Align L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (characterized)
to candidate HSERO_RS06870 HSERO_RS06870 cytochrome C biogenesis protein CcdA
Query= reanno::HerbieS:HSERO_RS06870 (306 letters) >FitnessBrowser__HerbieS:HSERO_RS06870 Length = 306 Score = 615 bits (1586), Expect = 0.0 Identities = 306/306 (100%), Positives = 306/306 (100%) Query: 1 MSTPLYRGVFPVAPTIFDANGKLDLEGQKRAIDFMIDAGSNGLCILANFSEQFVLSDEER 60 MSTPLYRGVFPVAPTIFDANGKLDLEGQKRAIDFMIDAGSNGLCILANFSEQFVLSDEER Sbjct: 1 MSTPLYRGVFPVAPTIFDANGKLDLEGQKRAIDFMIDAGSNGLCILANFSEQFVLSDEER 60 Query: 61 VQVQNTVLEHVAGRVPVIVTTTHYGSQICAERSRAAQDAGAAMVMVMPPYHGATFRVPEK 120 VQVQNTVLEHVAGRVPVIVTTTHYGSQICAERSRAAQDAGAAMVMVMPPYHGATFRVPEK Sbjct: 61 VQVQNTVLEHVAGRVPVIVTTTHYGSQICAERSRAAQDAGAAMVMVMPPYHGATFRVPEK 120 Query: 121 QIYEFYKHVSDAIDIPIMIQDAPVAGTPLSAPFLARMAKEIEQVSYFKIETAGAASKLRD 180 QIYEFYKHVSDAIDIPIMIQDAPVAGTPLSAPFLARMAKEIEQVSYFKIETAGAASKLRD Sbjct: 121 QIYEFYKHVSDAIDIPIMIQDAPVAGTPLSAPFLARMAKEIEQVSYFKIETAGAASKLRD 180 Query: 181 LIELGGDAVVGPWDGEEAITLIPDLDAGATGAMTGGGYPDGIRKIVDAYFAGDIEKAAEL 240 LIELGGDAVVGPWDGEEAITLIPDLDAGATGAMTGGGYPDGIRKIVDAYFAGDIEKAAEL Sbjct: 181 LIELGGDAVVGPWDGEEAITLIPDLDAGATGAMTGGGYPDGIRKIVDAYFAGDIEKAAEL 240 Query: 241 YMQWLPLINYENRQCGLSACKALMLEGGVIKSDMLRHPQPPLHPKVREGLLRVARRLDPL 300 YMQWLPLINYENRQCGLSACKALMLEGGVIKSDMLRHPQPPLHPKVREGLLRVARRLDPL Sbjct: 241 YMQWLPLINYENRQCGLSACKALMLEGGVIKSDMLRHPQPPLHPKVREGLLRVARRLDPL 300 Query: 301 VLSWGR 306 VLSWGR Sbjct: 301 VLSWGR 306 Lambda K H 0.321 0.138 0.413 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: 437 Number of extensions: 5 Number of successful extensions: 1 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: 306 Length of database: 306 Length adjustment: 27 Effective length of query: 279 Effective length of database: 279 Effective search space: 77841 Effective search space used: 77841 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: 48 (23.1 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