Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_007474687.1 CMTB2_RS05650 aldehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >NCBI__GCF_000170735.1:WP_007474687.1 Length = 491 Score = 171 bits (433), Expect = 5e-47 Identities = 119/374 (31%), Positives = 183/374 (48%), Gaps = 15/374 (4%) Query: 54 EDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEALG 113 ED RA+E A AF + + R A ++ + L E K++ A +T+E K S A Sbjct: 58 EDAKRALEVAKNAFENTKKSTLAQRIAWIEDVAKKLQEKKEEFAKYITLEVAKPISHARV 117 Query: 114 EVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWH----PLGVVGVISAFNFPVAVW 169 EV+ I+ + G T+P++ T P GVV I+ FNFP+ + Sbjct: 118 EVERCIENLKICAAEGYHILGETIPTDATFTGAKTTAFYKRVPAGVVVAITPFNFPLNLV 177 Query: 170 AWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVGAADVGERL 229 A AL+ G++VV KP+ P A A L ++ P L+ VV G ADVG L Sbjct: 178 AHKLGPALIAGNSVVLKPTPEAPYTAYAFAKLF--IESEYAIPNALS-VVYGDADVGSTL 234 Query: 230 VDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVVTPSADLDLTVNAAVFA 289 V SP ++S TGS +G+ + +A + LELGGN A + SA+LD + Sbjct: 235 VTSPIPRVISFTGSVAVGKIITQ--SAGIKKVSLELGGNAATFIESSANLDYAASRCAVG 292 Query: 290 AAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAAFGRM 349 A +GQ C +L+R+ V E + + ++L +L +G+PF++ T +GPL+NE A R Sbjct: 293 AFANSGQVCISLQRIYVDEKVYEEFAKKLGDEASKLKVGNPFEEDTFMGPLINEEAAIRA 352 Query: 350 REAVERATAEGGTLCAGGERQFPDAAPGAYYVRPALVRMPAQTAVVREETFAPILYVLTY 409 ++ A +EG + AGG+R+ G L + +V EE FAPI+ ++ Sbjct: 353 ENWIKSAVSEGARIIAGGKRE------GNILYPTILADVTDDMKIVCEEVFAPIVSLVKV 406 Query: 410 RDLDEAIRLNNEVP 423 R +EA+ N P Sbjct: 407 RGYEEAVEKMNNSP 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: 399 Number of extensions: 19 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: 491 Length adjustment: 34 Effective length of query: 462 Effective length of database: 457 Effective search space: 211134 Effective search space used: 211134 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 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