Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate HSERO_RS12985 HSERO_RS12985 L-lactate dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_1623 (390 letters) >FitnessBrowser__HerbieS:HSERO_RS12985 Length = 380 Score = 517 bits (1331), Expect = e-151 Identities = 260/382 (68%), Positives = 309/382 (80%), Gaps = 8/382 (2%) Query: 7 ITCIEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRT 66 +TC+ED R +A++RVP+ FYDYADSGSYTE TYRAN D +KLRQRVA+N++ RSTRT Sbjct: 4 MTCVEDFRLLAKKRVPKAFYDYADSGSYTESTYRANSKDLAALKLRQRVAINVDERSTRT 63 Query: 67 TMVGQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGR 126 TM+G DV MPVAIAPTGLTGMQ A+GE+LGA AA+ FGIPFTLSTMSICSIED+A T + Sbjct: 64 TMIGHDVTMPVAIAPTGLTGMQWANGEMLGAIAAEKFGIPFTLSTMSICSIEDVASVTTK 123 Query: 127 HPFWFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIA 186 PFWFQ+YVMRDR F++ LI+RAKAA CSAL LTLDLQILGQRHKD+KNG+S PPK T+ Sbjct: 124 -PFWFQLYVMRDRGFVKSLIERAKAAKCSALVLTLDLQILGQRHKDLKNGMSVPPKLTLE 182 Query: 187 NLINLATKPRWCLGMLGTKRRSFGNIVGHAK---GVGDLSSLSSWTAEQFDPQLNWGDVE 243 L++LA+KP W L LG R++FGN+ GH K G G + +LS WTA QFDP LNW DV Sbjct: 183 TLLDLASKPGWALRALG-GRKTFGNLAGHIKGGEGAGGVQTLSKWTASQFDPTLNWDDVA 241 Query: 244 WIKKRWGGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVA 303 WIK++WGGKLILKGI+D EDA+LAV SGADA++VSNHGGRQLDGA SSI ALP IA AV Sbjct: 242 WIKQQWGGKLILKGILDVEDAKLAVQSGADAIVVSNHGGRQLDGAMSSIEALPAIAQAV- 300 Query: 304 QMGGGIEVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKEL 363 G IEVW DGGIRSGQDVLKA ALGA+GT+IGR+FLY LGA G GV++ L+I++KEL Sbjct: 301 --GDQIEVWFDGGIRSGQDVLKAVALGARGTMIGRAFLYSLGAMGGEGVSQMLEIMRKEL 358 Query: 364 DITMAFCGHTNINTVDRSILLP 385 D++MA G +I V IL+P Sbjct: 359 DVSMALTGTKDIKDVGPQILIP 380 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: 543 Number of extensions: 27 Number of successful extensions: 5 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: 380 Length adjustment: 30 Effective length of query: 360 Effective length of database: 350 Effective search space: 126000 Effective search space used: 126000 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