Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_012757049.1 RLEG_RS07320 sorbosone dehydrogenase
Query= BRENDA::P30038 (563 letters) >NCBI__GCF_000023185.1:WP_012757049.1 Length = 506 Score = 179 bits (453), Expect = 3e-49 Identities = 149/488 (30%), Positives = 238/488 (48%), Gaps = 29/488 (5%) Query: 53 ALKDLKGRMEAIPCVVGDEEVWTSDVQYQVSPFNHGHKVAKFCYADKSLLNKAIEAALAA 112 AL D K R + + G E SD +V+P +HG V++F + +AI AA Sbjct: 9 ALNDHKAR-DFKMLIDGRWEAGASDPIERVAP-SHGVVVSRFPTGSRKDAERAISAA--- 63 Query: 113 RKEWDLKP-----IADRAQIFLKAADMLSGPRRAEILAKTMVGQGKTVIQAEIDAAAELI 167 RK +DL P ++R+ I LKAAD+++ R E+ + GK + Q + A + Sbjct: 64 RKAFDLGPWPRMTASERSAILLKAADLIAA-RAEELAFLDAIEAGKPITQVRGEIAGS-V 121 Query: 168 DFFRFNAKYAVELEGQQPISVPPSTNSTVYRGLEGFVAAISPFNFT--AIGGNLAGAPAL 225 D +R+ A A +L G+ ++ T V R G V+ I+P+NF +G L A A Sbjct: 122 DIWRYAAALARDLHGESYNTLGDGTLGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAA 181 Query: 226 MGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDTVTSSEHLCGINFT 285 G + KPS+ ++ + IL++AG+P ++ V GP G +TS + ++FT Sbjct: 182 -GCTTVVKPSELTSGSTLVLGEILQQAGIPDGVVNIVTGTGPEVGAIMTSHPDVDMVSFT 240 Query: 286 GSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESVVSGTLRSAFEYGG 345 GS K AQ T +++ E GGKN V AD+ + + + A+ G Sbjct: 241 GSTGVGKLTMSNAAQ------TLKKVSLELGGKNPQIVFPDADLGAFIDAAVFGAYFNAG 294 Query: 346 QKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVIDAKSFARIKKWLE 405 + C+A SRL + S+ + R+ E +KVGDP D T A+I + +I ++ Sbjct: 295 ECCNAGSRLILHKSIASDVVKRIAELSKAVKVGDPL-DPSTQVGAIITPQHLEKISGYVA 353 Query: 406 HARSSPSLTILAGGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGPVLSVYVYPDDKYKE 465 ARSS + G D +G F+ P I+E P + +EE+FGPVLSV + + E Sbjct: 354 GARSSGARVAHGGETLDLGMGQFMSPTILEEVTPDMAVAREEVFGPVLSVLTF--ETSAE 411 Query: 466 TLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRNAAGNFYINDKSTGSIVGQQPFGGARA 525 +++ +S YGL+ V+S+D D + +R AG ++N G+ + PFGG + Sbjct: 412 AIRIANS-IDYGLSAGVWSRDFDTCLTIGRSVR--AGTVWMNTFMDGA--SELPFGGYKQ 466 Query: 526 SGTNDKPG 533 SG + G Sbjct: 467 SGLGRELG 474 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: 620 Number of extensions: 31 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: 563 Length of database: 506 Length adjustment: 35 Effective length of query: 528 Effective length of database: 471 Effective search space: 248688 Effective search space used: 248688 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 (21.7 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