Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate GFF3587 Psest_3654 succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >FitnessBrowser__psRCH2:GFF3587 Length = 488 Score = 208 bits (530), Expect = 3e-58 Identities = 133/388 (34%), Positives = 204/388 (52%), Gaps = 11/388 (2%) Query: 38 HPLTGADLFGLRAHTPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLA 97 +P TG + + + RA+EAA A WR A R A ++R+ EL+ E+++DLA Sbjct: 34 NPATGELIGAVPNMGRGETRRAIEAAQAAQPAWRALTAKERAARLRRWYELMLENQEDLA 93 Query: 98 DLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVG 157 ++T E GK +EA GEV ++ ++LYG +P+ R++ P+GV Sbjct: 94 RIMTAEQGKPLAEARGEVAYAASFLEWFAEEGKRLYGDVIPAHAGDKRILVQKEPVGVTA 153 Query: 158 VISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQ 217 I+ +NFP A+ A AL G +V KP+ TP + A AAL + AG P GL Sbjct: 154 AITPWNFPSAMITRKAGPALAAGCAMVLKPAPQTPFSALALAALAE----RAGIPAGLLS 209 Query: 218 VVVGAA----DVGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVV 273 V+ A +VG L ++P V +S TGST +G + + A + LELGGN +V Sbjct: 210 VITADAATSREVGAELCENPIVRKLSFTGSTAVGIKLMQQCAPTLKKLSLELGGNAPFIV 269 Query: 274 TPSADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQD 333 ADLD V A+ + AGQ C R+ V + I D V++L+AA RL +G+ ++ Sbjct: 270 FDDADLDAAVEGAMISKYRNAGQTCVCANRIYVQDGIYDAFVDKLSAAVARLKVGNGAEE 329 Query: 334 TTLVGPLVNEAAFGRMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVRMPAQTA 393 GPL++ AA +++ ++ A +G TL AGG+ P A G ++ + + ++ A Sbjct: 330 GVTTGPLIDAAAVAKVQRHLQDALDKGATLLAGGK---PHALGGNFFEPTLVGGVTSEMA 386 Query: 394 VVREETFAPILYVLTYRDLDEAIRLNNE 421 V REETF P+ + +RD DE IR N+ Sbjct: 387 VAREETFGPLAPLFRFRDEDEVIRQAND 414 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: 469 Number of extensions: 27 Number of successful extensions: 2 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: 488 Length adjustment: 34 Effective length of query: 462 Effective length of database: 454 Effective search space: 209748 Effective search space used: 209748 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