Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013093619.1 BC1002_RS29445 ABC transporter
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000092885.1:WP_013093619.1 Length = 646 Score = 253 bits (647), Expect = 5e-72 Identities = 128/250 (51%), Positives = 178/250 (71%) Query: 7 EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66 E +L++ GI +F GL+AL+ V +T++RG V+GLIGPNG+GK+T NV+TG+Y P AG+ Sbjct: 389 EEILQLRGILMQFSGLKALNQVDLTVRRGTVHGLIGPNGSGKSTMMNVLTGIYVPTAGSI 448 Query: 67 ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126 E G ++A AGIARTFQN++LF EMTALENV+VG H + + + Sbjct: 449 EYRGMSLAGKTSSQIALAGIARTFQNVQLFGEMTALENVLVGLHHTFRAHIADVGLMSPR 508 Query: 127 FKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAA 186 ++ EE A +RA +L +VG+ A +AR L YG QR LEIARALA DPQ++ LDEPAA Sbjct: 509 YRREERAARERALGMLRFVGLEHVAGEEARNLPYGKQRLLEIARALALDPQVLLLDEPAA 568 Query: 187 GMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246 G+ A + +L +I ++R+ T++LIEH + +VM +CDRV+VLD+G++IAEGNPA++Q Sbjct: 569 GLTAPDIKELVAIIRKVRDHGITVVLIEHHMDVVMSVCDRVSVLDFGQKIAEGNPADIQS 628 Query: 247 NEKVIEAYLG 256 NEKVIEAYLG Sbjct: 629 NEKVIEAYLG 638 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: 428 Number of extensions: 18 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: 646 Length adjustment: 31 Effective length of query: 229 Effective length of database: 615 Effective search space: 140835 Effective search space used: 140835 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