Align Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized)
to candidate WP_092345435.1 BLU87_RS05345 1-pyrroline-5-carboxylate dehydrogenase
Query= SwissProt::P40047 (520 letters) >NCBI__GCF_900107645.1:WP_092345435.1 Length = 373 Score = 119 bits (297), Expect = 2e-31 Identities = 96/298 (32%), Positives = 145/298 (48%), Gaps = 14/298 (4%) Query: 71 KITTVYKAMEDDVDEAVAAAKKAFETKWSIVEPEVRAKALFNLADLVEKHQETLAAIESM 130 ++ T +KA +V A+ AA A + W + E RA ADL+ L +M Sbjct: 72 QLGTSHKAGPKEVQMAIDAAMAA-KPAWQSLRWEERAAIFLKAADLLAGPYRFLINAATM 130 Query: 131 DN-GKSLFCARGDVAL-VSKYLRSCGGWADKIYGNV-IDTGKNHFTYSIKEPL-GVCGQI 186 N K+ F A D A + +LR +A ++Y + + + + Y PL G + Sbjct: 131 LNISKNPFQAEIDAACELIDFLRFNVYFAQEVYADQPLHSPSPIWNYVQHRPLEGFVFAV 190 Query: 187 IPWNFPLLMWSWKIGPALATGNTVVLKPAETTPLSALFASQLCQEAGIPAGVVNILPGSG 246 P+NF + + PA+ GNTVV KPA + + +L QEAG+P GV+N +PGSG Sbjct: 191 APFNFTAIAGNLPTAPAIM-GNTVVWKPASSAVYAPYHFMKLLQEAGLPDGVINFVPGSG 249 Query: 247 RVVGERLSAHPDVKKIAFTGSTATGRHIMK-----VAAD---TVKKVTLELGGKSPNIVF 298 VG PD I FTGSTA + + K +AA+ T ++ E GGK Sbjct: 250 SDVGNVCLDSPDFNGIHFTGSTAVFQSMWKQIGNNIAANKYKTYPRIVGETGGKDFIFAH 309 Query: 299 ADADLDKAVKNIAFGIFYNSGEVCCAGSRIYIQDTVYEEVLQKLKDYTESLKVGDPFD 356 + AD+ I G F G+ C A SR Y+ ++++E VL ++K T+ +K+GD D Sbjct: 310 SSADVKALATGIVRGAFEYQGQKCSAASRAYVPESLWEPVLTEIKAQTDRIKMGDVAD 367 Lambda K H 0.317 0.134 0.390 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: 439 Number of extensions: 17 Number of successful extensions: 2 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: 520 Length of database: 373 Length adjustment: 32 Effective length of query: 488 Effective length of database: 341 Effective search space: 166408 Effective search space used: 166408 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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