Align Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized)
to candidate WP_013449840.1 SULKU_RS12970 phenylacetaldehyde dehydrogenase
Query= SwissProt::P94358 (485 letters) >NCBI__GCF_000183725.1:WP_013449840.1 Length = 481 Score = 324 bits (830), Expect = 5e-93 Identities = 189/477 (39%), Positives = 261/477 (54%), Gaps = 3/477 (0%) Query: 10 FINGKWTGGESGRTEDILNPYDQSVITTASLATGKQLEDAFDIAQKAQKEWAKSTTEDRK 69 FING+ G+ D +NP V LA+ + +E+A A A K WAK+T +++ Sbjct: 7 FINGQNKPSHPGKVIDDVNPATGEVFAKVHLASAEDIEEAISTAYAASKLWAKTTPREKE 66 Query: 70 AVLQKARGYLHENRDDIIMMIARETGGTIIKSTIELEQTIAILDEAMTYTGELGGVKEVP 129 AVL KA D+I ++ RE+G K+ E+ IL A + G Sbjct: 67 AVLLKAADIFESRTDEIRTILMRESGSVYAKAMFEIGLVADILRVAAGEARRVFGQTFTS 126 Query: 130 SDIEGKTNKIYRLPLGVISSISPFNFPMNLSMRSIAPAIALGNSVVHKPDIQTAISGGTI 189 +D G + R PLGVI+ ISPFN PM LS + A AIA GN+ V KP T I G I Sbjct: 127 ND-PGVLSYSTRRPLGVIAGISPFNAPMILSTKKFAMAIAAGNAFVLKPSSHTPICG-LI 184 Query: 190 IAKAFEHAGLPAGVLNVMLTDVKEIGDGMLTNPIPRLISFTGSTAVGRHIGEIAGRAFKR 249 + F+ AGLP GVLN++ ++G+ T+P +I+ TGST VG+ + A K+ Sbjct: 185 FGEIFKEAGLPDGVLNIIPCSSGDLGETFQTDPRIAMITLTGSTRVGKLVAASAAMHLKK 244 Query: 250 MALELGGNNPFAVLSDADVDRAVDAAIFGKFIHQGQICMIINRIIVHQDVYDEFVEKFTA 309 +ELGG +P VL DADVD AVD A F F+HQGQICM +RIIV +++YDEF EKF A Sbjct: 245 CTVELGGKSPTIVLGDADVDYAVDTATFSIFLHQGQICMAGSRIIVEENIYDEFCEKFAA 304 Query: 310 RVKQLPYGDQTDPKTVVGPLINERQIEKALEIIEQAKTDGIELAVEGKRVGNVLTPYVFV 369 +VK L G+ DP T++GPLI E Q +I+ A G L + G P V Sbjct: 305 KVKTLKVGNPEDPSTIIGPLIEEAQCRFIDGLIDDAVAKGATLLSGREHEGCFYKPTVVS 364 Query: 370 GADNNSKIAQTELFAPIATIIKAGSDQEAIDMANDTEYGLSSAVFTSDLEKGEKFALQID 429 I E F P A IIKA I++AN++ YGLSS++ T +L + + +I+ Sbjct: 365 NVTEEMVIFHEEAFGPAAAIIKARDLDHVIELANNSNYGLSSSIITDNLSAALRLSEEIE 424 Query: 430 SGMTHVNDQSVNDSPNIAFGGNKASGVGRFGNPWVVEEFTVTKWISIQKQ-YRKYPF 485 SGM H+N ++ D +I FGG K SG+GR G + +EE T KW++++ R YPF Sbjct: 425 SGMVHINGPTIQDEAHIPFGGVKESGMGREGGHFAIEEMTELKWVTVEAAGNRHYPF 481 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: 596 Number of extensions: 28 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: 481 Length adjustment: 34 Effective length of query: 451 Effective length of database: 447 Effective search space: 201597 Effective search space used: 201597 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