Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_035245208.1 G494_RS0101615 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_000429965.1:WP_035245208.1 Length = 507 Score = 191 bits (485), Expect = 5e-53 Identities = 137/456 (30%), Positives = 222/456 (48%), Gaps = 19/456 (4%) Query: 64 VVGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERAAVLFRAVAKVRRKKHEFSALLVKE 123 V+G V ++ + A+ +A A+ +WR +R LF + K+ + + + + Sbjct: 31 VIGEVPMTSEKTSLAAVDSAHGAYASWRKLSVSKRVGFLFDMRQAMVNKEEQLAVSIALD 90 Query: 124 AGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGERN-QYVYTPTGVTVVIPPW 182 K +EA + I+ +E A + L +G+ ++ N + V GV + P+ Sbjct: 91 QAKHISEARGEVRRVIEIIEA-ACSIPTLIQGETLDGIAKNINGRVVKQALGVFGGVAPF 149 Query: 183 NFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNFVPGSGAEV 242 NF + I GNT + KP++ +P+ + + +E GLPKGVVN V G+ + Sbjct: 150 NFPALVFGWFIPYAIGVGNTFIYKPSTQSPLFMQEMGTIFQEIGLPKGVVNIVHGNRSIP 209 Query: 243 GDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTVVVDEDCDI 302 G + ++ K S + GS ++ E + K+ + G K+ +V ED + Sbjct: 210 GTWY-ENDKISGVCLVGSTNTAKKMAEACGRGG------KRSMLLGGAKNFLVAMEDVNW 262 Query: 303 ELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEVLKRVIEITESKKVGEPDSADVYMGP 362 ++ + S +G AGQ+C AGS ++YDE+++RVIE ++ VG+ DVYMGP Sbjct: 263 DVFIDNFIHSCYGSAGQRCLAGSVVAAVPEIYDELVERVIEASKKVSVGDAMDPDVYMGP 322 Query: 363 VIDQASFNKIMDYIEIGKEEG-RLVSGGKGDD-----SKGYFIEPTIFADLDPKARLMQE 416 VI + I +YIEIG E+G L G+ + GYF+ PT+F D+ P R+ QE Sbjct: 323 VISAKAKENIENYIEIGIEQGSTLALDGRNPEMPEKNKDGYFVGPTVFTDVTPCRRIAQE 382 Query: 417 EIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLYFNRNCT 476 EIFGPV A K+ D+ L++ ++G + T+N+ + + E VG + N Sbjct: 383 EIFGPVAAIMKIKDLDDVLQLIRQQKFGNGACIFTQNQYYTEKFIAEADVGMVGVNVGVC 442 Query: 477 GAIVGYHPFGGFKMS--GTDSKAGGPDYLALHMQAK 510 A Y PFGG K S GTD K G D + Q K Sbjct: 443 -APHPYLPFGGIKDSHLGTD-KVQGKDGIDFFTQNK 476 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: 581 Number of extensions: 27 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: 507 Length adjustment: 35 Effective length of query: 481 Effective length of database: 472 Effective search space: 227032 Effective search space used: 227032 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