Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >NCBI__GCF_000021485.1:WP_012607209.1 Length = 506 Score = 248 bits (632), Expect = 4e-70 Identities = 156/478 (32%), Positives = 239/478 (50%), Gaps = 20/478 (4%) Query: 14 FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 FI G WV GQ V P G+ + A + A++AA W + ERA Sbjct: 22 FIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIADKWGKTSPAERA 81 Query: 74 TKLRRWYELIIENQDDLARLMTLEQGKPLAEA-KGEIVYAASFIEWFAEEAKRIYGDVIP 132 L + + I N + LA T++ GKP+ E +I A +FA + G + Sbjct: 82 NILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEGGI-- 139 Query: 133 GHQPDKRLIV--IKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAF 190 D+ + +P+GV I PWNFP M + K PAL AG +VLKPA TP S Sbjct: 140 -SDIDENTVAYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPISIL 198 Query: 191 ALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIK 250 LAEL +P GV ++V+G + G L ++ + K++FTGST GR + A + Sbjct: 199 ILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAANSLI 257 Query: 251 KVSLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDA 304 +LELGG +P I F DD+ LDKA+EG ++ + N G+ C C +R IQ+ +YD Sbjct: 258 PATLELGGKSPNIFFADVMDKDDSFLDKAIEGLVLFAF-NQGEVCTCPSRALIQESIYDK 316 Query: 305 FAEKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGK----- 359 F E+ + +K GN L+ T G ++ + K+ ++ +GA VL GG Sbjct: 317 FMERCLDRIKAIKQGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEGAQVLIGGSQAIVD 376 Query: 360 -PMEGNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYA 418 ++G ++ L N + +EE FGP+ + FKDEA+ ++++NDT +GL + ++ Sbjct: 377 GDLDGGYYVQPTLFKGHNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGAGVWS 436 Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476 R+ +R+ A++ G V +N A FGG K SG+GRE K ++ Y + K L Sbjct: 437 RNGNVAYRMGRAIKAGRVWINCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQQTKNL 494 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: 576 Number of extensions: 28 Number of successful extensions: 7 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: 506 Length adjustment: 34 Effective length of query: 446 Effective length of database: 472 Effective search space: 210512 Effective search space used: 210512 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