Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate BPHYT_RS24640 BPHYT_RS24640 alcohol dehydrogenase
Query= SwissProt::O34215 (441 letters) >FitnessBrowser__BFirm:BPHYT_RS24640 Length = 426 Score = 407 bits (1047), Expect = e-118 Identities = 215/416 (51%), Positives = 268/416 (64%), Gaps = 7/416 (1%) Query: 7 ALVLGTLSFAALADDQANDALVKRGEYLARAGDCVACHSVKGGQPFAGGLPMATPIGTIY 66 AL L FA A+ ALV+RG YLA+AGDCVACH+ G+PFAGGLPM TP+G IY Sbjct: 11 ALCLTLPLFAQTPARAADQALVQRGAYLAKAGDCVACHTAPKGKPFAGGLPMTTPMGQIY 70 Query: 67 STNITPDKTTGIGDYSYDDFQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFM 126 +TNITPD TGIG Y+ +DF +A+R GVAK+G LYPAMPYPSYA V+D+DMKALYAYFM Sbjct: 71 TTNITPDPQTGIGGYTEEDFARAMREGVAKDGHNLYPAMPYPSYAKVNDDDMKALYAYFM 130 Query: 127 HGVAPVAQANKDSDIPWPLSMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLG 186 GVAPV QAN++ DI WPL+MRWPL W VF D +Q +D RG YL++GLG Sbjct: 131 SGVAPVQQANREPDIKWPLNMRWPLKFWNMVFL-DKGVYQDKPGKDVAWNRGAYLIQGLG 189 Query: 187 HCGACHTPRSITMQEKALSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQ 246 HCG+CHTPR I QEKAL G+ +L+G +DGW A+NL G++ GLGRW++ DL+ Sbjct: 190 HCGSCHTPRGIAFQEKALDESGS-AFLTGGL--LDGWFAANLTGEHNVGLGRWNDQDLQA 246 Query: 247 FLRYGRNDHTAAFGGMTDVVEHSLQHLSDDDITAIARYLKSL-GAKDASQTVFTQDDQVA 305 FL+ G N H +AFG MT V+ +S Q L+D DI A++ YLKSL A + + D Q Sbjct: 247 FLKTGANRHASAFGSMTSVINNSTQGLNDTDIAAMSTYLKSLPPAGGSGAPPYKYDPQAT 306 Query: 306 KALWKGDDSQTGASVYVDSCAACHKTDGSRLSALLPGAAWQPGGAGEPDPTSLIHIVLTG 365 K + GA VY C CH DG + +L + P E DP+SLI++ L G Sbjct: 307 KVSLNRPANDAGARVYTAYCMHCHGVDGRGFAPMLAPLSGNP-NVLEKDPSSLINVTLNG 365 Query: 366 GTLPGVQGAPTAITMPAFGWRLNDQQVADVVNFIRGSWGNGAKATVTAKDVASLRK 421 + G P MP + LNDQQ+ADV+ F+R W NGA A VTA DVA LRK Sbjct: 366 TEDLVIGGIPAPYPMPKYAPVLNDQQIADVLTFVRAGWNNGAPA-VTADDVAKLRK 420 Lambda K H 0.317 0.133 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: 686 Number of extensions: 45 Number of successful extensions: 9 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: 441 Length of database: 426 Length adjustment: 32 Effective length of query: 409 Effective length of database: 394 Effective search space: 161146 Effective search space used: 161146 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