Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_038201580.1 Q392_RS04005 alpha-hydroxy-acid oxidizing protein
Query= reanno::Smeli:SM_b20850 (378 letters) >NCBI__GCF_000745855.1:WP_038201580.1 Length = 389 Score = 275 bits (704), Expect = 1e-78 Identities = 148/374 (39%), Positives = 220/374 (58%), Gaps = 2/374 (0%) Query: 4 ILEIRDLKALARRRVPKLFFDYADSGAWTEGTYRANEEDFAGIKLRQRVLVDMSDRSLET 63 ++ I DL+ LA+RR+PK+ +DY + GA E T R N F L R++ R L Sbjct: 12 VVNIEDLRRLAKRRLPKVIWDYLEGGAEDEVTLRRNRAAFDRYHLLPRMVTGKGSRDLSI 71 Query: 64 TMIGQKVSMPVALAPTGLTGMQHADGEMLAAQAAEAFGVPFTLSTMSICSIEDVASVTTK 123 T+ GQ+++ P + PTGL G+ D +++ A+AA A GV F+LS S IE VA V+ Sbjct: 72 TLFGQRLAAPFMIGPTGLNGIYVPDADLMLARAAAAAGVGFSLSAGSNNDIEAVARVSDG 131 Query: 124 PFWFQLYVMREREFVLDLIDRAKAAKCSALVMTLDLQILGQRHKDLRNGLSAPPRLTPKH 183 P +FQLY RE L+ RA+AA AL++T+D I G R +D+RN + +P+ Sbjct: 132 PKFFQLYPWGGREVATRLLARARAAGYCALMVTVDSLIPGNRERDVRNRFAHALHFSPRI 191 Query: 184 LWMMATRPGWCMK-MLGTNRRTFRNIVGHAKSVADLSSLQAWTNEQFDPQLSWKDVEWIK 242 +W T P W + F N+ +D +L A+T Q +P SW+D+ W++ Sbjct: 192 VWDAVTHPHWVVSTWFARGMPRFENLAEFLPPGSDAYALAAYTRAQRNPFYSWEDIAWLR 251 Query: 243 ERWGGPLILKGILDPEDAKMAAKTGADAIIVSNHGGRQLDGAHSSISMLPRIVEAVGDQI 302 +W GPL++KGIL +DA++AA GADA++VSNHGGR LDG +++ +LP +V A G + Sbjct: 252 SQWTGPLVIKGILTADDARLAASHGADAVVVSNHGGRSLDGMPATLDVLPSVVAASGG-M 310 Query: 303 EVHLDGGIRSGQDVLKAIALGAKGTYIGRPFLYGLGALGKEGVTLALDIIRKEMDTTMAL 362 V +D G R G D++KA+ALGA G +GR LYG+ A G+ G AL+I+ +E D M L Sbjct: 311 PVLVDSGFRRGSDIVKALALGAHGVLLGRAPLYGVAAAGEAGAGRALEILLQETDRVMGL 370 Query: 363 CGKRRITEVGRDII 376 G + +GR ++ Sbjct: 371 LGVDSVGALGRQLV 384 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: 372 Number of extensions: 10 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: 378 Length of database: 389 Length adjustment: 30 Effective length of query: 348 Effective length of database: 359 Effective search space: 124932 Effective search space used: 124932 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 24 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