Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25526 (482 letters) >NCBI__GCF_000745975.1:WP_035239838.1 Length = 484 Score = 660 bits (1703), Expect = 0.0 Identities = 314/480 (65%), Positives = 395/480 (82%) Query: 1 MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60 +K+ ++ LF + I EW+ A++G+ +DVTNPA G LG+VP GADET+ AI+AAN + Sbjct: 2 LKIKNTALFCRHCFIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANES 61 Query: 61 LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120 L AWR+ TA ER+ ILR W++L+ME+Q+DLA +MT EQGKPLAE++GEI+YAA+F EWFA Sbjct: 62 LDAWRSKTAGERSAILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFA 121 Query: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180 EE KR+YGD IP A +RL+VIKQP+GV AAITPWNFP+AMITRKAG ALAAGCTMVLK Sbjct: 122 EEAKRVYGDVIPQTVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLK 181 Query: 181 PASQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQ 240 PA+ TPFSALA+A+L +AGVP GVFNVVTGS+ A+G ELT+NP+VRKL+FTGST++G++ Sbjct: 182 PATATPFSALAIAKLGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKK 241 Query: 241 LMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDG 300 LM CA +K++S+ELGGNAPFIVFDDAD+D AVEGA+A K+RN+GQTCVCANR+YVQ G Sbjct: 242 LMRDCAGTMKRLSMELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAG 301 Query: 301 VYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKA 360 VYD F KL AV +L +G+G D+GV GPLID AV VE HI DA++KG +V+ GG Sbjct: 302 VYDEFCRKLTAAVQELKVGNGFDDGVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTR 361 Query: 361 HERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYA 420 H G FF PTI+ DV + +V++EETFGPLAP+F+F E +V+ +ANDTEFGLAAYFY Sbjct: 362 HALGRTFFAPTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYT 421 Query: 421 RDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCI 480 RD++R +R+GE LEYG+VGIN+GIISN VAPFGG+K SG GREGSKYG++DYLEIKYMC+ Sbjct: 422 RDMARSWRIGEKLEYGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 481 Lambda K H 0.318 0.135 0.395 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: 708 Number of extensions: 17 Number of successful extensions: 1 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: 482 Length of database: 484 Length adjustment: 34 Effective length of query: 448 Effective length of database: 450 Effective search space: 201600 Effective search space used: 201600 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 (21.7 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