Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_026167652.1 B149_RS0114960 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000375485.1:WP_026167652.1 Length = 251 Score = 130 bits (327), Expect = 2e-35 Identities = 74/242 (30%), Positives = 128/242 (52%), Gaps = 17/242 (7%) Query: 17 VAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYLGKSIKGK 76 V +GG+QA+ V+F + EGE++ LIG NGAGKTT ITG ++G + Y ++I G Sbjct: 11 VRFGGLQALTDVNFSLGEGEVMGLIGPNGAGKTTVFNVITGVYRASEGKVTYDDRTITGL 70 Query: 77 GAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADI-------------- 122 + ++ G+ + +F++MT EN + + R K G+ + Sbjct: 71 RPYQVLAMGVARTFQNIRLFSQMTALENCMVAQHSRS-KTGVFGAVLRSPSQKREERKIR 129 Query: 123 -EKMFTI-FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDK 180 + M + F L + +D+ A M G Q+ L + RAL S+PK +LLDEP+ GL+P Sbjct: 130 EQSMKALEFMGLADYRDEAASNMPYGHQRRLEIARALASEPKTILLDEPAAGLNPSESRS 189 Query: 181 IFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYL 240 + + + + LG+ +++VE + + + + V++ G++ G + + DPKV AYL Sbjct: 190 LMDSIGHISDLGINVLMVEHDMKVVMGVCRKIVVLDHGVMIAEGSPEDIQKDPKVIEAYL 249 Query: 241 GE 242 G+ Sbjct: 250 GQ 251 Lambda K H 0.317 0.136 0.373 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: 156 Number of extensions: 8 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: 242 Length of database: 251 Length adjustment: 24 Effective length of query: 218 Effective length of database: 227 Effective search space: 49486 Effective search space used: 49486 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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