Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate GFF2711 HP15_2655 methylmalonate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >FitnessBrowser__Marino:GFF2711 Length = 503 Score = 199 bits (507), Expect = 1e-55 Identities = 139/390 (35%), Positives = 195/390 (50%), Gaps = 11/390 (2%) Query: 38 HPLTGADLFGLRAHTPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLA 97 +P TG + EDVD AV AA AF W TP R ++ +F ELL HK DLA Sbjct: 27 NPATGQVTGRVALAGREDVDAAVAAADAAFPAWADTPPIRRARVMFKFLELLNTHKDDLA 86 Query: 98 DLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVG 157 +T E GK+ ++A GEV IDI +FA G+ + L G G T PLGVV Sbjct: 87 RAITAEHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPLGVVA 146 Query: 158 VISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQ 217 ++ FNFP V W VA+ G+T V KPS PL+ +A + DL + AG P G+ Sbjct: 147 GVTPFNFPAMVPMWMFPVAIAAGNTFVLKPS---PLDPSASLMIADL-LKQAGLPDGVFN 202 Query: 218 VVVGAADVGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGG-NNAAVVTPS 276 VV G D L++ P V +S GST + + + A+ G+ I LGG N VV P Sbjct: 203 VVQGDKDAVNALIEHPDVQALSFVGSTPIANLLYEK-GAKHGKRIQALGGAKNHMVVMPD 261 Query: 277 ADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTL 336 ADLD V+A + AA G+AG+RC + ++ D+AD +V RL L + + Q Sbjct: 262 ADLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAERARSLKVKNGEQLDAE 321 Query: 337 VGPLVNEAAFGRMREAVERATAEGGTLCAGGE----RQFPDAAPGAYYVRPALV-RMPAQ 391 +GP+V AA R+ +++ AEG L G D +++ +L + Sbjct: 322 MGPIVTAAAHQRITGYIDKGVAEGAELVVDGRGFDASNTGDGCADGFWMGGSLFDHVTPD 381 Query: 392 TAVVREETFAPILYVLTYRDLDEAIRLNNE 421 + REE F P+L + D+ AIRL N+ Sbjct: 382 MTIYREEIFGPVLACVRVPDIATAIRLIND 411 Lambda K H 0.320 0.135 0.406 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: 515 Number of extensions: 28 Number of successful extensions: 3 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: 496 Length of database: 503 Length adjustment: 34 Effective length of query: 462 Effective length of database: 469 Effective search space: 216678 Effective search space used: 216678 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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