Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_028310075.1 H566_RS0101815 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000482785.1:WP_028310075.1 Length = 507 Score = 335 bits (858), Expect = 3e-96 Identities = 193/481 (40%), Positives = 277/481 (57%), Gaps = 16/481 (3%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FING++ + + F+ + P+ K AR + DI+ A+ AA + W+ +S A+ Sbjct: 23 FINGQFVPPVDGQYFDVISPINGKVFTKAARSNAADIELALDAAHAAQVK--WARTSHAE 80 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R +L K+AD +E + E LA ET+D GKPIR +L DIP A R++A + G + Sbjct: 81 RANILLKIADRLEQNLERLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGVLRAQEGTL 140 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 + + +A EP+GV+ I+PWNFP+L+ WKL PAL AGNSV+LKP+E +P+S + Sbjct: 141 SQIDENTVAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALGAGNSVVLKPAESTPISILV 200 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 L L + LP GVLNVV GFG +AG L+ I IAFTGST TG+ ++ A +N+ Sbjct: 201 LVELIADL-LPPGVLNVVNGFGRDAGMPLATSKRIAKIAFTGSTATGR-VIAQAAANNLI 258 Query: 263 RVWLEAGGKSANIVFADCPDLQQA----ASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318 LE GGKS NI F D A A +NQG+VC + TR L++ESI D F Sbjct: 259 PATLELGGKSPNIFFEDVMAADDAFLDKAIEGMVLFAFNQGEVCTSPTRALIQESIYDRF 318 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLDGRNAGLAA 377 + + ++ + G+PLD T +G D + S+I G+ +G QLL+ G L+ Sbjct: 319 IERVLKRVAAIKQGNPLDTETQIGAQASAVQQDKILSYIGIGKEEGAQLLIGGSKPELSG 378 Query: 378 AIG------PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431 + PT+F + + +EEIFGPVL VT F + +AL +AND+ YGLGA VWT Sbjct: 379 DLAGGYYVQPTLFKGHN-KLRIFQEEIFGPVLSVTTFKDDAEALSIANDTVYGLGAGVWT 437 Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 RD SRA+R R ++AG V+VNNY+ FGGYK+SG GR+ L+ + + K + + Sbjct: 438 RDGSRAYRFGRDIQAGRVWVNNYHAYPAHAAFGGYKESGIGRETHKIILDHYQQTKNMLV 497 Query: 492 S 492 S Sbjct: 498 S 498 Lambda K H 0.317 0.133 0.389 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: 568 Number of extensions: 24 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: 495 Length of database: 507 Length adjustment: 34 Effective length of query: 461 Effective length of database: 473 Effective search space: 218053 Effective search space used: 218053 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 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