Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate RR42_RS33950 RR42_RS33950 dihydroxy-acid dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >FitnessBrowser__Cup4G11:RR42_RS33950 Length = 577 Score = 1035 bits (2676), Expect = 0.0 Identities = 513/584 (87%), Positives = 544/584 (93%), Gaps = 8/584 (1%) Query: 1 MSATKPRLRSTQWFGTNDKNGFMYRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHF 60 M +K +LRS QWFG+ DKNGFMYRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHF Sbjct: 1 MPESKSKLRSAQWFGSADKNGFMYRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHF 60 Query: 61 RKLAEHVKRGISEAGGFPVEFPVFSNGESNLRPSAMLTRNLASMDVEEAIRGNPIDAVVL 120 RKLAEHVKRG+ EAGGFPVEFPVFSNGESNLRP+AMLTRNLA+MDVEEAIRGNPIDAVVL Sbjct: 61 RKLAEHVKRGVYEAGGFPVEFPVFSNGESNLRPTAMLTRNLAAMDVEEAIRGNPIDAVVL 120 Query: 121 LAGCDKTTPALLMGAASCDVPAIVVSGGPMLNGKLEGKNIGSGTAVWQLHEALKAGEIDV 180 L GCDKTTPALLMGAASCDVPAIVV+GGPMLNGKL+GKNIGSGTAVWQLHE+LKAGEI+V Sbjct: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKLDGKNIGSGTAVWQLHESLKAGEINV 180 Query: 181 HHFLSAEAGMSRSAGTCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIR 240 H FLSAEAGMSRSAGTCNTMGTASTMACMAEALG +LPHNAAIPAVDSRRYVLAHMSGIR Sbjct: 181 HQFLSAEAGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDSRRYVLAHMSGIR 240 Query: 241 IVEMALEGLVLSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWMRIG 300 IVEMA EGL LSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDW RIG Sbjct: 241 IVEMAKEGLTLSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWTRIG 300 Query: 301 RDTPTIVDLMPSGRFPMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSLWDNVREAP 360 RDTPTIVDLMPSGRF MEEFYYAGGLPAVLRRLGE LLP+PDALTVNG++LW NV++AP Sbjct: 301 RDTPTIVDLMPSGRFLMEEFYYAGGLPAVLRRLGEANLLPHPDALTVNGRTLWQNVKDAP 360 Query: 361 NYDEEVIRPLDRPLIADGGIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYK 420 N ++EVIR LD PL+ADGGIR+LRGNLAPRGAVLKPSAA+P LLKHRGRAVVFENL+HYK Sbjct: 361 NTNDEVIRALDNPLMADGGIRVLRGNLAPRGAVLKPSAATPGLLKHRGRAVVFENLEHYK 420 Query: 421 ATINDEALDIDASSVMVLKNCGPRGYPGMAEVGNMGLPPKLLRQGVKDMVRISDARMSGT 480 I DE LD+DASSVMVLKNCGP+GYPGMAEVGNMGLPPKLLRQGVKDMVRISDARMSGT Sbjct: 421 ERIVDETLDVDASSVMVLKNCGPKGYPGMAEVGNMGLPPKLLRQGVKDMVRISDARMSGT 480 Query: 481 AYGTVVLHVAPEAAAGGPLAAVRNGDWIELDCEAGTLHLDITDDELHRRLSD-VDPTAAP 539 AYGTVVLHVAPEAAAGGPLAAVR+GDWIELDCEAGTLHLDI D+EL RR+++ VD AA Sbjct: 481 AYGTVVLHVAPEAAAGGPLAAVRDGDWIELDCEAGTLHLDIDDEELARRMAERVDTRAA- 539 Query: 540 GVAGQLGKGGYARLYIDHVLQADEGCDLDFLVGTRGAEVPSHSH 583 G+GGY RLY+DHVLQADEGCDLDFLVG RGA VP HSH Sbjct: 540 ------GEGGYRRLYVDHVLQADEGCDLDFLVGCRGAAVPRHSH 577 Lambda K H 0.319 0.136 0.412 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: 1292 Number of extensions: 49 Number of successful extensions: 2 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: 583 Length of database: 577 Length adjustment: 36 Effective length of query: 547 Effective length of database: 541 Effective search space: 295927 Effective search space used: 295927 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 (21.7 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