Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate BPHYT_RS17845 BPHYT_RS17845 amino acid dehydrogenase
Query= reanno::azobra:AZOBR_RS08020 (436 letters) >FitnessBrowser__BFirm:BPHYT_RS17845 Length = 424 Score = 366 bits (940), Expect = e-106 Identities = 191/423 (45%), Positives = 261/423 (61%), Gaps = 5/423 (1%) Query: 1 MRVIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGL 60 M+ IVLG GVIGV+TA++L + G EVTV++R+P AL TS+ NAG ++PGY PWAAPG+ Sbjct: 1 MKTIVLGGGVIGVATAFYLRQQGCEVTVIEREPDVALSTSFGNAGVIAPGYVTPWAAPGM 60 Query: 61 MAKAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLR 120 AK +K++ SPL+ RP +D A W W + L + + +NK RM R+A YSRDCL Sbjct: 61 PAKILKYLFKPASPLIFRPTLDAAQWRWIARWLHECDLERFRVNKQRMQRIAYYSRDCLH 120 Query: 121 VLRDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALR 180 R Y R++G LQ+FR++ V+ A +AVL + + + C +EP L Sbjct: 121 EFRARYPFDYG-RSQGYLQLFRSEYDVELAQPALAVLRDAGIAHREVSAAQCVEIEPGLS 179 Query: 181 LVKEKIVGGLLLPGDETGDCFRFTNALAAMATELGVEFRYNTGIRKLESDGRRVTGVVTD 240 ++ + GL LP DE GDC RFT L A+ V FR++T + L+ G V V + Sbjct: 180 WARQAPLSGLYLPDDEAGDCARFTRELRAICERNDVRFRFDTRVTSLDVHGGAVRAVRIE 239 Query: 241 ----AGTLTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVDAAGAPESTVMDE 296 A L AD+ VVA+G S L+ G+ +P+YPVKGYS TLP+ D AP +MDE Sbjct: 240 SERGAEMLYADAVVVALGVDSAGLLARLGVKVPLYPVKGYSATLPVTDEEKAPRGALMDE 299 Query: 297 THKIAVTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLFPTGGDLSKAEFWTGLR 356 + K A+TR G+ +RV GTAEL TLR L V++D FP + + A FW G R Sbjct: 300 SLKTAITRFGNNLRVAGTAELGNRQTTLREQALQTLMKVLNDWFPHAANPTSAHFWVGRR 359 Query: 357 PNTPDGTPIVGPTPVRNLFLNTGHGTLGWTMAAGSGRVVADVVGGRQTEIDMDGLTVARY 416 P TPDG P++GP+ V L+LN GHG+ GW M+ GSGRVVAD++ R+ EID+DGLT+ARY Sbjct: 360 PMTPDGAPLLGPSGVEKLWLNLGHGSTGWAMSMGSGRVVADLITHRKPEIDLDGLTLARY 419 Query: 417 GRS 419 +S Sbjct: 420 RKS 422 Lambda K H 0.319 0.136 0.408 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: 481 Number of extensions: 23 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: 436 Length of database: 424 Length adjustment: 32 Effective length of query: 404 Effective length of database: 392 Effective search space: 158368 Effective search space used: 158368 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 (21.7 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