Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_012756139.1 RLEG_RS02225 aldehyde dehydrogenase
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_000023185.1:WP_012756139.1 Length = 486 Score = 262 bits (670), Expect = 2e-74 Identities = 171/470 (36%), Positives = 246/470 (52%), Gaps = 15/470 (3%) Query: 49 TENKIVSINPANKEEVVGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERAAVLFRAVAK 108 +E + NP + E++ V+ ++QD E+AI AA AF W P +R +L VA Sbjct: 19 SEGWLEKFNP-HSGELLYHVADSSQDDVEQAITAARSAFPAWAELTPVKRGQILMDIVAL 77 Query: 109 VRRKKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGERNQY 168 ++R+ E + + E GKP +A +T AI EY+A + + L + G+ + Sbjct: 78 MKRRSDELAECIALETGKPPQDAKGETGGAIMQAEYFAGEGMRLYARSLTSGTPGKYSHT 137 Query: 169 VYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFVEVLEESGLP 228 V P GV +I P N A +A T ++ GNTVVLK A +P IA F E+ +E+GLP Sbjct: 138 VRQPRGVAGLIVPANTPIANIAWKTFPALICGNTVVLKAAEDSPRIAQLFAELTKEAGLP 197 Query: 229 KGVVNFVPGSGAEVGDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQTHLKQVIAEM 288 GV N V G G G LV + II+FTGS VG RI E A K L ++ E+ Sbjct: 198 DGVFNVVHGRGEPAGSTLVTDERVDIISFTGSTGVGRRIAEVAGK------RLARISLEL 251 Query: 289 GGKDTVVVDEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEVLKRVIEITESK 348 GGK+ VV +D D++ A SAF AGQ+C+AGSR +V + VY+E R+ S Sbjct: 252 GGKNPFVVCDDADLDQAVHWAALSAFSNAGQRCAAGSRMLVFKSVYEEFRDRLTAKARSL 311 Query: 349 KVGEPDSADVYMGPVIDQASFNKIMDYIEIGKEE-GRLVSGGKGDDSK----GYFIEPTI 403 K+G D +GP++ ++ IE KE+ G+++ GG+ D+ GY++EPT+ Sbjct: 312 KLGVAAGCD--LGPLVSLRQQQSVLSAIERAKEQGGQVLCGGRTPDAPELAGGYYVEPTV 369 Query: 404 FADLDPKARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHINRAKQE 463 L + L +E+FGPV V S EAL+VAN TEYGLT AV T+N D Q Sbjct: 370 IDGLATTSDLSCKEVFGPVTTLHPVGSMTEALDVANATEYGLTAAVHTRNVDRAMWFAQR 429 Query: 464 FHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTIS 513 G N G+ + PFGGF SG ++ G + L ++ + K IS Sbjct: 430 VKAGVANVNMGTYGS-EPHMPFGGFGSSGNGTREPGVEALDVYSELKNIS 478 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: 557 Number of extensions: 33 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: 486 Length adjustment: 34 Effective length of query: 482 Effective length of database: 452 Effective search space: 217864 Effective search space used: 217864 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