Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate GFF1057 Psest_1090 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__psRCH2:GFF1057 Length = 238 Score = 154 bits (389), Expect = 2e-42 Identities = 92/227 (40%), Positives = 131/227 (57%), Gaps = 6/227 (2%) Query: 1 MTTNILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRV 60 M + L+V L YG + G+DL V GELVTL+G NGAG++TTL+AI + R Sbjct: 5 MDRDQLRVSDLHAFYGESHILHGVDLVVGRGELVTLLGRNGAGRSTTLRAIMNMV--GRR 62 Query: 61 EGHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADI 120 G I G G + ++ + + PE RG+F +S++ENLL+ + Sbjct: 63 TGSIVVNGNETIGMPAHQIPRLGVGYCPEERGIFASLSVEENLLLPPTVRSG----GMSL 118 Query: 121 DKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIF 180 D+ + +FP L ER LSGGEQQMLAMAR L + LLLLDE + GL+P++V+K+ Sbjct: 119 DELYEMFPNLYERRFSQGTRLSGGEQQMLAMARILRTGANLLLLDEITEGLAPVIVQKLG 178 Query: 181 EVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQM 227 EV+ + +G+TI+LVEQN + A A R YVME G I + +A + Sbjct: 179 EVLIKLKQRGLTIVLVEQNFRFAAPLADRHYVMEHGRIIEEIEAADL 225 Lambda K H 0.317 0.134 0.365 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: 153 Number of extensions: 5 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: 241 Length of database: 238 Length adjustment: 23 Effective length of query: 218 Effective length of database: 215 Effective search space: 46870 Effective search space used: 46870 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 (21.6 bits) S2: 46 (22.3 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