Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_012568883.1 RC1_RS18020 aldehyde dehydrogenase
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_000016185.1:WP_012568883.1 Length = 490 Score = 235 bits (600), Expect = 2e-66 Identities = 150/445 (33%), Positives = 231/445 (51%), Gaps = 14/445 (3%) Query: 74 DHAEKAIQAAAKAFETWRYTDPEERAAVLFRAVAKVRRKKHEFSALLVKEAGKPWNEADA 133 D + A+ AAA A W P R +L VA +R + + L+ E GKP +A Sbjct: 47 DDVDAAVAAAAAAQPAWAALTPVRRGEILREVVAALRAARDGLADLVALETGKPPKDARG 106 Query: 134 DTAEAIDFMEYYARQMIELAKGKPVNSREGERNQYVYTPTGVTVVIPPWNFLFAIMAGTT 193 +TA A+ +++A + + L ++ G + V P G+ +I P N A +A Sbjct: 107 ETAGALLQGDFWAGEGLRLYGRTLSSAMPGRYSGTVRQPIGIAGLIVPANTPIANIAWKV 166 Query: 194 VAPIVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTS 253 ++ GN VLK + AP++A + + E +GLP GV+N V G GAE G LV HP Sbjct: 167 FPALLCGNAAVLKASEDAPLLALRIARIAEAAGLPPGVLNVVQGLGAEAGAALVGHPDVG 226 Query: 254 IITFTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTVVVDEDCDIELAAQSIFTSA 313 +++FTGS VG I E A + L +V E+GGK+ VV +D D++ A SA Sbjct: 227 VVSFTGSTAVGRWIAEAAGR------RLARVSLELGGKNAFVVCDDADLDKAVHWAVLSA 280 Query: 314 FGFAGQKCSAGSRAVVHEKVYDEVLKRVIEITESKKVGEPDSADVYMGPVIDQASFNKIM 373 F AGQ+C+AGSR +V ++VY+ R +E S ++G D+ D +GPVI+ ++ Sbjct: 281 FSNAGQRCAAGSRLIVMDRVYEAFRDRFVERARSLRLGVTDADD--LGPVINARQLATML 338 Query: 374 DYIEIGKEEG-RLVSGGK----GDDSKGYFIEPTIFADLDPKARLMQEEIFGPVVAFSKV 428 ++ ++ G R+++GG + G ++ PT+ LDP L E+FGP+ A +V Sbjct: 339 ARLDDARQAGARVLTGGHRLTGPGHATGCYLAPTVLEGLDPGHPLSDCELFGPITALYRV 398 Query: 429 SSFDEALEVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLYFNRNCTGAIVGYHPFGGF 488 + F AL++AN T YGLT A+ T++ D Q G N G+ PFGGF Sbjct: 399 ADFQGALDLANRTAYGLTAAIHTRSLDRALTFCQRVRAGVANANIGTFGS-EPQMPFGGF 457 Query: 489 KMSGTDSKAGGPDYLALHMQAKTIS 513 +SG S+ G + L ++ + KTIS Sbjct: 458 GLSGNGSREPGTEALDVYSELKTIS 482 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: 559 Number of extensions: 26 Number of successful extensions: 4 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: 490 Length adjustment: 34 Effective length of query: 482 Effective length of database: 456 Effective search space: 219792 Effective search space used: 219792 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