Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_011423489.1 RHE_RS00470 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_000092045.1:WP_011423489.1 Length = 494 Score = 347 bits (889), Expect = e-100 Identities = 191/480 (39%), Positives = 275/480 (57%), Gaps = 20/480 (4%) Query: 14 FIDGKFVPS-LDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +I+G + P KTFD +NPAT E L ++ + GAAE A+ AA A W A E Sbjct: 23 YINGVWTPGDAAAKTFDVLNPATGELLASLPDMGAAETRAAIDAAYAA-QPAWAARPAKE 81 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +LRK DLI+ + L+ + + + GKP P A + + YI EA Sbjct: 82 RSQILRKWFDLIVANADALAAILTAEMGKP--------FPEARGEILYAAAYIEWYAEEA 133 Query: 133 TQMDDVALN--------YAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAE 184 ++ + I++PVGV+G I PWN P ++ K+APALA G TVV KPAE Sbjct: 134 KRIYGETIPAPSQDKRMIVIKQPVGVVGTITPWNFPAAMIARKIAPALAVGCTVVSKPAE 193 Query: 185 LTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIM 244 TP+TA LA + AG+P GV NL+ G + G L + V ISFTG T G+I+M Sbjct: 194 QTPLTAIALAVLAEQAGIPAGVFNLIVGLDGPAIGRELCGNDKVRKISFTGSTEVGRILM 253 Query: 245 ASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAY 304 A +K++S ELGG P ++F D++LD +E + S + N G+ C+C +R+Y++ Y Sbjct: 254 RQCADQIKKVSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRLYIQSGVY 313 Query: 305 EAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE 364 +AF K AK ++ VGD F ++G LI ++ +V ++ AV +G ILTGGKR + Sbjct: 314 DAFAAKLAAKVADMSVGDGFRPGVEIGPLIDEQGLAKVEDHVGDAVAKGAKILTGGKRID 373 Query: 365 GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424 G G F PT++TG+TRD V +EE FGPV + F+T E+V+ Q NDT +GL+A + Sbjct: 374 G--AGTFFAPTVLTGVTRDMTVAREETFGPVAPLFRFETAEDVITQANDTEFGLAAYFYA 431 Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484 DL++ RVA +E G+V +NT + PFGG+KQSG+GREG H + Y E+ +CI Sbjct: 432 GDLKKVWRVAEALEYGMVGINTGLMSSEMAPFGGIKQSGLGREGSRHGADDYLEMKYLCI 491 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: 607 Number of extensions: 27 Number of successful extensions: 4 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: 494 Length adjustment: 34 Effective length of query: 452 Effective length of database: 460 Effective search space: 207920 Effective search space used: 207920 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