Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013402123.1 CALHY_RS00760 ATP-binding cassette domain-containing protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000166355.1:WP_013402123.1 Length = 317 Score = 99.4 bits (246), Expect = 8e-26 Identities = 71/239 (29%), Positives = 126/239 (52%), Gaps = 9/239 (3%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +++V+ L YG A+ + FEV++GE+V +G NGAGK+TTM ITG LS +G Sbjct: 1 MIKVEHLTKKYGQHYAIHDISFEVQKGEIVGFLGPNGAGKSTTMNIITGYLSPTEGTAYV 60 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRK-DKAGILADIEKMFT 127 G I + + VK+ + +PE ++ MT+ E L + I+K DK ++K+ Sbjct: 61 DGFDILEEP--EEVKKRIGYLPENPPLYMDMTVQEYLDFVSDIKKVDKKEKKRSMDKIME 118 Query: 128 IFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRD 187 + +++L +S G +Q + + +AL+ P VL+LDEP++GL P + +I V++ Sbjct: 119 TV-GIAHVRNRLIKNLSKGYKQRVGLAQALIGNPPVLILDEPTIGLDPKQIIEIRSVIKS 177 Query: 188 VYALGVTIVLVEQNASRALAIADRGYVMESGLI----TMTGPGQQLLNDPKVRAAYLGE 242 + + TI+L A+ +R ++ G I T ++L + K++ LG+ Sbjct: 178 LRS-EHTIILSSHILPEVSAVCERVLIINKGKIVASDTPENLSKRLTHGSKLQLRVLGQ 235 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: 151 Number of extensions: 7 Number of successful extensions: 3 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: 317 Length adjustment: 25 Effective length of query: 217 Effective length of database: 292 Effective search space: 63364 Effective search space used: 63364 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: 47 (22.7 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