Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate GFF481 PGA1_c04920 l-lactate dehydrogenase IldD
Query= reanno::Smeli:SM_b20850 (378 letters) >FitnessBrowser__Phaeo:GFF481 Length = 388 Score = 511 bits (1316), Expect = e-149 Identities = 253/373 (67%), Positives = 301/373 (80%) Query: 1 MTQILEIRDLKALARRRVPKLFFDYADSGAWTEGTYRANEEDFAGIKLRQRVLVDMSDRS 60 M I I DLK + RRVP++F+DYA+SG+WTE T+R N DF I+LRQRV VDM+ RS Sbjct: 1 MPVITNINDLKRIYERRVPRMFYDYAESGSWTEQTFRDNTNDFEKIRLRQRVAVDMAGRS 60 Query: 61 LETTMIGQKVSMPVALAPTGLTGMQHADGEMLAAQAAEAFGVPFTLSTMSICSIEDVASV 120 + MIGQ VSMPVALAP GLTGMQHADGE+ AA+AAE FGVPFTLSTMSI SIE+VA Sbjct: 61 TASQMIGQDVSMPVALAPVGLTGMQHADGEIKAARAAETFGVPFTLSTMSINSIEEVAEA 120 Query: 121 TTKPFWFQLYVMREREFVLDLIDRAKAAKCSALVMTLDLQILGQRHKDLRNGLSAPPRLT 180 TTKPFWFQLY M++ ++V LI RAK A+CSALV+TLDLQILGQRHKDL+NGLSAPP+LT Sbjct: 121 TTKPFWFQLYTMKDDDYVRRLIQRAKDARCSALVITLDLQILGQRHKDLKNGLSAPPKLT 180 Query: 181 PKHLWMMATRPGWCMKMLGTNRRTFRNIVGHAKSVADLSSLQAWTNEQFDPQLSWKDVEW 240 PK + + T+ W ++ML RR F NIVGH + ++D SSL AWT EQFDP L W + Sbjct: 181 PKTIANLMTKWSWGLQMLSAKRRNFGNIVGHVEGISDASSLGAWTAEQFDPSLDWSKIAK 240 Query: 241 IKERWGGPLILKGILDPEDAKMAAKTGADAIIVSNHGGRQLDGAHSSISMLPRIVEAVGD 300 + E W G +ILKGILD EDAKMAAK GADAI+VSNHGGRQLDGA SSI MLP I++AVGD Sbjct: 241 LIELWDGKVILKGILDVEDAKMAAKLGADAIVVSNHGGRQLDGALSSIQMLPAIMDAVGD 300 Query: 301 QIEVHLDGGIRSGQDVLKAIALGAKGTYIGRPFLYGLGALGKEGVTLALDIIRKEMDTTM 360 QIEVHLD GIRSGQDVLKA+ALGAKGT IGR F+YGLGA+G+ GVT AL+++ KE+DTTM Sbjct: 301 QIEVHLDSGIRSGQDVLKALALGAKGTMIGRAFVYGLGAMGQHGVTRALEVLHKELDTTM 360 Query: 361 ALCGKRRITEVGR 373 ALCG++ + ++GR Sbjct: 361 ALCGEKSVADLGR 373 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: 494 Number of extensions: 18 Number of successful extensions: 1 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: 388 Length adjustment: 30 Effective length of query: 348 Effective length of database: 358 Effective search space: 124584 Effective search space used: 124584 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