Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate AZOBR_RS05475 AZOBR_RS05475 protein fixB
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__azobra:AZOBR_RS05475 Length = 359 Score = 231 bits (590), Expect = 2e-65 Identities = 126/324 (38%), Positives = 193/324 (59%), Gaps = 6/324 (1%) Query: 71 YRGITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEK---ADELLKYG 127 Y+GI V V+ G +H V++EL+G+AR+LA +G V A+++G + E + YG Sbjct: 21 YKGIWVIVEQERGSVHSVSWELVGEARKLADKLGVEVGAVVLGADSPELNAICGDAFTYG 80 Query: 128 VDKVFVYDKPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLT 187 D V+ P L + +PY V+ D + KP +L+GAT +GR LA +A TGLT Sbjct: 81 ADVVYKVTDPVLADYRTDPYTRVMTDVVNTYKPEIVLLGATTLGRDLAGAIATTLATGLT 140 Query: 188 ADCTILEM-KENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDV 246 ADCT L++ +N L RP FGG ++ I T RPQ TVR +V + P+R + G V Sbjct: 141 ADCTELDIYMDNRSLAATRPTFGGTLLCTIQTLAYRPQMATVRPRVMSMPDRDDSRTGRV 200 Query: 247 EMM--DIEKAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIG 304 + ++ + +++ + +++ L+ A+ IVA G+G+ ++L ++ + A+ +G Sbjct: 201 VEVFPNLRETDVITKVLSFIADREQTEAQLAFADIIVAAGKGLGKPENLKLVFDLAKVLG 260 Query: 305 ATVACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSD 364 V TRP ++AGW Q+G +G+TV+PKL IA GISGA+Q GM+ S+ I+AIN+D Sbjct: 261 GEVGVTRPLVQAGWTGFDRQVGQTGKTVRPKLYIAAGISGAIQHRVGMEKSDLILAINTD 320 Query: 365 PKAPIFNIAHCGMVGDLYEILPEL 388 P APIF+ AH G+VGD ILP L Sbjct: 321 PNAPIFDFAHLGLVGDALTILPAL 344 Lambda K H 0.319 0.137 0.395 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: 18 Number of successful extensions: 4 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: 418 Length of database: 359 Length adjustment: 30 Effective length of query: 388 Effective length of database: 329 Effective search space: 127652 Effective search space used: 127652 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 (21.7 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