Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate 5208068 Shew_0580 succinylglutamic semialdehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-12387 (496 letters) >FitnessBrowser__PV4:5208068 Length = 487 Score = 171 bits (434), Expect = 4e-47 Identities = 139/428 (32%), Positives = 204/428 (47%), Gaps = 24/428 (5%) Query: 52 TPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEA 111 TPE V+ AVEAA A W R A+V+ + + L HK D+A+++ E GK + E Sbjct: 36 TPEQVNAAVEAARAAQFDWFMLGFDARLAIVEAYRDQLEAHKGDIAEVIAQETGKPQWET 95 Query: 112 LGEVQEMIDICDFAVGLSRQLYGR---TMPSERPGHRLMETWHPLGVVGVISAFNFPVAV 168 E MI +GLS Y + T ++ P R + P GVV V +NFP + Sbjct: 96 ATEAGAMIG----KIGLSVAAYHKRTGTSENDTPAGRAVLRHKPHGVVAVFGPYNFPGHL 151 Query: 169 WAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVGAADVGER 228 + AL+ G+TVV+KPSELTP A L+ AG P G+ +V G + G+ Sbjct: 152 PNGHIVPALLAGNTVVFKPSELTP----KTAELMLKLWEKAGLPAGVINLVQGEVETGKA 207 Query: 229 LVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTI-LELGGNNAAVVTPSADLDLTVNAAV 287 L P++ + TGS+R G + + A G+ + LE+GGNN ++ D V+ + Sbjct: 208 LASHPQIDGLFFTGSSRTGHILHQQYAGHPGKILALEMGGNNPLIIKGVKDTLAAVHDII 267 Query: 288 FAAAGTAGQRCTTLRRLIVHEDI-ADTVVERLTAAFERLPIGD-PFQDTTLVGPLVNEAA 345 +A ++GQRCT RRL V + D ++ +L A +++ +G Q +G +++EAA Sbjct: 268 QSAYISSGQRCTCARRLYVEKGAEGDALLAKLAEAVKQIKVGPWNAQPQPFMGSMISEAA 327 Query: 346 FGRMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVRMPAQTAVVREETFAPILY 405 M EA GGT + G V P L+ + + EE F P+L Sbjct: 328 AKGMVEAQRNLINLGGTPLV----ELKHLEAGTGLVSPGLIDVTQVIELPDEEYFGPLLQ 383 Query: 406 VLTYRDLDEAIRLNNEVPQACRQGSRTDGAPADDPRCRARRRAGGANC-PAVPGRSGT-- 462 V+ Y D DEAI+L N+ G D + D AR RAG N + G SG+ Sbjct: 384 VVRYTDFDEAIKLANDTRYGLSAGILAD-SREDYDYFLARIRAGIVNWNKQITGASGSAP 442 Query: 463 --GAGAGG 468 G GA G Sbjct: 443 FGGVGASG 450 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: 492 Number of extensions: 23 Number of successful extensions: 5 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: 487 Length adjustment: 34 Effective length of query: 462 Effective length of database: 453 Effective search space: 209286 Effective search space used: 209286 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