Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate 202865 SO3774 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, putative (NCBI ptt file)
Query= metacyc::MONOMER-12387 (496 letters) >FitnessBrowser__MR1:202865 Length = 1059 Score = 171 bits (433), Expect = 1e-46 Identities = 116/360 (32%), Positives = 183/360 (50%), Gaps = 13/360 (3%) Query: 56 VDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEALGEV 115 +++AV +AH AF +W TP VR + +++ +LL E++++L L T EAGK + + EV Sbjct: 602 IEQAVSSAHAAFGSWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDEV 661 Query: 116 QEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETW-HPLGVVGVISAFNFPVAVWAWNAA 174 +E +D C + +++L + P L E + GV IS +NFP+A++ + Sbjct: 662 REAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVS 721 Query: 175 VALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVGA-ADVGERLVDSP 233 AL G+TVV KP+E T + L AG P + Q + G A VG L Sbjct: 722 AALAAGNTVVAKPAEQTSIIGYRAVQLAH----QAGIPTDVLQYLPGTGATVGNALTADE 777 Query: 234 RVPLVSATGSTRMGRAVGPRVAARFGRTI---LELGGNNAAVVTPSADLDLTVNAAVFAA 290 R+ V TGST + + +A R G I E GG NA VV ++ + VN V ++ Sbjct: 778 RIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSS 837 Query: 291 AGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAAFGRMR 350 +AGQRC+ LR L + EDIAD V++ L A + L IG+P T VGP+++ A + Sbjct: 838 FTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSIKTDVGPVIDATAKANLD 897 Query: 351 EAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVRMPAQTAVVREETFAPILYVLTYR 410 ++ G + + P ++V P V + + V+ +E F PIL+V+ Y+ Sbjct: 898 AHIDHIKQVGKLI---KQMSLPAGTENGHFVAPTAVEIDS-IKVLEKEHFGPILHVIRYK 953 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: 921 Number of extensions: 41 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: 1059 Length adjustment: 40 Effective length of query: 456 Effective length of database: 1019 Effective search space: 464664 Effective search space used: 464664 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: 55 (25.8 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