Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate WP_028487974.1 Q394_RS0102985 fumarylacetoacetate hydrolase family protein
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >NCBI__GCF_000621325.1:WP_028487974.1 Length = 255 Score = 100 bits (250), Expect = 2e-26 Identities = 74/217 (34%), Positives = 109/217 (50%), Gaps = 18/217 (8%) Query: 65 PCVGKIGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRG-SKKTDW 123 PC + K I + N+ + A NL P P+ F K ++ + + + P G S + Sbjct: 51 PC--EPSKLIGLWNNFQERAVVENLHKPDHPLYFLKAANSFAADGELIPRPAGYSGMVVF 108 Query: 124 EVELGVVIGKPAKYIDEANALDYVAGYCVINDVSERE-WQIEKGGT-WDKGKGFDTFGPI 181 E ELG+VIGK K I A +Y+ GY +NDV+ RE +++ W + K FD FG Sbjct: 109 EGELGIVIGKRCKGIALEQAPEYIFGYTCVNDVTARELLKLDPAFVHWTRAKSFDQFGVF 168 Query: 182 GPWVVTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVIST 241 GP + T DP L + +E++G QN M F ++VS +S M+L+ GDVI+ Sbjct: 169 GPSIATG---LDPATLRVRVELNGVEKQNYPVADMFFSPYEIVSRISHDMTLEAGDVIAC 225 Query: 242 GTPPGV-GMGVKPNPVFLKPGQTIRLGIEGLGEQTQK 277 GT GV GM G T+ + I G+GE T + Sbjct: 226 GTSVGVCGMA---------DGDTVVVSIAGVGELTNR 253 Lambda K H 0.315 0.138 0.422 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: 200 Number of extensions: 10 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: 282 Length of database: 255 Length adjustment: 25 Effective length of query: 257 Effective length of database: 230 Effective search space: 59110 Effective search space used: 59110 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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