Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate Ga0059261_2633 Ga0059261_2633 Fe-S oxidoreductase
Query= reanno::Smeli:SMc00926 (443 letters) >FitnessBrowser__Korea:Ga0059261_2633 Length = 429 Score = 549 bits (1415), Expect = e-161 Identities = 273/431 (63%), Positives = 324/431 (75%), Gaps = 8/431 (1%) Query: 14 LQTNFSPEQLADPHVAESETILRKCVHCGFCTATCPTYVVLGDELDSPRGRIYLIKDMLE 73 +QT F+PEQLADP +A SE ++RKCVHCGFCTATCPTY +LGDELDSPRGRIYLIKDMLE Sbjct: 1 MQTRFTPEQLADPAMASSEGVIRKCVHCGFCTATCPTYALLGDELDSPRGRIYLIKDMLE 60 Query: 74 NGRAADSETVTHIDRCLSCLSCLTTCPSGVDYMHLVDHARAHIEKTYKRPFKDRLARSVI 133 N R ETV HIDRCLSCLSC+TTCPSGV+YMHLVDHARA+I + Y RP+ +R R ++ Sbjct: 61 NQRKPGPETVKHIDRCLSCLSCMTTCPSGVNYMHLVDHARAYIHENYGRPWHERAVRRLL 120 Query: 134 AATLPYPSRFRLALGAAGLARPLAGLLKRVPFLRTLGVMLDLAPSALPAARGAKPA-VYA 192 A LPYP RFR AL A L RP A L+ V + L ML +AP +PA A+ A V Sbjct: 121 AWVLPYPGRFRAALLLARLGRPFAPLVAGV---KPLAAMLAMAPKQVPAPVAAENASVPG 177 Query: 193 AKGTPRARVALLTGCAQPVLRPEINDATIRLLTGQGVEVVVSAGEGCCGALVHHMGRDEQ 252 AKG R+ALL GCA+PVL+PE A IRLL G +VV +AGEGCCGALVHHMGR+ Sbjct: 178 AKG----RIALLQGCAEPVLKPEYRAAAIRLLNRAGYDVVFAAGEGCCGALVHHMGREAD 233 Query: 253 ALQAGRHNIDVWLKAAEEDGLDAIIITASGCGTTIKDYGHMLRLDPAYAEKAARVSALAK 312 L A R N+D W++ + GL AI++TASGCGTTIKDYG MLR DPAYA KAA VS LAK Sbjct: 234 GLDAARRNVDAWMREIDGGGLAAIVVTASGCGTTIKDYGFMLRNDPAYAGKAALVSGLAK 293 Query: 313 DVTEYLATLDLPEQGARNLTVAYHSACSMQHGQKITSAPKQLLKRAGFSVREPAEGHLCC 372 D++E LA +DLP R LTVAYH ACS+QHGQK+T APK+LL AG++VR PAE HLCC Sbjct: 294 DISELLAQIDLPPGNGRGLTVAYHPACSLQHGQKVTDAPKRLLAAAGYAVRTPAEAHLCC 353 Query: 373 GSAGTYNILQPEISAKLKARKVRNIEATKPEVIATGNIGCITQIASGTEIPILHTVELLD 432 GSAGTYNILQPEI+ +L RK +++ + +VIATGN+GC QIA + P++HT+ELLD Sbjct: 354 GSAGTYNILQPEIADQLGDRKASHLDRLQADVIATGNVGCAMQIARFGDTPVVHTIELLD 413 Query: 433 WAYGGPKPAGL 443 WA GGP PA L Sbjct: 414 WATGGPAPAVL 424 Lambda K H 0.320 0.135 0.409 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: 623 Number of extensions: 28 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: 443 Length of database: 429 Length adjustment: 32 Effective length of query: 411 Effective length of database: 397 Effective search space: 163167 Effective search space used: 163167 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: 51 (24.3 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