Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate BWI76_RS05620 BWI76_RS05620 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS05620 BWI76_RS05620 NAD-dependent succinate-semialdehyde dehydrogenase Length = 482 Score = 787 bits (2033), Expect = 0.0 Identities = 392/482 (81%), Positives = 431/482 (89%), Gaps = 2/482 (0%) Query: 1 MQLKDAQLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKA 60 MQL D LFRQQA ING W DA +T+ VTNPA G+ +G VPKMG ETR AI+AA +A Sbjct: 1 MQLNDPTLFRQQAMINGRWRDASGKETLAVTNPANGQPLGNVPKMGAGETREAIDAAARA 60 Query: 61 LPAWRALTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFA 120 LPAWRALTAKERS+ LRRWFELM+E+QDDLARLMT EQGKPLAEAKGEI+YAASFIEWFA Sbjct: 61 LPAWRALTAKERSSILRRWFELMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120 Query: 121 EEAKRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180 EE KRIYGDTIPGHQ DKRL+VIKQPIGVTAAITPWNFP+AMITRKAGPALAAGCTMVLK Sbjct: 121 EEGKRIYGDTIPGHQADKRLLVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 Query: 181 PASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQ 240 PASQTP+SALAL ELA+RAGIP GV +VVTGSA EVGGELTGN LVRKLSFTGSTEIGRQ Sbjct: 181 PASQTPFSALALAELANRAGIPEGVFNVVTGSASEVGGELTGNPLVRKLSFTGSTEIGRQ 240 Query: 241 LMEECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDG 300 LME+CAKDIKKVSLELGGNAPFIVFDDADLDKAVEGA+ SK+RN GQTCVCANR+YVQD Sbjct: 241 LMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDS 300 Query: 301 VYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKL 360 VYD FAEKL AV+KL+IG+GL+ T GPLID KA+AKVQEHI DA+ KGA+V++GGK Sbjct: 301 VYDRFAEKLQQAVSKLQIGDGLQPNVTIGPLIDEKAIAKVQEHIADALGKGARVVTGGKA 360 Query: 361 IE--GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418 E GNFF+PTILVDVP A VAKEETFGPLAPLFRFKDEA+VIA +NDTEFGLA+YFYA Sbjct: 361 HELGGNFFQPTILVDVPGDAKVAKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYA 420 Query: 419 RDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCI 478 RD+ RVFRV EALEYG++GINTGLIS EVAPFGG+K+SGLGREGSKYGIEDYLEIKY+CI Sbjct: 421 RDLGRVFRVGEALEYGIIGINTGLISTEVAPFGGVKSSGLGREGSKYGIEDYLEIKYMCI 480 Query: 479 SV 480 + Sbjct: 481 GI 482 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: 807 Number of extensions: 22 Number of successful extensions: 2 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: 482 Length adjustment: 34 Effective length of query: 446 Effective length of database: 448 Effective search space: 199808 Effective search space used: 199808 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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