Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate BPHYT_RS18505 BPHYT_RS18505 amino acid dehydrogenase
Query= reanno::azobra:AZOBR_RS08020 (436 letters) >FitnessBrowser__BFirm:BPHYT_RS18505 Length = 409 Score = 311 bits (796), Expect = 3e-89 Identities = 162/409 (39%), Positives = 229/409 (55%), Gaps = 1/409 (0%) Query: 1 MRVIVLGSGVIGVSTAYFLAKAGHEVTVVDRQPGPALETSYANAGEVSPGYSAPWAAPGL 60 M V VLG GV+GV+TAYFLA+ G++VTVV++ A E S+AN G++S Y AP A P + Sbjct: 1 MHVCVLGGGVVGVTTAYFLAREGYQVTVVEKHTQAAAEASFANGGQLSYSYVAPLAGPSV 60 Query: 61 MAKAVKWMLMKHSPLVIRPKMDPAMWSWCLKLLANANERSYEINKGRMVRLAEYSRDCLR 120 ++ W+L + +PL RP +D W WC + L + ++RL YSR ++ Sbjct: 61 LSHLPGWLLSRTAPLRFRPSLDVDQWKWCCEFLRHCTSARSRQTTVELLRLGAYSRTVMQ 120 Query: 121 VLRDETGIRYDERAKGTLQVFRTQKQVDAAATDMAVLDRFKVPYSLLDVEGCAAVEPALR 180 L + + G L V+R + A M F V S LD + C AVEPAL Sbjct: 121 ELMTNESLDFAFNKSGKLVVYRNAEDFAGARKQMDFQAGFGVEQSALDADACIAVEPALE 180 Query: 181 LVKEKIVGGLLLPGDETGDCFRFTNALAAMATE-LGVEFRYNTGIRKLESDGRRVTGVVT 239 + +K+VGG+ +E GDC FT L+ +ATE GV F + T + L + +V T Sbjct: 181 SIHQKLVGGIYTASEEAGDCHLFTRELSRLATEKYGVRFLFGTQLHGLRQESGKVVAAQT 240 Query: 240 DAGTLTADSYVVAMGSYSPTLVKPFGLDLPVYPVKGYSLTLPIVDAAGAPESTVMDETHK 299 G + AD Y+VA+G+ SP L+ P G++L +YP+KGYSLT+P+ AP+ +V D HK Sbjct: 241 SEGDIIADDYIVALGNGSPNLLHPLGINLTMYPLKGYSLTVPVNLGNVAPKVSVTDLHHK 300 Query: 300 IAVTRLGDRIRVGGTAELTGFDLTLRPGRRGPLDHVVSDLFPTGGDLSKAEFWTGLRPNT 359 I RLGD++R+ G ++T R L P GD S + WTG RP T Sbjct: 301 IVYARLGDQLRIAGMVDMTPAGSKEDSARIRLLQSQAQATMPNAGDFSATQIWTGSRPTT 360 Query: 360 PDGTPIVGPTPVRNLFLNTGHGTLGWTMAAGSGRVVADVVGGRQTEIDM 408 PD P++G T NL+LNTG G+LG+T+AA S ++V D V GR T ID+ Sbjct: 361 PDSKPLLGATRFPNLWLNTGQGSLGFTLAAASAKLVTDAVRGRTTRIDI 409 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: 435 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: 409 Length adjustment: 32 Effective length of query: 404 Effective length of database: 377 Effective search space: 152308 Effective search space used: 152308 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: 50 (23.9 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