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) >FitnessBrowser__Koxy:BWI76_RS05620 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:
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