Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_013074996.1 BTUS_RS04875 aldehyde dehydrogenase
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_000092905.1:WP_013074996.1 Length = 478 Score = 242 bits (617), Expect = 3e-68 Identities = 145/464 (31%), Positives = 238/464 (51%), Gaps = 17/464 (3%) Query: 42 IDGERYETEN--KIVSINPANKEEVVGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERA 99 IDG E+EN + V++NPA + V+G V++ + ++A+ AA +AF W +R+ Sbjct: 8 IDGRFVESENGRRFVNVNPATGD-VLGEVAEGGKPEIDRAVAAARRAFGEWGRMPVAKRS 66 Query: 100 AVLFRAVAKVRRKKHEFSALLVKEAGKPWN-EADADTAEAIDFMEYYARQMIELAKGKPV 158 A+L R + + E + L + GKP + D A ++A + L + Sbjct: 67 AILNRIADLIEERSEELARLETLDTGKPLSLSRTLDIPRAAYNFRFFAAFVKGLGT-EAF 125 Query: 159 NSREGERNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKF 218 + N + P GV +I PWN ++ + GNT V+KPA P+ A K Sbjct: 126 QMDDVALNYVLRRPVGVAGLISPWNLPLLLLTWKVAPCLAAGNTCVIKPAELTPMTATKL 185 Query: 219 VEVLEESGLPKGVVNFVPGSGAEV-GDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPG 277 E+ +E+GLP GV+N V G G + G L +HP ++I+ TG G + AA Sbjct: 186 AEICQEAGLPDGVLNVVHGFGPDAAGSALTEHPDVNLISLTGETTTGKAVMRAAA----- 240 Query: 278 QTHLKQVIAEMGGKDTVVVDEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEV 337 T+LK+V E+GGK+ ++ D D++ A ++ S+F G+ C GSR V +YDE Sbjct: 241 -TNLKRVAFELGGKNPNIIFADADLDDAVETTVRSSFSNQGEVCLCGSRVYVERPIYDEF 299 Query: 338 LKRVIEITESKKVGEPDSADVYMGPVIDQASFNKIMDYIEIG-KEEGRLVSGGKGDD--S 394 L+R++E + VG+P +G +I + +++ +IE KE GR++ GG+ + + Sbjct: 300 LRRMVEKAKGLVVGDPFDEKTNVGALISEEHLHRVEGFIERAVKEGGRILVGGRRPEHMT 359 Query: 395 KGYFIEPTIFADLDPKARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNR 454 +GY++EPTI D+D + ++Q+E+FGPV+ S +E +E AN+T YGL+ + T N Sbjct: 360 RGYYLEPTIIVDVDRRCEIVQQEVFGPVITVQPFDSEEEVIEQANDTHYGLSATIWTTNL 419 Query: 455 DHINRAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAG 498 +R G ++ N + PFGG K SG + G Sbjct: 420 KRAHRVAARLEAGIIWINTWFLRDL--RTPFGGMKQSGIGREGG 461 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: 573 Number of extensions: 41 Number of successful extensions: 6 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: 478 Length adjustment: 34 Effective length of query: 482 Effective length of database: 444 Effective search space: 214008 Effective search space used: 214008 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