Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate N515DRAFT_1250 N515DRAFT_1250 L-lactate dehydrogenase (cytochrome)
Query= reanno::acidovorax_3H11:Ac3H11_1623 (390 letters) >FitnessBrowser__Dyella79:N515DRAFT_1250 Length = 379 Score = 444 bits (1142), Expect = e-129 Identities = 222/377 (58%), Positives = 278/377 (73%), Gaps = 4/377 (1%) Query: 7 ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66 IT + DLR +A+RRVPR F++YAD G+Y E T R N + + IK RQRV +N++ RS T Sbjct: 5 ITNVLDLRELARRRVPRAFFEYADRGAYDEVTLRGNRAALESIKFRQRVMMNVDQRSLAT 64 Query: 67 TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126 ++VGQ ++MP+AIAPTGLTG+QH GEILGA+AA GIPF LST+SICSIE + + + Sbjct: 65 SVVGQPISMPLAIAPTGLTGLQHGAGEILGARAATKAGIPFCLSTVSICSIEQVRDAV-Q 123 Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186 PFWFQ+YVMRDR F LI RA A CSAL LT DL + GQRH++IKNGLS PPK T+ Sbjct: 124 APFWFQLYVMRDRGFARDLIRRASDAGCSALMLTADLTVQGQRHREIKNGLSVPPKITLR 183 Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIK 246 NL ++ +KPRW ML RSFGN+ G +G L++L+ W A QFDP LNW D+EWI+ Sbjct: 184 NLFDVMSKPRWAWSMLRAPSRSFGNLAGRIQGTDSLTTLAQWIANQFDPTLNWQDLEWIR 243 Query: 247 KRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMG 306 + W GKLILKGIMD EDARLA G DA++VSNHGGRQLDGAP+SI LP IADAV G Sbjct: 244 ELWPGKLILKGIMDEEDARLAAAHGVDAIVVSNHGGRQLDGAPASIEVLPRIADAV---G 300 Query: 307 GGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDIT 366 ++V DGGI SGQDVLKA ALGA+ LIG++FLYGLGA GE GV R ++II++EL ++ Sbjct: 301 DKLDVLFDGGILSGQDVLKALALGARAGLIGKAFLYGLGALGEDGVARTIEIIRRELSVS 360 Query: 367 MAFCGHTNINTVDRSIL 383 MA G T++ + R +L Sbjct: 361 MALTGQTDVRRIGRDVL 377 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: 424 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: 379 Length adjustment: 30 Effective length of query: 360 Effective length of database: 349 Effective search space: 125640 Effective search space used: 125640 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