Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate Synpcc7942_1717 Synpcc7942_1717 glycolate oxidase subunit (Fe-S) protein
Query= reanno::Smeli:SMc00926 (443 letters) >FitnessBrowser__SynE:Synpcc7942_1717 Length = 433 Score = 324 bits (830), Expect = 4e-93 Identities = 181/427 (42%), Positives = 255/427 (59%), Gaps = 24/427 (5%) Query: 26 PHVAESETILRKCVHCGFCTATCPTYVVLGDELDSPRGRIYLIKDMLENGRAADSETVT- 84 P A + ++ CVHCGFC + CP+Y VLG E DSPRGR+YL+ D L+ GR S+TV Sbjct: 7 PIPAATPSLTDACVHCGFCLSDCPSYRVLGRETDSPRGRVYLM-DSLQQGRIELSDTVVE 65 Query: 85 HIDRCLSCLSCLTTCPSGVDYMHLVDHARAHIEKTYKRPFKDRLARSVIAATLPYPSRFR 144 H D CL CL+C + CPSGV Y L++ R I + ++RP+ + + R ++ A LPYP R R Sbjct: 66 HFDTCLGCLACTSACPSGVQYDQLIEEMRQRIAQEHRRPWPEAIWRKLLFAFLPYPERLR 125 Query: 145 --LALGAAGLARPLAGLLKRVPFLR---TLGVMLDLAPSALPAA-RGAKPAVYAAKGTPR 198 L LG + L L R P L+ L L P PA+ + P + A G R Sbjct: 126 PILRLGQLYQSSGLQNWLNRQPLLQKFPQLAAASALLPPLSPASFQDNWPTLLPALGDRR 185 Query: 199 ARVALLTGCAQPVLRPEINDATIRLLTGQGVEVVVSAGEGCCGALVHHMGRDEQALQAGR 258 RV LL GC Q + PE+N A IR+L G +VV+ +GCCGA+ HH G +QA R Sbjct: 186 YRVGLLLGCVQRLFNPEVNAAAIRVLRANGCDVVIPPQQGCCGAVAHHQGEMQQAQDLAR 245 Query: 259 HNIDVWLKAAEEDGLDAIIITASGCGTTIKDYGHMLRLDPAYAEKAARVSALAKDVTEYL 318 +++ E + LDAI++TASGCG T+K YG +L DP + ++A +++ +DV E+L Sbjct: 246 ----AVIRSFEAENLDAILVTASGCGHTLKHYGAILADDPEWCDRAQQLADRVQDVQEFL 301 Query: 319 ATLDL-----PEQGARNLTVAYHSACSMQHGQKITSAPKQLLKR-AGFSVREPAEGHLCC 372 AT+ L P Q + L V Y AC M HGQKI + P+QLL++ G +REP + LCC Sbjct: 302 ATVGLTTPLHPLQ-EQPLVVVYQDACHMLHGQKIRNQPRQLLQQIPGIELREPVDAQLCC 360 Query: 373 GSAGTYNILQPEISAKLKARKVRNIEATKPEVIATGNIGCITQI-----ASGTEIPILHT 427 GSAG YN+LQP I+A+L +K R++ T ++IA+ NIGC QI A ++P+LH Sbjct: 361 GSAGIYNLLQPAIAAELGQQKARSLAETGAQMIASANIGCYVQIRHHLQAQSKDLPVLHP 420 Query: 428 VELLDWA 434 ++++D A Sbjct: 421 LQIIDRA 427 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: 513 Number of extensions: 24 Number of successful extensions: 8 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: 433 Length adjustment: 32 Effective length of query: 411 Effective length of database: 401 Effective search space: 164811 Effective search space used: 164811 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