Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF4159 HP15_4099 branched-chain amino acid ABC transporter, ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Marino:GFF4159 Length = 269 Score = 204 bits (518), Expect = 2e-57 Identities = 108/243 (44%), Positives = 164/243 (67%), Gaps = 8/243 (3%) Query: 7 KVLLQVKGLKVAYG-GIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGN 65 + LL++ ++V Y +Q ++G+ V +G +V+L+GSNGAGK+TT+K+++G L++ DG Sbjct: 2 EALLEIDNIEVVYNKSVQVLRGLSLRVPKGAIVALLGSNGAGKSTTLKSVSGLLTLEDGE 61 Query: 66 I-----EYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILA 120 + + GK +KG LV++GL V EGR VF +T+ ENL Y L+ Sbjct: 62 VTAGEVRFRGKDVKGVPPERLVRDGLFHVMEGRRVFEDLTVEENLIAATYALSGSKPSLS 121 Query: 121 D-IEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVD 179 D E ++ FPRL+ER+ QLAG +SGGEQQMLA+GRAL++QP +++LDEPS+GL+P++V+ Sbjct: 122 DSYELVYNYFPRLKERRKQLAGYLSGGEQQMLALGRALIAQPDLIMLDEPSLGLAPLLVE 181 Query: 180 KIFEVVRDV-YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAA 238 +IF +V + G I+LVEQNA+ +LAIA GY+ME+G I + GP +L + V+ Sbjct: 182 EIFTIVARINREQGTAILLVEQNAAVSLAIASYGYIMENGKIVIDGPADKLTANEDVQEF 241 Query: 239 YLG 241 YLG Sbjct: 242 YLG 244 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: 191 Number of extensions: 8 Number of successful extensions: 4 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: 269 Length adjustment: 24 Effective length of query: 218 Effective length of database: 245 Effective search space: 53410 Effective search space used: 53410 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 17 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