Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_012049216.1 SWIT_RS15260 aldehyde dehydrogenase family protein
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_000016765.1:WP_012049216.1 Length = 478 Score = 255 bits (652), Expect = 2e-72 Identities = 163/466 (34%), Positives = 238/466 (51%), Gaps = 15/466 (3%) Query: 38 PLIINGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEER 97 P I GER+ + NP+ LV + + + L ++AI +A A W +PE R Sbjct: 6 PHRIGGERIAGPAAAERRNPSDLSDLVATTPEGDDALIDRAIAAAAAAQPGWAARSPEAR 65 Query: 98 ANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEI 157 +IL +AAA++ R + L E GK E A+ A Y+ + + L+ G+ + Sbjct: 66 GDILDRAAALLIERADDLGVLLAREEGKTCAEGRAEVVRAARIFRYFGGEALRLH-GRSL 124 Query: 158 LS-RPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAK 216 S RPG + P+GV I+PWNF +AI + GN VVLKPA TP + + Sbjct: 125 ASVRPGLEVSTRQEPLGVVGLITPWNFPIAIPAWKTAPALAFGNAVVLKPAGITPAIISA 184 Query: 217 FVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPG 276 + LEDAGLP G+ N V G+ G L++ + + ++FTGS VG RL AA Sbjct: 185 MADALEDAGLPPGLFNLVFAPGSVAG-RLIEDSRVAALSFTGSTGVGRRLAVAAA----- 238 Query: 277 QNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEV 336 H KRV +EMGGK+ +VV DADLD A L AF SGQ+C+A SR ++ ++D Sbjct: 239 -EHGKRVQLEMGGKNPLVVLDDADLDRAVAIALDGAFFGSGQRCTASSRLIVTDGIHDRF 297 Query: 337 LEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKE-GRLMTGGE--GDSS 393 + A L VG + D +GPV E+ + I +Y+ I ++ GR+ GGE + Sbjct: 298 VAALTEAAAKLRVGHALDPDTQIGPVASEEQRDTIEAYLSIAVEQGGRIACGGERLRRPT 357 Query: 394 TGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNR 453 G+F+ P +I E + +EEIFGPV + + DFD AL +AN + +GL+ ++T + Sbjct: 358 EGYFLAPALITGTTAEMRVNREEIFGPVASVVRVADFDEALAVANGSAFGLSAGIVTTSL 417 Query: 454 AHIEQAKREFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGG 498 AH + G + N G V YH PFGG K S + G Sbjct: 418 AHAGAFRARTQAGMVMVNAPTAG--VDYHVPFGGTKASSMGPREQG 461 Lambda K H 0.316 0.134 0.388 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: 575 Number of extensions: 30 Number of successful extensions: 3 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: 515 Length of database: 478 Length adjustment: 34 Effective length of query: 481 Effective length of database: 444 Effective search space: 213564 Effective search space used: 213564 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