Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate H281DRAFT_05401 H281DRAFT_05401 Cytochrome c, mono- and diheme variants
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__Burk376:H281DRAFT_05401 Length = 431 Score = 405 bits (1040), Expect = e-117 Identities = 207/406 (50%), Positives = 269/406 (66%), Gaps = 7/406 (1%) Query: 14 SAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPD 73 S A+ AA A QALVQ+G YLA+AGDC ACHTA GKPFAGGLPM TP+G IY+TNITPD Sbjct: 23 SPASAAASAADQALVQRGAYLAKAGDCAACHTAPKGKPFAGGLPMNTPMGQIYTTNITPD 82 Query: 74 -KTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVA 132 +TGIG Y+ +DF +A+R GVAK G LYPAMP+PSYA+V+D DM+ALYA+FM GVAPV Sbjct: 83 AQTGIGSYTEQDFARAMREGVAKDGHNLYPAMPYPSYAKVNDEDMKALYAFFMSGVAPVQ 142 Query: 133 RDNQDSDIPWPLSMRWPLSIWRWMF-APSVETPAPAAGSDPVISRGAYLVEGLGHCGACH 191 + N++SDI WP++MRWPL +W +F V P G D +RGAYL++GLGHCG+CH Sbjct: 143 QANRESDIKWPMNMRWPLKLWNMVFLEKGVYQNKP--GKDVAWNRGAYLIQGLGHCGSCH 200 Query: 192 TPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRS 251 TPR + QEKAL + GS FL+G L+ W A +L G+H GLG WS++ L FLKTG + Sbjct: 201 TPRGIAFQEKALDET-GSAFLTGGL-LDNWYATNLTGEHNVGLGRWSDQDLQAFLKTGAN 258 Query: 252 DRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPA-NDPKDQPHQYDKQVAQALWNGD 310 ++ FG M+ V+ +S Q + D D+ A+ YLKSLPA P++YD Q + N Sbjct: 259 RHASAFGSMTSVINNSTQNLNDGDIAAMTTYLKSLPAVGGNGAPPYKYDPQTTKVSLNRP 318 Query: 311 DSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHS 370 + GA VY C CH DG G+ + LAGNP + DA+SLI++ L G Sbjct: 319 ANDAGARVYTAYCMHCHGVDGRGFAPMLAPLAGNPNVLEKDASSLINVTLNGTEDLVIGG 378 Query: 371 APSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416 P+ + MP +A L+DQ++ADV+ F+R+ W N A AV DV LR Sbjct: 379 IPAPYPMPKYAPVLNDQQIADVLTFVRAGWNNGAPAVTAADVTKLR 424 Lambda K H 0.316 0.131 0.404 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: 642 Number of extensions: 39 Number of successful extensions: 6 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: 434 Length of database: 431 Length adjustment: 32 Effective length of query: 402 Effective length of database: 399 Effective search space: 160398 Effective search space used: 160398 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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