Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate 199537 SO0342 conserved hypothetical protein (NCBI ptt file)
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__MR1:199537 Length = 397 Score = 206 bits (524), Expect = 9e-58 Identities = 144/388 (37%), Positives = 208/388 (53%), Gaps = 45/388 (11%) Query: 3 QTRIPCLLMRGGTSKGAYFLHDDLP----APGPLRDRVLLAVMGSPD--ARQIDGIGGAD 56 Q ++ MRGGTSKG +F DLP PGP RD +LL V+GSPD A+QIDG+GGA Sbjct: 9 QIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGAT 68 Query: 57 SLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAA-- 114 S TSK I+ S + + DVDYLF QV +D+ VD+ NCGN+ A VG FA+ GL+ A Sbjct: 69 SSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDAAR 128 Query: 115 ---SGASTPVRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAG- 170 +G T VRI+ N G+ +A VP DG V+ GD +DGV AA + + F + A Sbjct: 129 IPRNGVCT-VRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAAD 187 Query: 171 --ASCGALLPTGNSRDCVE--GV---EVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADS 223 G + PTGN D +E G+ T I+ G+P + + AEDLG TG E + + +D+ Sbjct: 188 DDGEGGCMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDN 247 Query: 224 ALKTRLEAIRLQLGPRMNL-----GDVSQRNVPKMCLLSAPR-----NGGTVN------- 266 A + E IR RM L S+++ PK+ ++ P+ +G TV Sbjct: 248 AALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLL 307 Query: 267 TRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEF----- 321 R+ + H ++ AV++ TA I G++ + GG+++ + HPSG Sbjct: 308 VRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVN--LAAGGGEKEAVRFGHPSGTLRVGAQ 365 Query: 322 TVEISLEHGVIKGCGLVRTARLLFDGVV 349 V+ + E VIK + R+AR+L +G V Sbjct: 366 AVQENGEWTVIKAI-MSRSARVLMEGFV 392 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: 408 Number of extensions: 33 Number of successful extensions: 6 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: 397 Length adjustment: 30 Effective length of query: 331 Effective length of database: 367 Effective search space: 121477 Effective search space used: 121477 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: 50 (23.9 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