Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 276 bits (705), Expect = 2e-78 Identities = 174/487 (35%), Positives = 256/487 (52%), Gaps = 32/487 (6%) Query: 14 YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73 +I G+W+ A GQT + +P G VI TV + + A++AA A AW + ERS Sbjct: 22 FIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAARGAWGRTSPAERS 81 Query: 74 AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG-EIAYAASFIEWFAEEAKRIYG---- 128 L R + + + D LA + T + GKP+ E K ++ A +FA + G Sbjct: 82 LALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEGGISE 141 Query: 129 ---DTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQT 185 DT+ H +P+GV A I PWNFP M K PALAAG ++LKPA QT Sbjct: 142 IDHDTVAYH--------FHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQT 193 Query: 186 PYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEEC 245 P S + LV++ +P GVL+V+ G E G L N + K++FTG T GR +M+ Sbjct: 194 PMSVMVLVDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLIMQYA 252 Query: 246 AKDIKKVSLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRIYVQD 299 +++I V+LELGG +P I F DD DKA+EG + N G+ C C +R VQ+ Sbjct: 253 SENIIPVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFAL-NQGEVCTCPSRALVQE 311 Query: 300 GVYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGG- 358 +YD F E+ A V K+K GN L+ T G + K+ +++ +GAKVL+GG Sbjct: 312 KIYDRFMERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGGG 371 Query: 359 ------KLIEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGL 412 +L G + +PTIL K + +EE FGP+ + FKD+ E + ++NDT +GL Sbjct: 372 RADVGPELAGGFYVQPTILEGHNKMR-IFQEEIFGPVLSVTSFKDDEEALEIANDTLYGL 430 Query: 413 ASYFYARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLE 472 + + R+ +R +R A+E G V N + A FGG K SG+GRE K ++ Y + Sbjct: 431 GAGVWTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQK 490 Query: 473 IKYLCIS 479 K + +S Sbjct: 491 TKNMLVS 497 Lambda K H 0.317 0.134 0.384 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: 556 Number of extensions: 29 Number of successful extensions: 5 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 (21.6 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