Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate WP_043531966.1 JH15_RS15380 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25526 (482 letters) >NCBI__GCF_000759345.1:WP_043531966.1 Length = 483 Score = 679 bits (1751), Expect = 0.0 Identities = 325/481 (67%), Positives = 394/481 (81%) Query: 1 MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60 M LND LFRQ I+G W DA + I+VTNPA D+LG+VPK+ DE AAIDAA+RA Sbjct: 1 MNLNDPTLFRQHCYIDGCWADAEDKATIEVTNPATNDRLGTVPKLSKDEVSAAIDAADRA 60 Query: 61 LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120 LP W+A TAKERA+ILR WF+L MEHQ+DLA+++TLEQGKPL EA+GEI+Y ASFIEWF Sbjct: 61 LPLWKAKTAKERASILRRWFDLCMEHQEDLAQILTLEQGKPLQEARGEIAYGASFIEWFG 120 Query: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180 EE KR+YGD IP H D+R++V K+P+GV AAITPWNFP AMITRKA A+AAGCT+++K Sbjct: 121 EEAKRVYGDVIPAHAKDRRIVVTKEPVGVVAAITPWNFPNAMITRKAAAAMAAGCTVIVK 180 Query: 181 PASQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQ 240 PAS TP+SALALAELA RAGVP GV NVVTGSA VG ELT+NP VRKLSFTGSTE+G+ Sbjct: 181 PASSTPYSALALAELAERAGVPRGVLNVVTGSASVVGGELTANPRVRKLSFTGSTEVGKI 240 Query: 241 LMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDG 300 L+ +CAK +KKVS+ELGGNAPFI+F+DADLD+AV G +ASKFRN GQTCVCANR++V D Sbjct: 241 LLGECAKTVKKVSMELGGNAPFIIFEDADLDQAVAGVMASKFRNTGQTCVCANRIFVHDK 300 Query: 301 VYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKA 360 +YD F ++L AVS +G GL++GV++GPLI+ AV KVE+HI DA+ KGA V GGK Sbjct: 301 IYDDFTDRLATAVSAQKVGSGLEDGVSLGPLINPAAVEKVEQHIEDAIAKGASVYLGGKR 360 Query: 361 HERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYA 420 HE GNFFQPTIL +V +++ + +ETFGP+APL RF DE DVI QANDT GLA+YFY Sbjct: 361 HELQGNFFQPTILTNVSSDSMLMHDETFGPVAPLLRFTDEDDVIRQANDTTLGLASYFYT 420 Query: 421 RDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCI 480 RD+ RV+RV EALE GIVGIN GIIS+E+APFGG+K SG+GREGSKYGI+DY+EIKY+C+ Sbjct: 421 RDVGRVWRVAEALECGIVGINEGIISSELAPFGGVKESGIGREGSKYGIDDYIEIKYLCM 480 Query: 481 G 481 G Sbjct: 481 G 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: 704 Number of extensions: 18 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: 482 Length of database: 483 Length adjustment: 34 Effective length of query: 448 Effective length of database: 449 Effective search space: 201152 Effective search space used: 201152 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 Sep 24 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