Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate Ac3H11_832 D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
Query= reanno::acidovorax_3H11:Ac3H11_4848 (445 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_832 Length = 414 Score = 380 bits (975), Expect = e-110 Identities = 197/414 (47%), Positives = 262/414 (63%), Gaps = 20/414 (4%) Query: 26 VIVIDRQPDAALETSFANAAQISVSYCEPWANREAPLKALKWMFDKEAPLLFRPQMDWQQ 85 V VIDRQ ETSFAN QISVS+ EPWAN APLK L+W+ ++APLLFR + D +Q Sbjct: 1 VTVIDRQGAPGAETSFANGGQISVSHAEPWANPSAPLKVLQWLGKEDAPLLFRIRADMRQ 60 Query: 86 WRWGLQFLAQCNDTAFERNVQQIVALGAYSHAALKDLVGTTGIEYNRLERGIAHFYTDQK 145 W WGL FL C N++QIV LG YS L+ L TGI+Y++ +GI HFYT+QK Sbjct: 61 WLWGLSFLRNCTPARTRHNIEQIVRLGTYSRDTLQQLRAATGIQYDQRTQGILHFYTNQK 120 Query: 146 SFDAAGHAVELMRKHGVQRRLVSRDELLQIEPAFRAYGDKITGGTYTSTDESGDARVFTQ 205 FD A E MR G +R+++S DE +++EPA ++ G TYT+ DESGDA FT+ Sbjct: 121 EFDGALAPAEQMRALGCERQVISADEAVRLEPALAHIRPQLAGATYTAEDESGDANQFTR 180 Query: 206 ELARRCIARGAQFLYGHDVLRLNKIGNAIDSVAVMARQPGGGGKKDFILKADAVVVACGS 265 ELA+ C A G QF GH + L + G ID V V + G+ + + + DA V+A GS Sbjct: 181 ELAKLCEAAGVQFRMGHHITALREAGGRIDHVEVTTAE----GRFERV-RGDAFVLAMGS 235 Query: 266 YSAPLLRSVGVDLPIYPGKGYSATFPLLRPEGAPMVSTIDDGKKIAMSRL-----GNHLR 320 +S L + +G+ LPIYP KGYS T P+ A VS DD K+ SR G+ LR Sbjct: 236 FSPLLAQPLGIRLPIYPAKGYSVTMPVKDASKAHQVSLTDDEFKLVFSRYTSERGGDRLR 295 Query: 321 VAGTIELNGWDLTLDSSLARARCHMLSRRIEAILPGVCDTRTPEEGGDPQYWTGLRPATP 380 +AGT ELNG+D L+ + RC + RR+E + PG D Q+W+GLRPATP Sbjct: 296 IAGTAELNGYDRHLN----QVRCEAIVRRVEQLFPGAGD------ASQAQFWSGLRPATP 345 Query: 381 TNIPFIGRTRVGKLWVNAGHGTLGWTHGAGSGKALAELISGQVPAMNFGFCGME 434 +N+P IG+T+VG L++N GHGTLGWTH GSGKALA+++SG+VP ++F F G++ Sbjct: 346 SNVPLIGKTKVGNLFLNTGHGTLGWTHACGSGKALADIVSGRVPEVDFAFQGLQ 399 Lambda K H 0.321 0.137 0.424 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: 534 Number of extensions: 23 Number of successful extensions: 5 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: 445 Length of database: 414 Length adjustment: 32 Effective length of query: 413 Effective length of database: 382 Effective search space: 157766 Effective search space used: 157766 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