Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >NCBI__GCF_000828635.1:WP_041097806.1 Length = 479 Score = 303 bits (776), Expect = 8e-87 Identities = 174/472 (36%), Positives = 267/472 (56%), Gaps = 13/472 (2%) Query: 10 RQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTA 69 R Q +IDG WV TI+V +P G +L TVP+ AA+ +A+ AA A AW A Sbjct: 4 RTQFYIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPA 63 Query: 70 KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGD 129 ERA L++ E + D++A+ +TLE G P ++ + S F +K + Sbjct: 64 AERAAYLKKIQESLKARADEIAKTITLEMGMPYKFSQR--IQVGSPTASFGMYSKMLAD- 120 Query: 130 VIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSA 189 P + V+++ +GV AAITPWN+P I K ALAAGCT+VLKP+ P +A Sbjct: 121 -FPFEEKVGNSKVVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNA 179 Query: 190 FALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDI 249 F LAE+ AG+PAGVF++++G +G + ++ V +SFTGST G ++ + + Sbjct: 180 FLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRVSELASATV 239 Query: 250 KKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKL 309 K+V+LELGG + I+ DDAD + AV+G + + Y N+GQTC R+ + Y A A KL Sbjct: 240 KRVALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRY-AEAAKL 298 Query: 310 KVAVAK-LKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM------E 362 V A+ ++G+ + G T GPL + +V+++I +++G +L GG + + Sbjct: 299 AVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPEGVNPD 358 Query: 363 GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLG 422 G + +PTI V ++++A+EE FGP+ + + DE D ++++N T +GLA ++ Sbjct: 359 GYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSATDE 418 Query: 423 RVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 +VA + G V +N G N APFGG K SG GRE KYG+ED+LE K Sbjct: 419 HAEQVARRMRTGQVEINGGTF-NMYAPFGGYKQSGNGRELGKYGLEDFLEFK 469 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: 569 Number of extensions: 27 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: 479 Length adjustment: 34 Effective length of query: 446 Effective length of database: 445 Effective search space: 198470 Effective search space used: 198470 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 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