Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate GFF2557 PS417_13035 aldehyde dehydrogenase
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__WCS417:GFF2557 Length = 1175 Score = 226 bits (576), Expect = 3e-63 Identities = 151/389 (38%), Positives = 207/389 (53%), Gaps = 36/389 (9%) Query: 25 QALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPD-KTGIGDYSFE 83 +A +++G LA GDC CHTA G AGGL M+TP G +YS+NITPD KTGIG +S+ Sbjct: 794 KATLERGRLLAAVGDCAVCHTAPGGATNAGGLAMQTPFGTLYSSNITPDVKTGIGAWSYP 853 Query: 84 DFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVARDNQDSDIPWP 143 F++A+R G+ + G LYPA P+ ++ +++ADMQALYAY M V PV S P P Sbjct: 854 AFERAMRDGIGRDGRNLYPAFPYTAFRNINEADMQALYAYLMSQV-PV------SQAPTP 906 Query: 144 LSMRWPLSI------WRWMFAPSVETPAPAAGSDPVISRGAYLVEGLGHCGACHTPRALT 197 +MR+P +I W + E +P +RG YLV GLGHC ACH+PR L Sbjct: 907 NAMRFPFNIRPLMAGWNALNLRRGEI-SPQPERSEQWNRGNYLVNGLGHCAACHSPRNLM 965 Query: 198 MQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRSDRSAVF 257 EK GG FL+G ++GW A +L G K W+E+QL +L TG SD V Sbjct: 966 GAEK-----GGKSFLAGGT-VDGWEAPALNGLSKAST-PWTEDQLFTYLSTGYSDAHGVA 1018 Query: 258 GGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQVAQALWNGDDSKPGAA 317 G VV + + AD+ A+A YL SL + + P A + N D G Sbjct: 1019 AGPMGPVVSELSKLPKADIRAMAVYLASLKGDAAAEAP----AVTAANVPNPD----GRR 1070 Query: 318 VYIDNCAACHRTDGHG--YTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHSAPSTF 375 V+ C ACH DG G V P+ A N + S +LI ++L+G + PAT Sbjct: 1071 VFEGACKACH-ADGLGPKLFGVSPSFATNTNVHSDQPDNLIKVILQGISKPATQDLG--- 1126 Query: 376 TMPAFAWRLSDQEVADVVNFIRSSWGNQA 404 MP F LS+ +VAD+ ++R+ + A Sbjct: 1127 YMPGFKDSLSNSQVADLAAYLRAQFAPNA 1155 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: 1414 Number of extensions: 93 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: 434 Length of database: 1175 Length adjustment: 39 Effective length of query: 395 Effective length of database: 1136 Effective search space: 448720 Effective search space used: 448720 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: 55 (25.8 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