Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= BRENDA::Q9RW56 (523 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 214 bits (546), Expect = 4e-60 Identities = 157/473 (33%), Positives = 225/473 (47%), Gaps = 23/473 (4%) Query: 38 KHYPLIIDGQEVDTEGK--IQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKW 95 +H I GQ V +G I NP T V+ + T DA+ A + A AF +W Sbjct: 3 QHSRFYIGGQWVAPDGNAFIDVENPA-TETVIARVPEGTATDADRAARAAAAAFPAWAAL 61 Query: 96 DMDARARILLKAAAILKRRRLEACALMSIEVGKNYAEAD-VEVAEAIDFLEYYARSAMKY 154 R L K A LK R+ E L++ EVG A V+ I AR A + Sbjct: 62 SGAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAE- 120 Query: 155 AGFGSSETTWFEGEENGLMSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAED 214 GF ++ ++ +P G I+PWNFP A + AG VV+KP+E Sbjct: 121 -GFAEERIG-----QSLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEV 174 Query: 215 AGLIAGFMVDILREAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEV 274 A L A + +++ AGLPAGV + G G VGE L H ++FTGS A G + V Sbjct: 175 APLNAFLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAV 234 Query: 275 AAKVQPGQKWIKRVIMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVV 334 AA +KRV +ELGGK +V AD+ A+ G F +GQ CSA++RL+V Sbjct: 235 AAAT------VKRVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVP 288 Query: 335 DSVYDEVVNGFVERAKALKMGTG-EENANVTAVVNQMSFNKIKGYLELAPSEGKVLLGGE 393 Y E V+ A A +G E + + +V+ + +++ +E A ++G LL G Sbjct: 289 QERYAEAAALAVQAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGG 348 Query: 394 ATGEANGKQGYYIQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLT 453 + GYY++PT+ G V ++ LA+EE+FGPV+A+L +D +A IAN T+YGL Sbjct: 349 SAAPEGLPTGYYVRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLA 408 Query: 454 GGVCSNSRERLEQARAEFEVGNLYFNRKITGAIVG-VQPFGGYNMSGTDSKAG 505 V S R G + I GA + PFGG+ SG + G Sbjct: 409 AAVWSAEEARALAFARRLRAGQV----DINGAFFNLLAPFGGFKQSGYGRELG 457 Lambda K H 0.317 0.134 0.391 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: 561 Number of extensions: 25 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: 523 Length of database: 476 Length adjustment: 34 Effective length of query: 489 Effective length of database: 442 Effective search space: 216138 Effective search space used: 216138 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 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