Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate 3607536 Dshi_0948 L-lactate dehydrogenase (cytochrome) (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_1623 (390 letters) >FitnessBrowser__Dino:3607536 Length = 390 Score = 508 bits (1308), Expect = e-148 Identities = 254/378 (67%), Positives = 308/378 (81%), Gaps = 4/378 (1%) Query: 7 ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66 IT IEDL+ I +RRVP+MFYDYA+SGS+TE T+R N SDF +KLRQR+A++M+ RST+T Sbjct: 4 ITEIEDLKRIYKRRVPKMFYDYAESGSWTEQTFRENSSDFDLLKLRQRIAMDMDNRSTKT 63 Query: 67 TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126 TMVGQ+VAMPVA+AP GLTGMQHADGEI A+AA+ FG+PFTLSTMSICSIED+A HT Sbjct: 64 TMVGQEVAMPVALAPVGLTGMQHADGEIKAARAAEKFGVPFTLSTMSICSIEDVAAHT-E 122 Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186 PFWFQVY ++D DF++RL DRAK A CSAL +T+DLQ+LGQRH+D+KNGLSAPPK T A Sbjct: 123 TPFWFQVYTLKDDDFMKRLFDRAKEAKCSALVITVDLQLLGQRHRDLKNGLSAPPKLTPA 182 Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIK 246 ++ N+ TK +W LGMLGTKRR FGNIVGHAKGV D SSLSSWTAE FD L+W ++ + Sbjct: 183 SIANMMTKVQWGLGMLGTKRRFFGNIVGHAKGVTDPSSLSSWTAEAFDQSLDWERIKQFR 242 Query: 247 KRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMG 306 W G +ILKGI+D EDA++A+N GADA++ SNHGGRQLDGA SSI LP I DAV G Sbjct: 243 SWWDGPVILKGILDPEDAKMALNVGADAIVCSNHGGRQLDGALSSIRMLPQIMDAV---G 299 Query: 307 GGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDIT 366 IEV +D GIRSGQDVLKA ALGA+GT+IGR++ YGLGA GEAGVTRAL++I KELD++ Sbjct: 300 DKIEVHLDSGIRSGQDVLKAVALGARGTMIGRAWTYGLGAMGEAGVTRALEVIHKELDLS 359 Query: 367 MAFCGHTNINTVDRSILL 384 M CG ++ +D S LL Sbjct: 360 MGLCGRRSVEDLDASNLL 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: 488 Number of extensions: 16 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: 390 Length adjustment: 31 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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