Align Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized)
to candidate WP_029134950.1 A3GO_RS0120300 phenylacetaldehyde dehydrogenase
Query= SwissProt::P94358 (485 letters) >NCBI__GCF_000428045.1:WP_029134950.1 Length = 480 Score = 345 bits (886), Expect = 2e-99 Identities = 194/476 (40%), Positives = 273/476 (57%), Gaps = 2/476 (0%) Query: 10 FINGKWTGGESGRTEDILNPYDQSVITTASLATGKQLEDAFDIAQKAQKEWAKSTTEDRK 69 FING+W + G D +NP V A K +E A A A W K+ R+ Sbjct: 7 FINGEWVETQDGEVLDDINPSTGEVFARVHQAGPKDVEHAITAASAASVAWGKTQPAVRE 66 Query: 70 AVLQKARGYLHENRDDIIMMIARETGGTIIKSTIELEQTIAILDEAMTYTGELGGVKEVP 129 +L KA L +I ++ E G T K+ E + +L A + G + +P Sbjct: 67 EILIKAADCLQARIHEIADVLIDEAGSTFGKAMFEASFVVNLLRSAAGEARRIFG-ETMP 125 Query: 130 SDIEGKTNKIYRLPLGVISSISPFNFPMNLSMRSIAPAIALGNSVVHKPDIQTAISGGTI 189 SD + R PLGVI+ I+PFNFP L+ + +A AIA GN+ V KP +TA++G Sbjct: 126 SDGPDIFSMSVRRPLGVIAGIAPFNFPFLLACKKVALAIAAGNAFVLKPSEETAVTG-LK 184 Query: 190 IAKAFEHAGLPAGVLNVMLTDVKEIGDGMLTNPIPRLISFTGSTAVGRHIGEIAGRAFKR 249 IA+ FE AGLP GVLNV+ E+G ++ +P ++I+FTGST VG+ + A + K+ Sbjct: 185 IAEIFEQAGLPKGVLNVIPGSGPEVGGRLVDDPRVKMITFTGSTVVGKKLAVQAAQQLKK 244 Query: 250 MALELGGNNPFAVLSDADVDRAVDAAIFGKFIHQGQICMIINRIIVHQDVYDEFVEKFTA 309 + LELGG +P VL+DAD+D AVDAA FG F+HQGQ+CM +++IV VYD F +KF A Sbjct: 245 ITLELGGKSPLIVLADADLDYAVDAACFGIFLHQGQVCMANSKLIVEAAVYDAFCDKFAA 304 Query: 310 RVKQLPYGDQTDPKTVVGPLINERQIEKALEIIEQAKTDGIELAVEGKRVGNVLTPYVFV 369 +VK L GD P TV+GPLI Q + ++ A G L G N P V Sbjct: 305 KVKSLKVGDPRQPNTVIGPLIRGAQCQVIDRHVQDALDKGARLLTGGSSESNFYQPTVMA 364 Query: 370 GADNNSKIAQTELFAPIATIIKAGSDQEAIDMANDTEYGLSSAVFTSDLEKGEKFALQID 429 + +I + E F P+ +IIKA + A+ +AND+EYGLSSAV T+DL+K + +L+++ Sbjct: 365 DVGPDMQIYREESFGPVVSIIKADDHEAALYIANDSEYGLSSAVITNDLQKAMELSLRLE 424 Query: 430 SGMTHVNDQSVNDSPNIAFGGNKASGVGRFGNPWVVEEFTVTKWISIQKQYRKYPF 485 +GM H+ND +V D P++ FGG K SG GR G + +EE T KWI+IQ R +PF Sbjct: 425 AGMVHINDCTVFDEPHVPFGGVKKSGFGREGGRYSMEEMTEVKWITIQMGKRHFPF 480 Lambda K H 0.316 0.134 0.380 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: 589 Number of extensions: 15 Number of successful extensions: 3 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: 485 Length of database: 480 Length adjustment: 34 Effective length of query: 451 Effective length of database: 446 Effective search space: 201146 Effective search space used: 201146 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