Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_057508907.1 ABB28_RS12160 methionine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_001431535.1:WP_057508907.1 Length = 335 Score = 157 bits (397), Expect = 4e-43 Identities = 90/252 (35%), Positives = 147/252 (58%), Gaps = 10/252 (3%) Query: 19 LLEIRNLTKSYD----GQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAG 74 ++E + L KSY A+ + LTI +GE+F ++G SG GKSTL+RM+ E PS G Sbjct: 1 MIEFQRLHKSYAVAGRAISALQPLDLTIQEGEVFGIIGHSGAGKSTLIRMINRLEDPSGG 60 Query: 75 QIMLDGVDLSQVPP-----YLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASR 129 ++++ G D++ + R I M+FQ + L TV N+AF L+ P+A+I +R Sbjct: 61 RLLIAGEDVTALETAGLRTLRRRIGMIFQHFNLLSSRTVASNVAFPLELAGTPRAQIDAR 120 Query: 130 VNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQ 189 V E+L V +Q A + P QLSGGQ+QRV +AR+LA P++LL DE ALD + + Sbjct: 121 VAELLQTVGLQAHADKYPAQLSGGQKQRVGIARALATGPQILLCDEATSALDPQTTASVL 180 Query: 190 LEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEF 249 + I +G+T V++TH+ + + R+A+++ G+ V++G +++ HP + F Sbjct: 181 ALLSKINRELGLTIVLITHEMDVIRRVCDRVAVLDAGEMVEMGPVTDVFLHPQHPTTRRF 240 Query: 250 IG-SVNVFEGVL 260 + S ++ EG L Sbjct: 241 VSESEHIDEGTL 252 Lambda K H 0.321 0.137 0.400 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: 261 Number of extensions: 12 Number of successful extensions: 2 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: 377 Length of database: 335 Length adjustment: 29 Effective length of query: 348 Effective length of database: 306 Effective search space: 106488 Effective search space used: 106488 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