Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate GFF3053 PS417_15625 lactate dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_1623 (390 letters) >FitnessBrowser__WCS417:GFF3053 Length = 386 Score = 582 bits (1501), Expect = e-171 Identities = 286/383 (74%), Positives = 332/383 (86%), Gaps = 4/383 (1%) Query: 7 ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66 IT IEDLR +AQ+RVPRMFYDYADSGS+TE TYRANESDF IK RQRVA N++ RS R Sbjct: 4 ITTIEDLRKLAQKRVPRMFYDYADSGSWTESTYRANESDFASIKFRQRVARNIDERSIRA 63 Query: 67 TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126 TM+GQ++AMPVA+APTGL GMQHADGEIL A+AA AFG+ +TLSTMSICS+EDIAEH G+ Sbjct: 64 TMIGQEMAMPVALAPTGLAGMQHADGEILTARAAAAFGLRYTLSTMSICSLEDIAEHVGQ 123 Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186 PFWFQ+YVMRDR FIE+LI+RAKAA AL LTLDLQILGQRHKD+ NGLSAPPK T+ Sbjct: 124 -PFWFQLYVMRDRAFIEQLIERAKAAGVDALVLTLDLQILGQRHKDLINGLSAPPKLTLP 182 Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIK 246 N++N+ATKPRW +GMLGT+RR FGNIVGH KGV D+SSLSSWTA+QFDP+L+W DVEWIK Sbjct: 183 NILNMATKPRWVMGMLGTQRRGFGNIVGHVKGVADMSSLSSWTAQQFDPRLSWDDVEWIK 242 Query: 247 KRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMG 306 K WGGKLI+KGI+D EDA LA N+GADAL+VSNHGGRQLDGAPSSI+ LP I +AV G Sbjct: 243 KCWGGKLIIKGILDVEDAHLAANAGADALVVSNHGGRQLDGAPSSISQLPAIVEAV---G 299 Query: 307 GGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDIT 366 IEVW+DGGIRSGQDVLKA ALGA+GT+IGR LYGLGA GEAGVT+AL+II +ELD++ Sbjct: 300 ERIEVWLDGGIRSGQDVLKAMALGAKGTMIGRPHLYGLGAMGEAGVTKALEIIARELDVS 359 Query: 367 MAFCGHTNINTVDRSILLPGTYP 389 MA CG+ +I V+R ILLPGT+P Sbjct: 360 MALCGYNDIRDVNREILLPGTFP 382 Lambda K H 0.320 0.137 0.412 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: 519 Number of extensions: 15 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: 390 Length of database: 386 Length adjustment: 30 Effective length of query: 360 Effective length of database: 356 Effective search space: 128160 Effective search space used: 128160 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: 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