Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 175 bits (444), Expect = 3e-48 Identities = 123/388 (31%), Positives = 184/388 (47%), Gaps = 17/388 (4%) Query: 39 PLTGADLFGLRAHTPE----DVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQ 94 P TG GL A P+ + RA++AA A+ WR A R A++ + +L+ H+ Sbjct: 47 PATG----GLIASVPDLGATETRRAIDAAEAAWNPWRQRTAKDRAAVMMAWHDLIMAHQD 102 Query: 95 DLADLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLG 154 LA L++ E GK +EA+GE+ + ++ YG +P+ RL+ P+G Sbjct: 103 ALARLLSAEQGKPLAEAMGEISYGASFISWFAEEGKRAYGDLIPTTASDRRLLVMKQPIG 162 Query: 155 VVGVISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKG 214 VV ++ +NFP+A+ A AL G VV KP+E TPL+ A A L AG PKG Sbjct: 163 VVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDTPLSALALAELAH----RAGLPKG 218 Query: 215 LNQVVV--GAADVGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAV 272 L +V A VG + + +V +S TGSTR+G+ + + A + LELGGN + Sbjct: 219 LFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQCAETVKKVSLELGGNAPFI 278 Query: 273 VTPSADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQ 332 V DLD V A+ + +GQ C R +V I + +L + +G Sbjct: 279 VFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAGIYEDFAVKLAEKAAAMAVGHALS 338 Query: 333 DTTLVGPLVNEAAFGRMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVRMPAQT 392 GPL+N AA ++ V A ++G + GG P A G ++ L + Sbjct: 339 GVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGR---PHALGGGFWQPTVLADVTPAM 395 Query: 393 AVVREETFAPILYVLTYRDLDEAIRLNN 420 REETF P+ +L + EAI L N Sbjct: 396 LCFREETFGPVAPLLRFETEAEAIALAN 423 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: 514 Number of extensions: 21 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: 499 Length adjustment: 34 Effective length of query: 462 Effective length of database: 465 Effective search space: 214830 Effective search space used: 214830 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