Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate PfGW456L13_3320 L-arabonate dehydratase (EC 4.2.1.25)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3320 (578 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3320 Length = 578 Score = 1166 bits (3016), Expect = 0.0 Identities = 578/578 (100%), Positives = 578/578 (100%) Query: 1 MSDKKPTLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHF 60 MSDKKPTLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHF Sbjct: 1 MSDKKPTLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHF 60 Query: 61 RQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVL 120 RQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVL Sbjct: 61 RQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVL 120 Query: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGKDIGSGTVVWQLSEQVKAGTISI 180 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGKDIGSGTVVWQLSEQVKAGTISI Sbjct: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGKDIGSGTVVWQLSEQVKAGTISI 180 Query: 181 DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR 240 DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR Sbjct: 181 DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR 240 Query: 241 AVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIG 300 AVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIG Sbjct: 241 AVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIG 300 Query: 301 RGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSIGENTRDAP 360 RGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSIGENTRDAP Sbjct: 301 RGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSIGENTRDAP 360 Query: 361 IYGEDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAATPELMQHRGRAVVFENFDMY 420 IYGEDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAATPELMQHRGRAVVFENFDMY Sbjct: 361 IYGEDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAATPELMQHRGRAVVFENFDMY 420 Query: 421 KARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSG 480 KARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSG Sbjct: 421 KARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSG 480 Query: 481 TAYGTVVLHVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIADTELAARMADLQPPQNL 540 TAYGTVVLHVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIADTELAARMADLQPPQNL Sbjct: 481 TAYGTVVLHVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIADTELAARMADLQPPQNL 540 Query: 541 IVGGYRQLYIDHVLQADQGCDFDFLVGCRGAEVPRHSH 578 IVGGYRQLYIDHVLQADQGCDFDFLVGCRGAEVPRHSH Sbjct: 541 IVGGYRQLYIDHVLQADQGCDFDFLVGCRGAEVPRHSH 578 Lambda K H 0.319 0.136 0.410 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: 1338 Number of extensions: 48 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: 578 Length of database: 578 Length adjustment: 36 Effective length of query: 542 Effective length of database: 542 Effective search space: 293764 Effective search space used: 293764 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: 53 (25.0 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