Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_029134199.1 A3GO_RS0115615 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >NCBI__GCF_000428045.1:WP_029134199.1 Length = 454 Score = 288 bits (738), Expect = 2e-82 Identities = 165/445 (37%), Positives = 248/445 (55%), Gaps = 4/445 (0%) Query: 32 NPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERATKLRRWYELIIENQDDLA 91 NPATG + + ++ A + A A W ALT +RA LR + + LA Sbjct: 7 NPATGHEIQSYEQLSADDLSTLCVNASHAQGDWMALTIDQRAALLREVARQLETGKRQLA 66 Query: 92 RLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIPGHQPDKRLIVIKQPIGVTA 151 +L+T E GK + EA+ E+ A ++A+ A + D + + ++V KQP+G+ Sbjct: 67 KLITSEMGKLIGEAESEVEKCAWVCHYYADTANQFLADEVIESDASRSMLV-KQPLGLVL 125 Query: 152 AITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFALAELAQRAGIPAGVFSVVSG 211 AI PWNFP + R A PAL AG ++LK AS P A L +L Q AG P+ VFS + Sbjct: 126 AIMPWNFPFWQVFRCAAPALMAGNGVLLKHASNVPGCALMLEQLFQDAGFPSSVFSTLLI 185 Query: 212 SAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKVSLELGGNAPFIVFDDADLD 271 S+G + ++L ++ + +S TGS GR + S K++KK+ LELGG+ F+V DDADLD Sbjct: 186 SSGQV-ADLVADAQIHAISLTGSEAAGRSVASVAGKNLKKLVLELGGSDAFVVLDDADLD 244 Query: 272 KAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVAVAKLKIGNGLEAGTTTGPL 331 AV+ A+ S++ N GQ+C+ A R + DG+ D F EK A+ L++G+ L+A TT GP+ Sbjct: 245 AAVKAAVQSRFLNCGQSCIAAKRFVVVDGIGDRFVEKFHAAINNLRVGDPLDAETTLGPM 304 Query: 332 IDEKAVAKVQEHIADALSKGATVLAGGK--PMEGNFFEPTILTNVPNNAAVAKEETFGPL 389 + + + D++ +GA +LAGG+ P G F+ T+L V +EE FGP+ Sbjct: 305 ARDDLRETLHRQVTDSIDQGALLLAGGQFLPRPGWFYAATLLDQVTPGMPAYEEELFGPV 364 Query: 390 APLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAEALEYGMVGVNTGLISNEVAP 449 A + R DE D + ++ND+ FGL + D R A + G VN + S+ P Sbjct: 365 AAVIRATDEQDALRIANDSRFGLGGSVWTGDAARGEEFARRMACGSAFVNGLVKSDPRLP 424 Query: 450 FGGIKASGLGREGSKYGIEDYLEIK 474 FGGIK SG GRE S+ GI++++ K Sbjct: 425 FGGIKHSGYGRELSRLGIQEFINAK 449 Lambda K H 0.317 0.135 0.390 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: 438 Number of extensions: 22 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: 480 Length of database: 454 Length adjustment: 33 Effective length of query: 447 Effective length of database: 421 Effective search space: 188187 Effective search space used: 188187 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: 51 (24.3 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