Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_082115713.1 AAW01_RS11260 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= metacyc::MONOMER-12387 (496 letters) >NCBI__GCF_001010925.1:WP_082115713.1 Length = 1202 Score = 147 bits (372), Expect = 2e-39 Identities = 127/435 (29%), Positives = 201/435 (46%), Gaps = 46/435 (10%) Query: 54 EDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEALG 113 E V RA EA F W +T R +++ +LL + ++L L+ EAGK A+ Sbjct: 620 ESVKRAAEA----FPGWSSTSVHERAECLEKAADLLEDRMENLLGLIMREAGKSAPNAIA 675 Query: 114 EVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVGVISAFNFPVAVWAWNA 173 EV+E +D + +R ++ LG V IS +NFP+A++ Sbjct: 676 EVREAVDFLRYYAQQARDS--------------LDGADALGPVVCISPWNFPLAIFVGEV 721 Query: 174 AVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVGAADVGERLVDSP 233 + AL G+TV+ KP+E TPL A ++ +AG P+ + Q+V G +G LV SP Sbjct: 722 SAALAAGNTVLAKPAEETPLIAAQAIGIMH----EAGVPEDVVQLVPGDGRIGAALVGSP 777 Query: 234 RVPLVSATGSTRMGRAVGPRVAARF--GRT----ILELGGNNAAVVTPSADLDLTVNAAV 287 + V+ TGST + + + ++A R G + I E GG NA VV SA + V V Sbjct: 778 DICGVTFTGSTEVAKIIQRQLAERLLPGGSPLPFIAETGGQNAMVVDSSALPEQVVRDVV 837 Query: 288 FAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAAFG 347 +A +AGQRC+ LR L + D+AD +++ L A L +G + + VGP++ A Sbjct: 838 ASAFDSAGQRCSALRVLCLQADVADDMLDMLRGAMAELRVGATDRLSVDVGPVITAEAKE 897 Query: 348 RMREAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVRMPAQTAVVREETFAPILYVL 407 + +E + G + + + +A +V P ++ + + + R E F P+L+V+ Sbjct: 898 TIETHIEDMRSRGFKV---EQLELDEATGYGTFVAPTIIEIDSVDQLGR-EVFGPVLHVV 953 Query: 408 TY--RDLDEAIRLNNEVPQACRQGSRTD--------GAPADDPRCRARRRAGGANCPAVP 457 Y +DL + ++ N G T A A+ R GA P Sbjct: 954 RYARKDLPQLMQAINATGYGLTFGLHTRIDETIAQVTAQAEVGNIYVNRNVIGAIVGVQP 1013 Query: 458 ----GRSGTGAGAGG 468 G SGTG AGG Sbjct: 1014 FGGQGLSGTGPKAGG 1028 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: 1149 Number of extensions: 55 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: 1202 Length adjustment: 41 Effective length of query: 455 Effective length of database: 1161 Effective search space: 528255 Effective search space used: 528255 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 24 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