Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate PfGW456L13_812 D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
Query= reanno::psRCH2:GFF3724 (432 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_812 Length = 436 Score = 745 bits (1923), Expect = 0.0 Identities = 367/433 (84%), Positives = 398/433 (91%), Gaps = 1/433 (0%) Query: 1 MRVLVLGSGVVGTASAYYLARAGFEVVVVDRQPAVAMETSFANAGQVSPGYASPWAAPGV 60 MRV+VLGSGV+GT SAYYLARAGFEVVVVDRQPA AMETSFANAGQVSPGYASPWAAPGV Sbjct: 3 MRVMVLGSGVIGTTSAYYLARAGFEVVVVDRQPAAAMETSFANAGQVSPGYASPWAAPGV 62 Query: 61 PLKAMKWLLQRHAPLAIKLTGDVDQYLWMAQMLRNCTAARYAVNKERMVRLSEYSRDCLD 120 PLKA+KWLLQRHAPLAIK T D+DQYLWMAQMLRNCTA+RYAVNKERMVRLSEYSRDCLD Sbjct: 63 PLKAIKWLLQRHAPLAIKATADIDQYLWMAQMLRNCTASRYAVNKERMVRLSEYSRDCLD 122 Query: 121 ELRAETGIAYEGRQLGTTQLFRTQAQLDAAAKDIAVLERSGVPYELLDRAAIGRVEPALA 180 ELRAETGIAYEGR LGTTQLFRTQAQLD AAKDIAVL+ SGVP+ELLDR I RVEPALA Sbjct: 123 ELRAETGIAYEGRSLGTTQLFRTQAQLDGAAKDIAVLKESGVPFELLDREGIARVEPALA 182 Query: 181 KVAHKLSGALRLPNDQTGDCQMFTSRLAEMALALGVEFRFGQNIQRLEHAGDRIAGVWID 240 V L+GALRLPNDQTGDCQMFT++LAEMA LGV+FRFGQ+IQRL+ AGDRI GVWID Sbjct: 183 SVTDILAGALRLPNDQTGDCQMFTTKLAEMAANLGVQFRFGQDIQRLDFAGDRINGVWID 242 Query: 241 GKLETADRYVLALGSYSPQMLKPLGIRAPVYPLKGYSLTVPISDPAMAPQSTVLDETYKV 300 GKLETADRYVLALGSYSPQ+LKPLGI+APVYPLKGYSLTVPI++PAMAP ST+LDETYKV Sbjct: 243 GKLETADRYVLALGSYSPQLLKPLGIKAPVYPLKGYSLTVPITNPAMAPTSTILDETYKV 302 Query: 301 AITRFDQRIRVGGMAEIAGHDLSLNPRRRETLEMVVGDLYPQGGDPAEAVFWTGLRPATP 360 AITRFD RIRVGGMAEIAG DLSLNPRRRETLEM+V DLYPQGG+ AEA FWTGLRP TP Sbjct: 303 AITRFDNRIRVGGMAEIAGFDLSLNPRRRETLEMIVNDLYPQGGNLAEASFWTGLRPTTP 362 Query: 361 DGTPIIGATAYRNLYLNTGHGTLGWTMACGSGRVLADLLASKRPQISTDGLDIFRYG-KH 419 DGTPI+GAT ++NL+LNTGHGTLGWTMACGSGR+LADL+A ++PQIS +GLDI RYG K Sbjct: 363 DGTPIVGATPFKNLFLNTGHGTLGWTMACGSGRLLADLMAKRKPQISAEGLDISRYGNKT 422 Query: 420 KETRKHAHPAAAH 432 +E+ KH PA AH Sbjct: 423 QESAKHVSPAPAH 435 Lambda K H 0.320 0.135 0.405 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: 707 Number of extensions: 16 Number of successful extensions: 2 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: 432 Length of database: 436 Length adjustment: 32 Effective length of query: 400 Effective length of database: 404 Effective search space: 161600 Effective search space used: 161600 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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