Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate BWI76_RS14180 BWI76_RS14180 hypothetical protein
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__Koxy:BWI76_RS14180 Length = 361 Score = 484 bits (1247), Expect = e-141 Identities = 253/357 (70%), Positives = 281/357 (78%), Gaps = 3/357 (0%) Query: 1 MGQTRIPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTS 60 M Q RIPCLLMRGGTSK A FL DDLP RD VLLA MGSPD RQIDGIGGAD LTS Sbjct: 1 MAQRRIPCLLMRGGTSKAACFLADDLPVDPASRDAVLLATMGSPDTRQIDGIGGADPLTS 60 Query: 61 KVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTP 120 KVAIIR S R DAD+DYLFAQV VD A VDYGQNCGNILA VGPFA+ERGLV T Sbjct: 61 KVAIIRRSARPDADIDYLFAQVNVDRAVVDYGQNCGNILAVVGPFAIERGLVDCVAPLTR 120 Query: 121 VRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTG 180 VRIFMENTGQIAVA+VP G VEYAGDTRIDGVPG A+ +V+ F DVAG+SCGALLPTG Sbjct: 121 VRIFMENTGQIAVAEVPCNTGGVEYAGDTRIDGVPGTASKIVLNFLDVAGSSCGALLPTG 180 Query: 181 NSRDCVEGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQLGPRM 240 + D +G+EVTCIDNGMPVVL+ A DLG TGYE E L+AD LK RLE IRLQ GPRM Sbjct: 181 QASDRFDGIEVTCIDNGMPVVLIRASDLGRTGYETREQLDADDELKQRLETIRLQAGPRM 240 Query: 241 NLGDVSQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGSVAQG 300 NLGDV+QR VPKM L++ PR GG +++R+FIPHRCHASIGVFGAVSVA+ACLI GSVAQ Sbjct: 241 NLGDVTQRTVPKMTLIARPRAGGAISSRTFIPHRCHASIGVFGAVSVASACLIPGSVAQA 300 Query: 301 LASTSGGDRQRLAVEHPSGEFTVEISL-EHGVIKGCGLVRTARLLFDGVVCIGRDTW 356 LAS L+VEHP+GEF+V + L ++G + GCGL+RTARLLF G VCI D W Sbjct: 301 LASLE--RTPELSVEHPTGEFSVALRLDDNGQLAGCGLLRTARLLFAGDVCIPADVW 355 Lambda K H 0.320 0.138 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: 525 Number of extensions: 17 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: 361 Length of database: 361 Length adjustment: 29 Effective length of query: 332 Effective length of database: 332 Effective search space: 110224 Effective search space used: 110224 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: 49 (23.5 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