Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_084934895.1 HA51_RS12930 triosephosphate isomerase
Query= BRENDA::Q7X216 (265 letters) >NCBI__GCF_002095475.1:WP_084934895.1 Length = 257 Score = 130 bits (327), Expect = 3e-35 Identities = 86/257 (33%), Positives = 132/257 (51%), Gaps = 16/257 (6%) Query: 5 IWLGTSWKMNKPLSQAMAWCETLA--ARMPEGCHPAIQPFVIPSFTAIQPVSHFLQTHQL 62 IWLG S KM Q + WC +A A++P + + FV+P++ AI V+ + Sbjct: 6 IWLGVSLKMYFGYQQTLDWCRKVAGLAQLPAVKNGEVGLFVLPAYPAIPAVADIFA--KT 63 Query: 63 PLLTGAQNMHEADQGAWTGEISAAMLAETGATLVELGHSERRAAFNESDAAINRKVHSAL 122 P+ G Q++ +A+ GAWTGE+SA+ML E G +L E+GH+ERR F+E I KV +L Sbjct: 64 PVRFGGQDVCQAENGAWTGEVSASMLQELGCSLAEIGHAERRRHFHEDKVQIAAKVAMSL 123 Query: 123 GHGLRPLICIGDSAEEKRWQVSRESVVRQMKIALYGLSHQQAL--RTLIAYEPVWAIGEH 180 HGL P++CIG+ E++ ++ Q + QQ L AYEP WAIG Sbjct: 124 RHGLTPVLCIGE--EQQAEPAQAIALCEQQLAEALADAAQQGLSGEVFFAYEPQWAIG-- 179 Query: 181 GTPASPQEAGVIHQALRQALCERFGHETGTRIPLLYGGXVTLQNAVELLRQQEINGLFIG 240 +PQ A + A ++ G + ++YGG ++ L ++NGLF+G Sbjct: 180 ----APQPAPDSYIRAVCAGLQQLKTPNGITLKIIYGGSAG-PGLIQRL-GADVNGLFLG 233 Query: 241 RAAWDAQGYCDIVQRVT 257 R A D I++ + Sbjct: 234 RFAHDPNALAQIIEEAS 250 Lambda K H 0.321 0.133 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: 198 Number of extensions: 13 Number of successful extensions: 4 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: 265 Length of database: 257 Length adjustment: 25 Effective length of query: 240 Effective length of database: 232 Effective search space: 55680 Effective search space used: 55680 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 (21.9 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