Align L-rhamnose isomerase (EC 5.3.1.14) (characterized)
to candidate WP_011655154.1 RL_RS31865 L-rhamnose catabolism isomerase
Query= BRENDA::Q75WH8 (430 letters) >NCBI__GCF_000009265.1:WP_011655154.1 Length = 430 Score = 790 bits (2039), Expect = 0.0 Identities = 385/430 (89%), Positives = 408/430 (94%) Query: 1 MAEFRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVG 60 M E RIA D+VA +ND+RA+ALK DYEALGA LARRGVDIEAVT +V +FFVAVPSWGVG Sbjct: 1 MTESRIAPDLVATDNDKRATALKADYEALGATLARRGVDIEAVTRQVAEFFVAVPSWGVG 60 Query: 61 TGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALG 120 TGGTRFARFPGTGEPRGIFDKLDDCAVI QLT+ATPNVSLHIPWDKAD ELKA+G+ALG Sbjct: 61 TGGTRFARFPGTGEPRGIFDKLDDCAVINQLTQATPNVSLHIPWDKADASELKAKGNALG 120 Query: 121 LGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKAIGSKALTVWI 180 LGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKA+GSKALTVWI Sbjct: 121 LGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKALGSKALTVWI 180 Query: 181 GDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYL 240 GDGSNFPGQS+FT+AFERYL++MA+IYK LPDDWKLFSEHKMYEPAFYST+VQDWGTNYL Sbjct: 181 GDGSNFPGQSHFTKAFERYLASMADIYKALPDDWKLFSEHKMYEPAFYSTIVQDWGTNYL 240 Query: 241 IAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPY 300 IAQTLGPKA CLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAI+PY Sbjct: 241 IAQTLGPKAYCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIDPY 300 Query: 301 RLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAA 360 RLFLVFNELVDAE RGV F+PAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDR A Sbjct: 301 RLFLVFNELVDAEQRGVNDFNPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRKA 360 Query: 361 LSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERP 420 LSGYQ+DNDALMA+ETLKRAYR DVEPILAEARRR GGA+DP+A YRASGYR +VAAERP Sbjct: 361 LSGYQDDNDALMASETLKRAYRADVEPILAEARRRAGGAIDPIAVYRASGYRRQVAAERP 420 Query: 421 ASVAGGGGII 430 AS AGGGGII Sbjct: 421 ASAAGGGGII 430 Lambda K H 0.318 0.135 0.400 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: 772 Number of extensions: 24 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: 430 Length of database: 430 Length adjustment: 32 Effective length of query: 398 Effective length of database: 398 Effective search space: 158404 Effective search space used: 158404 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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