Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_012759625.1 RLEG_RS21595 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_000023185.1:WP_012759625.1 Length = 493 Score = 350 bits (897), Expect = e-101 Identities = 191/480 (39%), Positives = 277/480 (57%), Gaps = 21/480 (4%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 +IDG + +TFD +NPAT E L ++ + GAAE A+ AA A G W A ER Sbjct: 23 YIDGVWTSGDATRTFDVLNPATGELLASLPDMGAAETRTAIDAAHAAQPG-WAARPAKER 81 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 +LRK DL++ +EL+ + + + GKP P A + + YI EA Sbjct: 82 STILRKWFDLMVANADELAAILTAEMGKP--------FPEARGEILYAAAYIEWYAEEAK 133 Query: 134 QM---------DDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAE 184 ++ DD + IR+PVGV+G I PWN P ++T K+APALA G TVV KPAE Sbjct: 134 RIYGETIPAPSDDKRM-IVIRQPVGVVGTITPWNFPAAMITRKIAPALAVGCTVVSKPAE 192 Query: 185 LTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIM 244 TP+TA LA + AG+P GV N++ G + G L + V ISFTG T G+I+M Sbjct: 193 QTPLTAIALAVLAEQAGIPAGVFNVIVGVDGPAIGRELCGNEKVRKISFTGSTEVGRILM 252 Query: 245 ASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAY 304 A +K++S ELGG P ++F D++LD +E + S + N G+ C+C +R+YV+ Y Sbjct: 253 RQCADQIKKVSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRLYVQSNVY 312 Query: 305 EAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE 364 +AF K AK E+ VGD F +G LI ++ +V ++ A+ +G +LTGGKR + Sbjct: 313 DAFAAKLAAKVAEMSVGDGFKPGVVIGPLIDEQGLAKVEDHVSDALAKGAKVLTGGKRID 372 Query: 365 GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424 G G F PT++TG+ R +V +EE FGPV + F+T E+V+ Q NDT +GL+A + Sbjct: 373 G--AGTFFTPTVLTGVARGMKVAREETFGPVAPLFRFETVEDVIAQANDTEFGLAAYFYA 430 Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484 DL++ RVA +E G++ +NT + PFGG+KQSG+GREG H + Y E+ +CI Sbjct: 431 GDLKKVWRVAEALEYGMIGINTGLMSSETAPFGGIKQSGLGREGSRHGADDYLEMKYLCI 490 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: 601 Number of extensions: 29 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: 493 Length adjustment: 34 Effective length of query: 452 Effective length of database: 459 Effective search space: 207468 Effective search space used: 207468 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