Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 312 bits (799), Expect = 2e-89 Identities = 188/464 (40%), Positives = 259/464 (55%), Gaps = 10/464 (2%) Query: 14 YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73 YI G+W+ D I V NPAT VI VP+ + RA AA A PAW AL+ ER Sbjct: 8 YIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGAERG 67 Query: 74 AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPG 133 A L++ + + QD+L RL+ +E G P+ A A + I FA A RI + Sbjct: 68 AFLQKIADGLKARQDELGRLIASEVGMPVKLATR--VQAGNPIFTFAACA-RIAAEGFAE 124 Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193 + + L V+K P G A ITPWNFP I K G ALAAGCT+VLKP+ P +A L Sbjct: 125 ERIGQSL-VLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAFLLA 183 Query: 194 ELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVS 253 E+ AG+PAGV ++VTG VG L + + +SFTGST G+++ A +K+VS Sbjct: 184 EVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVS 243 Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAV 313 LELGG + +V DADL AV+G + + N+GQ C R+ V Y A A Sbjct: 244 LELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAA 303 Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGK-----LIEGNFFEP 368 A +G+ L EG+ GPL+ G +V+ IE AV+ GA++L GG L G + P Sbjct: 304 AAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGYYVRP 363 Query: 369 TILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVA 428 T+ V AA+A+EE FGP+ + ++DEAE A++N T++GLA+ ++ + +R A Sbjct: 364 TVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARALAFA 423 Query: 429 EALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLE 472 L G V IN G N +APFGG K SG GRE ++G+ED+LE Sbjct: 424 RRLRAGQVDIN-GAFFNLLAPFGGFKQSGYGRELGRHGVEDFLE 466 Lambda K H 0.317 0.134 0.384 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: 586 Number of extensions: 20 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: 480 Length of database: 476 Length adjustment: 34 Effective length of query: 446 Effective length of database: 442 Effective search space: 197132 Effective search space used: 197132 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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