Align Maleylacetoacetate isomerase; MAAI; GSTZ1-1; Glutathione S-transferase zeta 1; EC 5.2.1.2; EC 2.5.1.18 (characterized)
to candidate H281DRAFT_05672 H281DRAFT_05672 RNA polymerase-associated protein
Query= SwissProt::P57113 (216 letters) >FitnessBrowser__Burk376:H281DRAFT_05672 Length = 203 Score = 70.9 bits (172), Expect = 2e-17 Identities = 55/176 (31%), Positives = 83/176 (47%), Gaps = 8/176 (4%) Query: 7 VLYSYFRSSCSWRVRIALALKGIDYEIVPINLIKDGGQQFSEEFQTLNPMKQVPALKIDG 66 VLYS S R R+ L KG+D+EI ++L E+ +NP QVP L Sbjct: 3 VLYSGTTCPFSQRCRLVLFEKGMDFEIRDVDLFNK-----PEDIAVMNPYGQVPILVERD 57 Query: 67 ITIGQSLAILEYLEETRPIPRLLPQDPQKRAIVRM-ISDLIASGIQPLQNLSVLKQVGQE 125 + + +S I EY++E P P+L+P DP +RA R+ + + + L K E Sbjct: 58 LILYESNIINEYIDERFPHPQLMPADPVQRARARLFLLNFEKELFVHVGTLENEKGKAAE 117 Query: 126 NQMPWAQKAITSGFNALEKILQSTAGKYCVGDEVSMADVCLAPQVANAERFKVDLS 181 A+ AI L I KY +G+E SM DV +AP + + + ++LS Sbjct: 118 KNHEKARLAIRDRLTQLAPIF--LKNKYMLGEEFSMLDVAIAPLLWRLDHYGIELS 171 Lambda K H 0.319 0.135 0.392 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: 96 Number of extensions: 5 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: 216 Length of database: 203 Length adjustment: 21 Effective length of query: 195 Effective length of database: 182 Effective search space: 35490 Effective search space used: 35490 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: 45 (21.9 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