Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_036264374.1 DL86_RS17780 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::Burk376:H281DRAFT_01117 (795 letters) >NCBI__GCF_000746085.1:WP_036264374.1 Length = 1033 Score = 143 bits (360), Expect = 5e-38 Identities = 155/507 (30%), Positives = 221/507 (43%), Gaps = 52/507 (10%) Query: 14 PAPEDDQPARQWLAQHEARFGHFIGGAWHAPASGAQFVSHAP-ASGERLADIAQGDAADI 72 P PED P R+ E IG A A A AP SG A+ A+ I Sbjct: 504 PLPEDLHPGRKTAKGVEFGDRQEIGALMAAIAREAGAFEAAPIVSGAAREGAARAIASPI 563 Query: 73 D-AALAAARAAQPGWL------ALGGKG---------RARHLYALARMVQRHSRLFAVLE 116 D +++ R A PG L A GG RA L A+ ++ + + L Sbjct: 564 DGSSIGLVREAAPGLLQEAMREARGGFKIWSRTPVGLRAACLDRAAQELEAQAPRWLHLL 623 Query: 117 ALDNGKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFADHAPL---------------GV 161 ++ GK + + + A F + +AQ FA AP+ GV Sbjct: 624 QIEAGKTLEDA--IGEWREAIDFCRY--YAQEARRRFASPAPMPGPTGEDNRLFCHGRGV 679 Query: 162 IGQIVPWNFPLLMLAWKIAPAIATGNCVVLKPAEYTPLTALLFAELAHQAGLPAGVLNVV 221 I PWNFPL + +IA A+A GN V+ KPAE TPL A L ++AG+PA VL+++ Sbjct: 680 FVCISPWNFPLSIFLGQIAAALAAGNSVLAKPAEQTPLIAAQAVSLLYRAGVPASVLHLL 739 Query: 222 TGDGSTGAALVEHPQVDKIAFTGSTEVG-KLIRSVTAGSG--KSLTLELGGKSPFIVFDD 278 GDG GAALV V +A TGS + K+ RS+ A SG L E GG + I Sbjct: 740 PGDGDVGAALVALDGVAGVAITGSMDTATKINRSLAAKSGPIAQLIAETGGVNAMIADAT 799 Query: 279 ADLDGAVEGVVDAIWFNQGQVCCAGSRLLVQEGIEARFIAKLKRRMETLRVGPSLDKSID 338 A + + VV + + + GQ C A L +QE + R IA +K L VG + Sbjct: 800 ALPEQVCDDVVASAFRSAGQRCSALRLLCLQEDVADRMIAMIKGAARELLVGDPRALGVH 859 Query: 339 MGAIVDPVQLERIHSLVETGRREGCAIWQ---AADTPLPANGCFYPPTLVTNVAPASTLA 395 +G ++D + + +E R CAI A + P G FY + ++ S L Sbjct: 860 VGPVIDLAAKRSLEAHIEDMR--ACAIVHYAGRAPSTAPPRG-FYLAPHIFELSSVSDL- 915 Query: 396 QEEIFGPVLVTMSFRTPDEAIAL--ANNSRYGLAASVWSETIGRALDVAPRLAAGVVWVN 453 + E FGP+L ++ + L + +GL V S ++ R AG +VN Sbjct: 916 RREAFGPILHVARYKASELGGLLDSIEAAGFGLTLGVHSRIDAVIDEIVERRLAGNCYVN 975 Query: 454 ATNLFDAAVG---FGGYRESGYGREGG 477 N+ A VG FGG+ SG G + G Sbjct: 976 -RNMIGAVVGTQPFGGFGLSGTGPKAG 1001 Score = 59.3 bits (142), Expect = 1e-12 Identities = 61/210 (29%), Positives = 87/210 (41%), Gaps = 4/210 (1%) Query: 544 DGTRVGEVGEGNRKDIRNAVQAARAAQK-WSQASTHNRAQVLFYLAENLAVRADEFAHQL 602 DG+ +G V E ++ A++ AR K WS+ RA L A+ L +A + H L Sbjct: 564 DGSSIGLVREAAPGLLQEAMREARGGFKIWSRTPVGLRAACLDRAAQELEAQAPRWLHLL 623 Query: 603 TVRNGATDAAAHAEVEASVTRLFTYAAWADK-FDGAVHTPPLRGVALAMH-EPLGVIGIA 660 + G T A E ++ YA A + F P G + GV Sbjct: 624 QIEAGKTLEDAIGEWREAIDFCRYYAQEARRRFASPAPMPGPTGEDNRLFCHGRGVFVCI 683 Query: 661 CPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIVTGKR 720 P PL F+ A ALA GN V+ P E PL ++ + VP V++++ G Sbjct: 684 SPWNFPLSIFLGQIAAALAAGNSVLAKPAEQTPLIAAQAVSLLYRAGVPASVLHLLPGDG 743 Query: 721 EALLPALARHDDVDAVWCFGSAADATLIER 750 + + AL D V V GS AT I R Sbjct: 744 D-VGAALVALDGVAGVAITGSMDTATKINR 772 Lambda K H 0.320 0.135 0.411 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: 1706 Number of extensions: 98 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 795 Length of database: 1033 Length adjustment: 43 Effective length of query: 752 Effective length of database: 990 Effective search space: 744480 Effective search space used: 744480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (26.2 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