Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_092344789.1 BLU87_RS03510 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-20632 (478 letters) >NCBI__GCF_900107645.1:WP_092344789.1 Length = 452 Score = 230 bits (587), Expect = 7e-65 Identities = 147/448 (32%), Positives = 217/448 (48%), Gaps = 9/448 (2%) Query: 21 ESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEVRSDLLDKVGSTIIARS 80 ESLNP+ T +V+ +V ++A A+ W S R LL K + R Sbjct: 4 ESLNPA-TGEVLETFDEWSDEQVATTIEAVHGAYQNWRTTSFAERKSLLLKAAVILRQRK 62 Query: 81 ADIGRLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQNLESTRPGVEIQTYRQAV 140 + ++A E GK + EG E + + Y+A A + ++ +R Sbjct: 63 DEFATMMALEMGKPVVEGRAEIEKCALVCNYYAENAEQMLAPEPIASDASRSYVAFRPQ- 121 Query: 141 GVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATANVLADIMAECGAPAGVFN 200 G+ + PWNFP AAPAL GN V+K A P A + + E G PA VF Sbjct: 122 GIVLAVMPWNFPFWQVFRFAAPALMAGNVGVLKHASNVPRCALAIEQVFVEAGYPADVFR 181 Query: 201 -MLFGRGSMGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQARVQLEMGGKNPLIVLDD 259 ++ G G + +I+H V + TGS G +VA + A + +E+GG +P IVL+D Sbjct: 182 TLMIGSGKVAQ-VIEHPYVVATTLTGSDIAGRKVAEKSGAMLKKSVMELGGSDPFIVLND 240 Query: 260 ADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLAEKVAALRVGDALDPNTQ 319 ADL+ A ++A+ +GQ C A+ R IV+DGI++ F+ +AAL++GD D TQ Sbjct: 241 ADLDLAASVAVTARCINSGQSCIAAKRFIVEDGIYETFLEKFKANMAALKMGDPCDETTQ 300 Query: 320 IGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNPGWYVRPTLIADTQAGMRINNE 379 +GP ED M +R ++ + ++G +V+ GG + + PT++ GM NE Sbjct: 301 VGPQAREDLMRELHRQVEGSVAKGAKVILGG----MPGEAAFYPPTILTQVSKGMPAYNE 356 Query: 380 EVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHARHFQRYARAGMTMVNLATA 439 E FGPVA IRVK EEAL +AN EFGL + T + R+G VN T Sbjct: 357 EFFGPVAIVIRVKDAEEALFVANDTEFGLGGSVWTRDIIKGEKIAGEIRSGAVFVNSMTK 416 Query: 440 GVDYHVPFGGTKSSSYGAREQGFAAVEF 467 D +PFGG S +G + EF Sbjct: 417 S-DPRLPFGGVGISGFGRELSHYGIKEF 443 Lambda K H 0.317 0.133 0.384 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: 442 Number of extensions: 22 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: 478 Length of database: 452 Length adjustment: 33 Effective length of query: 445 Effective length of database: 419 Effective search space: 186455 Effective search space used: 186455 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: 51 (24.3 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