Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_099618346.1 CLH62_RS11815 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_002744735.1:WP_099618346.1 Length = 489 Score = 372 bits (956), Expect = e-107 Identities = 202/476 (42%), Positives = 286/476 (60%), Gaps = 9/476 (1%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +F+ G+F+ + G+TF INPAT + + V + A+++A+ W MTA Sbjct: 10 NFVHGRFLANRTGETFPVINPATGQAIYEVEVADESVQQAAIESARAGF-AEWSAMTAIA 68 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +L + L+ ER +EL+ +E DTGKP + ++D+ A FF+ +I E Sbjct: 69 RSRILLRAVALLRERNDELAAVEVRDTGKPWQEAEAVDVVTGADTLEFFAGLAPSI--EG 126 Query: 133 TQMD-DVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTAT 191 Q D Y R P+G+ I WN PL + WK APALA GN ++ KP+E TPM A Sbjct: 127 NQQDLGGDFYYTRREPLGICAGIGAWNYPLQISCWKSAPALACGNAMIFKPSEETPMGAV 186 Query: 192 VLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTL 251 LAEI +AGVP GV N+V G G LT HP++ +SFTGE TGK +MA+AA TL Sbjct: 187 KLAEIFVEAGVPAGVFNVVQGAA--EVGQWLTHHPEIAKVSFTGEVATGKKVMAAAASTL 244 Query: 252 KRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311 K ++ ELGGK+P +IF D++L+ I M +F QGE+C G+R++V Y F+E+ Sbjct: 245 KDVTMELGGKSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFMERM 304 Query: 312 VAKT-KELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK--RPEGLEK 368 + +T K + GDP D T GALIS++H + V YI + EG T+ GG+ PE + Sbjct: 305 LERTRKNIKPGDPMDTNTNFGALISEKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDSKG 364 Query: 369 GYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLR 428 GYF+EPTI T T D +VKEEIFGPV++V+ F E+EV+ + N+T GL+A V+TND+R Sbjct: 365 GYFVEPTIFTDCTDDMTIVKEEIFGPVMSVLTFSNEDEVIARANNTDTGLAAGVFTNDIR 424 Query: 429 RAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484 RAHRV QI+AGI W+N++ P GG K SGIGRE G + Y+++ ++ I Sbjct: 425 RAHRVIHQIQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYI 480 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: 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: 489 Length adjustment: 34 Effective length of query: 452 Effective length of database: 455 Effective search space: 205660 Effective search space used: 205660 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 24 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