Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 166 bits (421), Expect = 1e-45 Identities = 117/392 (29%), Positives = 195/392 (49%), Gaps = 16/392 (4%) Query: 39 PLTGADLFGLRAH-TPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLA 97 P+ G +F AH T ED++ AV+AAH AF TW T + R ++ + + + ++ + LA Sbjct: 36 PIDGK-VFTKAAHSTKEDLELAVDAAHEAFKTWSKTSSTERSIILNKIAQRMEDNLEYLA 94 Query: 98 DLVTIEAGK-IRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVV 156 + TI+ GK +R ++ +D + G+ R G ++ L+ P+GVV Sbjct: 95 AVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSLSELDQNTVSLI-VHEPIGVV 153 Query: 157 GVISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLN 216 I +NFP+ + W A AL G+ VV KP+E TP+ + L++L I D P +N Sbjct: 154 AQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPV---SIMVLMEL-IGDLLPPGVVN 209 Query: 217 QVVVGAADVGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGN------NA 270 V +++G LV +P+V + TGST GR V LELGG ++ Sbjct: 210 VVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATENIIPVTLELGGKSPNIFFSS 269 Query: 271 AVVTPSADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDP 330 + A LD V AV A G+ CT RL++ EDI + + ++ + + IG P Sbjct: 270 VMAEDDAFLDKAVEGAVMFAL-NQGEICTCPSRLLIQEDIYEKFIAKVIERTKAIKIGSP 328 Query: 331 FQDTTLVGPLVNEAAFGRMREAVERATAEGGTLCAGGE-RQFPDAAPGAYYVRPALVRMP 389 T ++G ++ F ++ ++ EG + GGE + P G YY++P + + Sbjct: 329 LDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINELPGELGGGYYIKPTIFKGH 388 Query: 390 AQTAVVREETFAPILYVLTYRDLDEAIRLNNE 421 + + +EE F P+L V T++ ++EAI + N+ Sbjct: 389 NKMRIFQEEIFGPVLAVTTFKTVEEAIEIAND 420 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: 440 Number of extensions: 21 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: 501 Length adjustment: 34 Effective length of query: 462 Effective length of database: 467 Effective search space: 215754 Effective search space used: 215754 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