Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_022949182.1 H035_RS0111795 aldehyde dehydrogenase family protein
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_000421465.1:WP_022949182.1 Length = 506 Score = 252 bits (644), Expect = 2e-71 Identities = 166/491 (33%), Positives = 246/491 (50%), Gaps = 32/491 (6%) Query: 10 RQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTA 69 R YI G W+ NGQ + P TG V + + +A++AA A AW + Sbjct: 18 RYNNYIGGHWIAPVNGQYFENITPVTGTPFCEVARSTAEDIEKALDAAHAAKDAWGKTSP 77 Query: 70 KERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAK---- 124 R+ L + + M + + LA T + GKP+ E +I AA +FA + Sbjct: 78 AGRADLLLKIADRMEQQLEMLAVAETWDNGKPIRETLAADIPLAADHFRYFASAIRTQES 137 Query: 125 ---RIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181 I DTI H +P+GV I PWNFP M + K PALAAG +VLKP Sbjct: 138 SVCEIDADTIAYH--------FHEPLGVVGQIIPWNFPLLMASWKLAPALAAGNCVVLKP 189 Query: 182 ASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQL 241 A QTP S L L+EL IP GV++VV G E G L +S + K++FTG T GR + Sbjct: 190 AEQTPASILVLMELIGDL-IPPGVVNVVNGFGVEAGKPLARSSRIAKVAFTGETTTGRLI 248 Query: 242 MEECAKDIKKVSLELGGNAPFIVFDDAD------LDKAVEGAIISKYRNNGQTCVCANRI 295 M+ ++++ V+LELGG +P + F+D +DKA+EG S N G+ C C +R Sbjct: 249 MQYASQNLIPVTLELGGKSPNLFFEDVTAKQDTFVDKALEG-FASFALNQGEVCTCPSRA 307 Query: 296 YVQDGVYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVL 355 +Q +YD F + V ++ GN L+ T G + + K+ +I+ A +G + L Sbjct: 308 LLQASIYDDFIHRALERVKAIRQGNPLDTETMIGAQASAEQMEKILSYIDIARQEGTECL 367 Query: 356 SGGK-------LIEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDT 408 GG+ L G + +PTI V +EE FGP+ + F+DE E + ++NDT Sbjct: 368 IGGERAQLQGELAGGYYIQPTIFKG-HNQMRVFQEEIFGPVLAVTTFRDEEEALEIANDT 426 Query: 409 EFGLASYFYARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIE 468 +GL + + RDM+ +R+ ++ G V N + A FGG K SG+GRE K ++ Sbjct: 427 LYGLGAGVWTRDMNTAYRMGRGIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRETHKMMLD 486 Query: 469 DYLEIKYLCIS 479 Y + K L +S Sbjct: 487 HYQQTKNLLVS 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: 563 Number of extensions: 28 Number of successful extensions: 6 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 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