Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_004124037.1 RHSP_RS23215 triose-phosphate isomerase
Query= BRENDA::Q7X216 (265 letters) >NCBI__GCF_000359745.1:WP_004124037.1 Length = 256 Score = 201 bits (510), Expect = 2e-56 Identities = 117/252 (46%), Positives = 156/252 (61%), Gaps = 10/252 (3%) Query: 6 WLGTSWKMNKPLSQAMAWCETLAARMPEGCHPA-IQPFVIPSFTAIQPVSHFLQTHQLPL 64 W+GTSWKMNK L++A A+ E L R + A IQ FVIP FTA++ V L + + Sbjct: 8 WIGTSWKMNKTLAEARAFAEAL--RAADALRDARIQRFVIPPFTAVREVKAILS--ETSV 63 Query: 65 LTGAQNMHEADQGAWTGEISAAMLAETGATLVELGHSERRAAFNESDAAINRKVHSALGH 124 GAQNMH A++GAWTGEIS ML + +VELGHSERR F E++ + K +A+ H Sbjct: 64 KVGAQNMHWAEKGAWTGEISPLMLKDCNLDIVELGHSERREHFGETNETVGLKTEAAVRH 123 Query: 125 GLRPLICIGDSAEEKRWQVSRESVVRQMKIALYGLS-HQQALRTLIAYEPVWAIGEHGTP 183 GL PLICIG++ E++ + E + Q+ AL LS Q+ L+AYEPVWAIGE G P Sbjct: 124 GLIPLICIGETLEDRESGRATEILSEQVVGALEELSAAQKQADILLAYEPVWAIGEKGIP 183 Query: 184 ASPQEAGVIHQALRQALCERFGHETGTRIPLLYGGXVTLQNAVELLRQQEINGLFIGRAA 243 A P A QA A+ ++ G +IP LYGG V QN EL+ ++GLFIGR+A Sbjct: 184 AEPSYADA-RQAEIIAVAQKV---LGRKIPCLYGGSVNPQNCEELISCPNVDGLFIGRSA 239 Query: 244 WDAQGYCDIVQR 255 W+ +GY DI+ + Sbjct: 240 WNVEGYLDILAK 251 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: 205 Number of extensions: 8 Number of successful extensions: 5 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: 256 Length adjustment: 24 Effective length of query: 241 Effective length of database: 232 Effective search space: 55912 Effective search space used: 55912 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