Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_089301742.1 CHB84_RS12430 aldehyde dehydrogenase family protein
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_900188115.1:WP_089301742.1 Length = 477 Score = 236 bits (601), Expect = 2e-66 Identities = 159/472 (33%), Positives = 235/472 (49%), Gaps = 37/472 (7%) Query: 42 IDGE-RYETENKIVSINPANKEEVVGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERAA 100 +DG+ RYE+ I +PA+ EEV+G+V T+ + A+ AA +AF W ERA Sbjct: 13 VDGQTRYESSESIDVFDPAS-EEVIGSVPAGTRAEVDSAVAAARRAFPEWSARPVAERAE 71 Query: 101 VLFRAVAKVRRKKHEFSALLVKEAGKPWNEAD-------ADTAEAIDFMEYYARQMIELA 153 V+ + ++ +A + + G P A A T+EA+ +L Sbjct: 72 VVRAISNGIAARRDAIAADITADVGAPITFATKVQAVLPAATSEAV----------ADLL 121 Query: 154 KGKPVNSREGERNQYVYT-PTGVTVVIPPWNF-LFAIMAGTTVAP-IVTGNTVVLKPASA 210 + RE N V P GV I PWN+ L IMA +AP + G TVVLKP+ Sbjct: 122 SSGEFSFREEIGNSLVEREPVGVVAAITPWNYPLHQIMA--KIAPALAAGCTVVLKPSEV 179 Query: 211 APVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSIITFTGSREVGTRIFER 270 AP+ V+VL E+G+P GVVN V G+G EVG L H +++FTGS G + Sbjct: 180 APLCTRHLVDVLTEAGVPAGVVNIVHGTGPEVGAALAGHEDVDMVSFTGSTRGGRAVSAA 239 Query: 271 AAKVQPGQTHLKQVIAEMGGKDTVVVDEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVH 330 AA +K+V E+GGK VV +D D+ A + +AF GQ C+A +R +V Sbjct: 240 AADT------IKRVALELGGKSANVVLDDADLGKAVKLGVANAFLNGGQSCNAWTRMLVP 293 Query: 331 EKVYDEVLKRVIEITESKKVGEPDSADVYMGPVIDQASFNKIMDYIEIGKEEGRLVSGG- 389 E ++DE + E + G+P +GP++ + +K++ +I G E G ++ G Sbjct: 294 ESLHDEAVSLACEAAAKYEPGDPTDGSTRLGPLVSETQRDKVVGFIRSGVESGATLAFGG 353 Query: 390 ---KGDDSKGYFIEPTIFADLDPKARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLT 446 D GYF+ PT+FA + P + QEEIFGPV+ S D+A+ +AN+T YGL Sbjct: 354 PERPDDRDTGYFVRPTVFAGVRPDVTVAQEEIFGPVLCVIPYSDEDDAVRIANSTVYGLA 413 Query: 447 GAVITKNRDHINRAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAG 498 GAV + + + + G + N GA PFGG+K SGT + G Sbjct: 414 GAVFSGSDERALSVARRMRTGQVDIN---GGAFNPLAPFGGYKQSGTGREFG 462 Lambda K H 0.315 0.133 0.382 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: 595 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: 516 Length of database: 477 Length adjustment: 34 Effective length of query: 482 Effective length of database: 443 Effective search space: 213526 Effective search space used: 213526 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 (21.6 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