Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate BPHYT_RS03835 BPHYT_RS03835 D-lactate dehydrogenase
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__BFirm:BPHYT_RS03835 Length = 332 Score = 462 bits (1189), Expect = e-135 Identities = 234/330 (70%), Positives = 268/330 (81%), Gaps = 1/330 (0%) Query: 1 MRILFFSSQAYDSESFQASNHRHGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDLSRPV 60 MR++ FSS+ YD ++F +N H +ELH Q++HL ++TA+LAQG++VVC FVND++ V Sbjct: 1 MRMILFSSRQYDRDTFTEANATHRYELHCQESHLDSETAILAQGYDVVCPFVNDNVDAAV 60 Query: 61 LERLAAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRL 120 L RL AGGTR++ALRSAG+NHVDLAAAE LG+ V VPAYSPHAVAEHAVGLIL LNRRL Sbjct: 61 LARLHAGGTRMIALRSAGFNHVDLAAAERLGITVARVPAYSPHAVAEHAVGLILALNRRL 120 Query: 121 HRAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDP-YPNP 179 RA RTREGDFSLHGL GFDLHGK VGVIGTG IG F RIMAGFG ++LAYDP P Sbjct: 121 PRAVARTREGDFSLHGLLGFDLHGKTVGVIGTGMIGRVFGRIMAGFGMQVLAYDPGKPAA 180 Query: 180 RIQALGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVN 239 + ALG RY+ LDALLAESD+VSLHCPL DT HLI+ LA MK GAMLINTGRG LV Sbjct: 181 DLLALGARYVPLDALLAESDVVSLHCPLVPDTYHLINGPALAKMKRGAMLINTGRGGLVE 240 Query: 240 AAALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFL 299 + ALI ALK GQLG+LGLDVYEEE+ +FFED S+ PLQDDVLARLL FPNV+VTAHQAF Sbjct: 241 SNALIGALKDGQLGHLGLDVYEEESGLFFEDHSNLPLQDDVLARLLMFPNVIVTAHQAFF 300 Query: 300 TREALAAIADTTLDNIAAWQDGTPRNRVRA 329 TREA+ IA TTLDN+AAWQ GTPRN VRA Sbjct: 301 TREAMNEIAQTTLDNVAAWQAGTPRNVVRA 330 Lambda K H 0.323 0.137 0.402 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: 443 Number of extensions: 14 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: 329 Length of database: 332 Length adjustment: 28 Effective length of query: 301 Effective length of database: 304 Effective search space: 91504 Effective search space used: 91504 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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