Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_011386798.1 AMB_RS22540 alpha-hydroxy-acid oxidizing protein
Query= reanno::acidovorax_3H11:Ac3H11_1623 (390 letters) >NCBI__GCF_000009985.1:WP_011386798.1 Length = 384 Score = 216 bits (550), Expect = 9e-61 Identities = 127/362 (35%), Positives = 190/362 (52%), Gaps = 6/362 (1%) Query: 10 IEDLRAIAQRRVPRMFYDYADSGSYTEGTYRANESDFQRIKLRQRVAVNMEGRSTRTTMV 69 I DL +A+ R+P + + D GS EG R N + L + + +T ++ Sbjct: 9 IGDLAKLARWRIPGFAFGFLDGGSGEEGGLRRNRERLEAAVLAPKACTGAKPDTT-ASLF 67 Query: 70 GQDVAMPVAIAPTGLTGMQHADGEILGAKAAKAFGIPFTLSTMSICSIEDIAEHTGRHPF 129 G+D A+P AP G+ + +++ A+ A G P ST++ ++EDIA H Sbjct: 68 GRDYALPFGAAPVGMGNLLWPGADLMVARQAARLGFPVVASTVATTALEDIAAAAEGHA- 126 Query: 130 WFQVYVMRDRDFIERLIDRAKAANCSALQLTLDLQILGQRHKDIKNGLSAPPKPTIANLI 189 WFQ+YV R+ L+ RA AA L +T+D+ + G R +D++N P KP + Sbjct: 127 WFQLYVSREERINRDLLARAWAAGIRELVITVDVPVAGDRRRDVRNRFILPFKPGPRFVA 186 Query: 190 NLATKPRWCLGMLGTKRRSFGNIVGHAKGVGDLSSLSSWTAEQFDPQLNWGDVEWIKKRW 249 +A P W L L F N+ + G D +L+ + + Q L W DV ++ W Sbjct: 187 QVAMAPLWALSTLRAGSPGFPNLTRYV-GEVDGKTLAGFISSQIKDDLAWDDVRALRDLW 245 Query: 250 GGKLILKGIMDAEDARLAVNSGADALIVSNHGGRQLDGAPSSIAALPGIADAVAQMGGGI 309 G+L++KGIM A DAR A++ GAD + VSNHGGRQLD AP++I +L I A +G Sbjct: 246 QGRLLIKGIMTAADARTALDLGADGIWVSNHGGRQLDAAPAAIDSLAAIR---AALGKEA 302 Query: 310 EVWMDGGIRSGQDVLKARALGAQGTLIGRSFLYGLGAYGEAGVTRALQIIQKELDITMAF 369 + MDG IRSG+DV++A A GA GR+F YG A GE G RA ++ ++ T+ Sbjct: 303 VILMDGSIRSGEDVVRAGATGADFVFCGRAFYYGAAAAGEGGAARAADLLAADVRRTLTQ 362 Query: 370 CG 371 G Sbjct: 363 IG 364 Score = 23.9 bits (50), Expect = 0.008 Identities = 8/21 (38%), Positives = 12/21 (57%) Query: 213 VGHAKGVGDLSSLSSWTAEQF 233 + HA +GDL+ L+ W F Sbjct: 3 INHAASIGDLAKLARWRIPGF 23 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: 401 Number of extensions: 20 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 390 Length of database: 384 Length adjustment: 30 Effective length of query: 360 Effective length of database: 354 Effective search space: 127440 Effective search space used: 127440 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