Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_004313986.1 C665_RS13220 ABC transporter
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000310185.1:WP_004313986.1 Length = 597 Score = 223 bits (567), Expect = 1e-62 Identities = 111/253 (43%), Positives = 170/253 (67%), Gaps = 2/253 (0%) Query: 4 KSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63 K+ E++L+ +++RFGGL A +++ + ++ G++ LIGPNGAGK+T FN I+G+ TP + Sbjct: 344 KAGELILEAKDVTRRFGGLIANNNMSLEVRAGEILALIGPNGAGKSTMFNQISGVDTPTS 403 Query: 64 GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFR 123 G GKP E+A+ G++RTFQ+++L M+ LENV +G H+R+ G+ + +R Sbjct: 404 GEVLFLGKPVAGHDSREIARMGMSRTFQHVKLLPTMSVLENVAIGAHLRSDKGVLSSAWR 463 Query: 124 TKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDE 183 +AEEA I K A ++ VG+ ++ +A +L+ G QR LEIARAL DP L+ LDE Sbjct: 464 LD--RAEEARILKEAARQIERVGLAEYMYEEAGSLALGQQRILEIARALCADPCLLLLDE 521 Query: 184 PAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAE 243 PAAG+ EK L EL+ ++R + L++EHD+ VM L DRV V+++G++IAEG P E Sbjct: 522 PAAGLRFREKEALGELLRKLRAEGMATLIVEHDMDFVMSLVDRVVVMEFGQKIAEGLPDE 581 Query: 244 VQKNEKVIEAYLG 256 +Q+N V+EAYLG Sbjct: 582 IQQNPAVLEAYLG 594 Lambda K H 0.319 0.137 0.384 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: 399 Number of extensions: 19 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: 260 Length of database: 597 Length adjustment: 31 Effective length of query: 229 Effective length of database: 566 Effective search space: 129614 Effective search space used: 129614 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 (21.7 bits) S2: 50 (23.9 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