Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 361 bits (927), Expect = e-104 Identities = 193/480 (40%), Positives = 296/480 (61%), Gaps = 12/480 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +FI GK+VP++ G+TF+NI+P + TVA A +++LA+ AA A G W + + E Sbjct: 21 NFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAA-RGAWGRTSPAE 79 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R L ++ D I ++ + L+++E++D GKP + + D+P A +F +F+ +R Sbjct: 80 RSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEGGI 139 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +++D + Y P+GV+ I PWN PLL+ WKLAPALAAGN V++KPAE TPM+ V Sbjct: 140 SEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMSVMV 199 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 L ++ D +P GV+N+++GFG AG L ++ + ++FTGETTTG++IM A++ + Sbjct: 200 LVDMIGDL-LPPGVLNVINGFGV-EAGKPLAQNKRIAKVAFTGETTTGRLIMQYASENII 257 Query: 253 RLSYELGGKNPNVIFAD--SNLDEVIETTMK--SSF-INQGEVCLCGSRIYVERPAYEAF 307 ++ ELGGK+PN+ FAD D+ + ++ S F +NQGEVC C SR V+ Y+ F Sbjct: 258 PVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVQEKIYDRF 317 Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE--- 364 +E+ VA+ K++ G+P D T +GA S++ E++ Y+ + +EG +L GG R + Sbjct: 318 MERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGGGRADVGP 377 Query: 365 GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424 L G++++PTI+ G + R+ +EEIFGPV++V F +EE LE NDT YGL A VWT Sbjct: 378 ELAGGFYVQPTILEGHNK-MRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGLGAGVWT 436 Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484 + RA+R IEAG VW N + L FGG KQSGIGRE + Y + N+ + Sbjct: 437 RNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQKTKNMLV 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: 586 Number of extensions: 31 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: 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