Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_000166355.1:WP_013403450.1 Length = 343 Score = 132 bits (332), Expect = 1e-35 Identities = 82/260 (31%), Positives = 133/260 (51%), Gaps = 12/260 (4%) Query: 1 MARI-TLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLL 59 M RI L I H+ G + K+ L V+ G + ++GPSG GK+TL+ I+ L Sbjct: 1 MIRIKNLTKIYHSNGIDIKA-----LDNVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLE 55 Query: 60 QPSHGRILFDGKDVTNLSTQS-----RNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEA 114 +P+HG I DG ++T LS + + +FQ + + TV N+AFPL G+ + Sbjct: 56 KPTHGSIEIDGVEMTKLSPTELKEMRKKVGIIFQHFNLLSSRTVKGNVAFPLEIAGLDKK 115 Query: 115 DVDRRVRDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPH 174 +D RV+++LE++ L + L+ QKQ++ + R L N +L DE + +DP Sbjct: 116 TIDNRVKELLELVGLTNKTDSYPSQLSGGQKQRVGIARALANNP-KVLLCDEATSALDPE 174 Query: 175 MKWVLRSQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSH 234 + + LK ++++FG T+V VTH+ KV VM GQIV+ G E+F P Sbjct: 175 TTLSILNLLKEINREFGITIVVVTHEMNVVKQICNKVAVMEKGQIVEQGLLTEIFANPKT 234 Query: 235 TFVGYFIGSPGMNFMPARIE 254 F+ S + +P ++ Sbjct: 235 KIAQNFLRSLTFSELPEELK 254 Lambda K H 0.321 0.137 0.405 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: 247 Number of extensions: 14 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: 356 Length of database: 343 Length adjustment: 29 Effective length of query: 327 Effective length of database: 314 Effective search space: 102678 Effective search space used: 102678 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 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