Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate WP_013402451.1 CALHY_RS02540 fumarylacetoacetate hydrolase family protein
Query= metacyc::MONOMER-16233 (285 letters) >NCBI__GCF_000166355.1:WP_013402451.1 Length = 253 Score = 164 bits (415), Expect = 2e-45 Identities = 99/273 (36%), Positives = 147/273 (53%), Gaps = 29/273 (10%) Query: 3 FCRFGQRGQEKPGIIDADGKIRDLSGVVPELTIEALAAAKGAD--VASLPLVEGEPRYGV 60 FCRF + D KI G+V + ++++ D V + + GE + Sbjct: 4 FCRF-----------EKDNKIN--YGIVKDNIVQSIEGNIFGDWKVGNESYLLGEVKLLP 50 Query: 61 PVKGIGKIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKNSTHGDWEV 120 PV+ KIV +GLNY N +P EP++F+K S++ G D ++ P + +EV Sbjct: 51 PVEP-SKIVCVGLNYHSTIKRLNAAVPEEPVIFLKPPSAIIGDGDNIIFPSDVKELGYEV 109 Query: 121 ELGVVIGETCRFVSEDEALSKVAGYVLVNDVSERFNQKQRGTQWSKGKGHDTFCPVGPWL 180 EL V+I + + V+ +EAL V GY + ND++ + K G W+K K +DTF P+GPW+ Sbjct: 110 ELAVIIKDKIKSVNYNEALKHVFGYTIANDLTAK--DKMTGGPWTKAKSYDTFLPLGPWI 167 Query: 181 VTPDEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPP 240 T DP + + + +NG Q GNT M+F+VA LISY+S+ +TL PGD++ITGTPP Sbjct: 168 ATDL---DPNNAKLEMYINGNMTQNGNTSDMVFDVAYLISYISKIMTLCPGDVIITGTPP 224 Query: 241 GVGEGKKPQAIYLKAGDVMELGIEKLGTQRQQV 273 G G L GD +E IE +G R V Sbjct: 225 GAG--------LLNPGDYVEAKIEGIGVLRNYV 249 Lambda K H 0.316 0.137 0.411 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: 266 Number of extensions: 14 Number of successful extensions: 3 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: 285 Length of database: 253 Length adjustment: 25 Effective length of query: 260 Effective length of database: 228 Effective search space: 59280 Effective search space used: 59280 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: 42 (22.0 bits) S2: 47 (22.7 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