Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_000166355.1:WP_013403450.1 Length = 343 Score = 140 bits (352), Expect = 6e-38 Identities = 75/226 (33%), Positives = 124/226 (54%), Gaps = 5/226 (2%) Query: 16 LEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDVRMNDVDPS-- 73 ++ + V+L+I+ G+ +GPSG GKSTL+R I LE+ + G + ID V M + P+ Sbjct: 18 IKALDNVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLEKPTHGSIEIDGVEMTKLSPTEL 77 Query: 74 ---KRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDRK 130 ++ + ++FQ + L TV+ N+ F L AG+ + I+ RV E ++ L D Sbjct: 78 KEMRKKVGIIFQHFNLLSSRTVKGNVAFPLEIAGLDKKTIDNRVKELLELVGLTNKTDSY 137 Query: 131 PKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVYV 190 P QLSGGQ+QRV I RA+ +PK+ L DE S LD E + + + ++++ TIV V Sbjct: 138 PSQLSGGQKQRVGIARALANNPKVLLCDEATSALDPETTLSILNLLKEINREFGITIVVV 197 Query: 191 THDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGS 236 TH+ + +K+ VM G + + G +++ +P F+ S Sbjct: 198 THEMNVVKQICNKVAVMEKGQIVEQGLLTEIFANPKTKIAQNFLRS 243 Lambda K H 0.321 0.139 0.396 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: 267 Number of extensions: 13 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: 358 Length of database: 343 Length adjustment: 29 Effective length of query: 329 Effective length of database: 314 Effective search space: 103306 Effective search space used: 103306 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