Align Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; P5C dehydrogenase; Aldehyde dehydrogenase family 4 member A1; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_011763950.1 AZO_RS01105 aldehyde dehydrogenase
Query= SwissProt::Q8CHT0 (562 letters) >NCBI__GCF_000061505.1:WP_011763950.1 Length = 494 Score = 123 bits (308), Expect = 2e-32 Identities = 133/448 (29%), Positives = 197/448 (43%), Gaps = 43/448 (9%) Query: 96 ADKALLNRAIDAALAARKEWDLKPMA--DRAQVFLKAADMLSG--PRRAEVLAKTMVGQG 151 AD+AL++ A + A A KE D A DRA+V + AD++ PR + A Sbjct: 46 ADEALVDIAAENAWTAWKESDWARCAPRDRARVLRRWADLVEAEAPRLGVLEALGSTRPV 105 Query: 152 KTVIQAEIDAAAELIDFFRFNAKFAVELEGEQPISVPPSTNHT----VYRGLEGFVAAIS 207 + I ++ AE + FF A++A +L GE +T H V G + AI+ Sbjct: 106 RDAIAWDVPFTAEGLRFF---AEYADKLGGEVA-----ATRHDHLGMVIAEPYGLIGAIT 157 Query: 208 PFNFTAIGGNL-AGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGP 266 P+NF + + GA GN VL KPS+ ++ + + +AG+P I V DG Sbjct: 158 PWNFPLVMVSWKVGAALAAGNAVLLKPSELTPFSALRLAELAIQAGVPAGIFNIVQGDGR 217 Query: 267 TFGDTVTSSEHLCGINFTGSVPTFKHLWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSA 326 T G+ +T + + FTGS T + A + + T E GGK+ V Sbjct: 218 TTGEAITRHPRVSKMTFTGSTRTGAAIMSACALHGPKPVTL-----ELGGKSPQLVFDDV 272 Query: 327 -DVDSVVSGTLRSAFEYGGQKCSACSRLYVPKSLWPQIKGRLLEEHSRIKVG---DPAED 382 D+D + + + GQ C A SRL V + ++ G L+E I G D Sbjct: 273 RDLDKLAATIAGAITGNAGQVCVAGSRLIVQR----RVAGALVERIRAIFTGHRPGATWD 328 Query: 383 FGTFFSAVIDAKAFARIKKWLEHARSSPSLSILAGGQCNES--VGYYVEPCIIESKDPQE 440 +I A+ ARI +E A+++ + GG+ + G Y P +I+ D Sbjct: 329 EDATLPPIISAQQAARIAAIVERAQAAGG-RVKCGGRIVDGGYGGAYYLPTLIDGVDTAN 387 Query: 441 PIMKEEIFGPVLTVYVYPDDKYRETLQLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNAA 500 P + EEIFGPVLTV + D++ L S SYGL V D A R R A Sbjct: 388 PAVSEEIFGPVLTVQTFDDEEEGFALA---SHDSYGLAAGVHTSDVGRAMRAVR--RIEA 442 Query: 501 GNFYIN--DKSTGSVVGQQPFGGARASG 526 G ++N +S V+ P GG SG Sbjct: 443 GTVWVNRYGRSADFVI---PTGGYHQSG 467 Lambda K H 0.319 0.135 0.411 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: 658 Number of extensions: 29 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: 562 Length of database: 494 Length adjustment: 35 Effective length of query: 527 Effective length of database: 459 Effective search space: 241893 Effective search space used: 241893 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