Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate GFF2783 PGA1_c28260 glyoxylate reductase GyaR
Query= BRENDA::F8A9V0 (325 letters) >FitnessBrowser__Phaeo:GFF2783 Length = 328 Score = 142 bits (357), Expect = 1e-38 Identities = 100/300 (33%), Positives = 156/300 (52%), Gaps = 28/300 (9%) Query: 24 WDVEMTPDFLDETTVEKA---KGAQVVSLFVSDKADGPVLEALHSYGVGLLALRSAGYDH 80 +DV + D + E A K A V+ V+D+ D +L + L+A AG DH Sbjct: 26 FDVRLREDDTPMSRAELATALKDADVLVPTVTDEIDAGLLGQAGDR-LKLIANYGAGVDH 84 Query: 81 IDIETAKRLGIKVVNVPAYSPHAIADHTLAIMLALIRRLHRAHDKVRLGDFD---LDGLM 137 ID+ TA++ GI V N P AD +A+++A++RR+ ++ GD+ L+ Sbjct: 85 IDVATARQRGILVSNTPGVLTDDTADMAMALIMAVVRRIPEGLAVMQKGDWQGWSPTALL 144 Query: 138 GFDLNGKVAGVIGLGKIGRLVATRLKAFGCKVLGYDPY-IQPEIVENVD------LDTLI 190 G L G+ G++G+G IG+ VA R AFG +V ++ ++PEI + + LD ++ Sbjct: 145 GGRLAGRRLGILGMGSIGQAVAKRAAAFGMQVHYHNRRRLRPEIEQRFEATYWESLDQMV 204 Query: 191 TQADIISIHCPLTRENFHMFNEETFKRMKPGAILVNTARGGLIDTKALLEALKSGKLGGA 250 + D++SI+CP T FH+ N K MKP A++VNT+RG +ID AL L++ ++ GA Sbjct: 205 ARMDVLSINCPSTPSTFHLMNARRLKLMKPDAVIVNTSRGEVIDEHALTRMLRASEIAGA 264 Query: 251 ALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLANVVLTGHQAFLTREAVKNIEETTVENI 310 LDVYE+ + +P L + L NVVL H T E + E + NI Sbjct: 265 GLDVYEHGTDI-----------NPRLRE---LENVVLLPHMGSATLEGRLEMGEKVLLNI 310 Lambda K H 0.321 0.140 0.407 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: 223 Number of extensions: 9 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: 325 Length of database: 328 Length adjustment: 28 Effective length of query: 297 Effective length of database: 300 Effective search space: 89100 Effective search space used: 89100 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: 48 (23.1 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