 140 SEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPMSILA 199 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 +AE+ D +P GV+N+V+GFG AG L + + I+FTGETTTG++IM AA+ L Sbjct: 200 VAELIADL-LPPGVLNIVNGFGV-EAGKPLASNKRIAKIAFTGETTTGRLIMQYAAENLI 257 Query: 253 RLSYELGGKNPNVIFA------DSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306 ++ ELGGK+PN+ FA D+ LD+ +E S +NQGEVC C SR V+R Y+ Sbjct: 258 PVTLELGGKSPNIFFADVMAEDDAFLDKALE-GFASFALNQGEVCTCPSRALVQRSIYDK 316 Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRP--E 364 F+EK +A+ ++ G P D T +GA S++ E++ Y+ + +EG +L GG+R E Sbjct: 317 FMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERSVLE 376 Query: 365 G-LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423 G L++GY+++PT + G R RV +EEIFGPVV+V F+TEEE L+ NDT YGL A +W Sbjct: 377 GELKEGYYMQPTALEGHNR-MRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAGLW 435 Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483 T D RA+R I AG VW N + FGG KQSGIGRE + Y + N+ Sbjct: 436 TRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNLL 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: 579 Number of extensions: 35 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 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