Align Putative aldehyde dehydrogenase AldY; EC 1.2.1.3 (characterized)
to candidate WP_002880378.1 B506_RS08415 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Query= SwissProt::P94358 (485 letters) >NCBI__GCF_000387565.1:WP_002880378.1 Length = 476 Score = 254 bits (649), Expect = 5e-72 Identities = 161/470 (34%), Positives = 255/470 (54%), Gaps = 14/470 (2%) Query: 9 SFINGKWTGGESGRTEDILNPYDQSVITTASLATGKQLEDAFDIAQKAQKEWAKSTTEDR 68 +++NG+W +S +I P + T + + ++ D A+KA W + +R Sbjct: 7 NYVNGEWR--DSADAIEIFEPATGKSLGTVPAMSHEDVDYVMDSAKKALPAWRALSYVER 64 Query: 69 KAVLQKARGYLHENRDDIIMMIARETGGTIIKSTIELEQTIAILDEA----MTYTGEL-- 122 A LQKA L+ + + I +++E + S E+ +T I++ +T GE+ Sbjct: 65 AAYLQKAADILYRDAEKIGSTLSKEIAKGLKSSIGEVTRTAEIVEYTAKVGVTLDGEVME 124 Query: 123 GGVKEVPSDIEGKTNKIYRLPLGVISSISPFNFPMNLSMRSIAPAIALGNSVVHKPDIQT 182 GG E S + K + R P+G++ +ISPFN+P+NL+ IAPA+ GN V KP Q Sbjct: 125 GGNFEAAS--KNKLAVVRREPVGLVLAISPFNYPVNLAGSKIAPALMGGNVVAFKPPTQG 182 Query: 183 AISGGTIIAKAFEHAGLPAGVLNVMLTDVKEIGDGMLTNPIPRLISFTGSTAVGRHIGEI 242 AISG ++AKAF AGLPAGV N + + IGD ++ +P I+FTGS+AVG++IG++ Sbjct: 183 AISG-LLLAKAFAEAGLPAGVFNTITGRGRVIGDYIVEHPAVNFINFTGSSAVGKNIGKL 241 Query: 243 AGRAFKRMALELGGNNPFAVLSDADVDRAVDAAIFGKFIHQGQICMIINRIIVHQDVYDE 302 AG + + LELGG + VL DAD+D + G F + GQ C + R++V V DE Sbjct: 242 AG--MRPIMLELGGKDAAIVLEDADLDLTAKNIVAGAFGYSGQRCTAVKRVLVMDSVADE 299 Query: 303 FVEKFTARVKQLPYGDQTDPKTVVGPLINERQIEKALEIIEQAKTDGIELAVEGKRVGNV 362 VEK TA VK L G + + PLI+ + + +IE+A G + + KR GN+ Sbjct: 300 LVEKVTALVKDLTVGMPEEDADIT-PLIDTKSADYVQGLIEEAAEKGAKPLFDFKREGNL 358 Query: 363 LTPYVFVGADNNSKIAQTELFAPIATIIKAGSDQEAIDMANDTEYGLSSAVFTSDLEKGE 422 + P V + ++A E F P+ I+ S EA+ +AN++EYGL S+VF+ + EK Sbjct: 359 IYPMVMDQVTTDMRLAWEEPFGPVLPFIRVKSADEAVKIANESEYGLQSSVFSRNFEKAF 418 Query: 423 KFALQIDSGMTHVNDQSVNDSPNIAFGGNKASGVGRFGNPWVVEEFTVTK 472 + +++ G H+N+++ N F G K+SG G G + ++ T K Sbjct: 419 AISGKLEVGTVHINNKTQRGPDNFPFLGVKSSGAGVQGVKYSIQAMTRVK 468 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: 523 Number of extensions: 22 Number of successful extensions: 4 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: 476 Length adjustment: 34 Effective length of query: 451 Effective length of database: 442 Effective search space: 199342 Effective search space used: 199342 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: 51 (24.3 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