Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate HSERO_RS01205 HSERO_RS01205 2-hydroxy-acid oxidase
Query= reanno::Smeli:SM_b20850 (378 letters) >FitnessBrowser__HerbieS:HSERO_RS01205 Length = 393 Score = 254 bits (649), Expect = 3e-72 Identities = 142/359 (39%), Positives = 205/359 (57%), Gaps = 4/359 (1%) Query: 7 IRDLKALARRRVPKLFFDYADSGAWTEGTYRANEEDFAGIKLRQRVLVDMSDRSLETTMI 66 I +L+A+AR+RVP F+Y + GA E + R N E F I R LVD+S R + Sbjct: 17 IEELRAMARKRVPNFCFEYVEGGAEEEISLRHNREVFTRIGFLPRTLVDVSVRRQGRRLF 76 Query: 67 GQKVSMPVALAPTGLTGMQHADGEMLAAQAAEAFGVPFTLSTMSICSIEDVASVTTKPFW 126 GQ ++ P + PTG +G+ +G++ A AA + GVPF L+ +S S+E+V + W Sbjct: 77 GQDIASPFLIGPTGFSGLLAREGDVAMASAAASAGVPFVLTNVSTTSLEEVVRRSGAQVW 136 Query: 127 FQLYVMREREFVLDLIDRAKAAKCSALVMTLDLQILGQRHKDLRNGLSAPPRLTPKHLWM 186 Q+Y+ R+R FV + RA+AA LV+T D + G+R D RN S+P RL ++ Sbjct: 137 QQVYLYRDRAFVASVAQRAQAAGIGVLVLTTDSAVYGKREWDARN-FSSPRRLDWRNKLD 195 Query: 187 MATRPGWCMKML---GTNRRTFRNIVGHAKSVADLSSLQAWTNEQFDPQLSWKDVEWIKE 243 + P W + +L G R + + + A + L W DV+W++ Sbjct: 196 VLRHPRWLIDILYPHGFPRFANLGDLLPPDQTSVRGAAAAILGQSLSAALDWADVQWLRG 255 Query: 244 RWGGPLILKGILDPEDAKMAAKTGADAIIVSNHGGRQLDGAHSSISMLPRIVEAVGDQIE 303 W G L+LKG++ EDA+ A G D I++SNHGGRQLDGA S++ +LP +V AV Q+ Sbjct: 256 IWPGKLVLKGVMQVEDAQRAVALGVDGIVLSNHGGRQLDGALSTMDVLPEVVAAVKGQLT 315 Query: 304 VHLDGGIRSGQDVLKAIALGAKGTYIGRPFLYGLGALGKEGVTLALDIIRKEMDTTMAL 362 V LDGG R G D++KAIALGA +GR YGL A G+ G T AL+I+R E+D +AL Sbjct: 316 VMLDGGFRRGADIVKAIALGADAVLLGRATTYGLAAGGQAGATRALEILRSEVDRVLAL 374 Lambda K H 0.321 0.136 0.406 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: 374 Number of extensions: 13 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: 378 Length of database: 393 Length adjustment: 30 Effective length of query: 348 Effective length of database: 363 Effective search space: 126324 Effective search space used: 126324 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 (21.9 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