Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Pf6N2E2_1764 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1764 Length = 502 Score = 248 bits (632), Expect = 5e-70 Identities = 153/466 (32%), Positives = 234/466 (50%), Gaps = 19/466 (4%) Query: 41 INGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQ---TWRNVNPEER 97 ING + + +PA + L G + +A+ D+ A+ +A AF+ WR + P ER Sbjct: 29 INGHWLRAGATFEIIDPATELPL-GELDEADADIVGLAVDAARSAFEDRSAWRTMGPSER 87 Query: 98 ANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADA-DTAEAIDFLEYYARQMIELNRGKE 156 IL K A + + + E G P A A + A+ ID YYA +L G Sbjct: 88 ERILHKLADELEADSDVLADLIAAELGLPRGAALAFEVAKVIDVFRYYAGFPSKLT-GDT 146 Query: 157 ILSRPGEQNRYFYT-----PMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTP 211 I P + F+ P+GV I PWN L + + G T+V+KPA Sbjct: 147 IEIDPAMDDAEFFAYTTHEPVGVVGAILPWNAPLLVGSWKIAPALAAGCTLVVKPAEDVS 206 Query: 212 VVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAA 271 +V + E+ AGLP GV+N V G GA G L++H FTGS D+G R+Y+ AA Sbjct: 207 LVILRLAELASKAGLPDGVLNVVTGRGAVTGQALIEHTGIDKFAFTGSTDIGKRIYKAAA 266 Query: 272 VVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKD 331 + L RV +E+GGK+ V+V DAD+ A ++ ++AF SGQ C +GS+ + H Sbjct: 267 ------DRLVRVSLELGGKNPVIVLADADVKAIAPALCMAAFANSGQICVSGSKVMAHAS 320 Query: 332 VYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTGGEGD 391 + +E+L + AK L G P + + +GPV +K F+++M+YI G+ EG ++ G Sbjct: 321 IANELLGAMASFAKTLVPGSPFDPETVIGPVCSKKQFDRVMAYIRQGETEGNVIIGQRQS 380 Query: 392 SSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITR 451 +S GF+I PTII DL ++ ++ EEIFGPV+ D + +++ N + YGL + Sbjct: 381 TSPGFYINPTIITDLPAQSKLLSEEIFGPVITVETWTDEQNVIDLTNRSAYGLCATIWGS 440 Query: 452 NRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAG 497 N HI++ + G ++ N P GGF+ SG G Sbjct: 441 NHGHIQRLAKRLRTGTVFINSPAFPP--ANIPTGGFRQSGVGRDLG 484 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: 612 Number of extensions: 33 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: 502 Length adjustment: 34 Effective length of query: 481 Effective length of database: 468 Effective search space: 225108 Effective search space used: 225108 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 17 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