Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 199928 SO0742 iron(III) ABC transporter, ATP-binding protein (NCBI ptt file)
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__MR1:199928 Length = 349 Score = 105 bits (262), Expect = 1e-27 Identities = 74/243 (30%), Positives = 126/243 (51%), Gaps = 8/243 (3%) Query: 3 TNILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEG 62 T+ L + Q+ Y G Q +KG+DL + +GE++ L+G +G GKTT L+A+ G S +G Sbjct: 2 TSTLNLHQVHSDYQGQQILKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAIS--QG 59 Query: 63 HIEYLGQPLKGKKSFELVKDK-LAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADID 121 I+ G+ + G F + + + M+ + +F +++ EN+L G Q A +D Sbjct: 60 EIQINGKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFGV-AKLTTAQRKARLD 118 Query: 122 KWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFE 181 A+ +L+ A + LSGG+QQ +++ARAL P+LLLLDEP + + + Sbjct: 119 DMLALV-KLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMA 177 Query: 182 VIRNVSAQ-GITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDP--RVKAAYL 238 IR++ Q ++ + V + A A + G+I G+A+ + P R A +L Sbjct: 178 EIRSILKQRNVSAVFVTHSKDEAFVFADTLAIFSQGVIVQHGRAEDLYAAPNSRYVADFL 237 Query: 239 GEG 241 G G Sbjct: 238 GSG 240 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: 195 Number of extensions: 11 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: 241 Length of database: 349 Length adjustment: 26 Effective length of query: 215 Effective length of database: 323 Effective search space: 69445 Effective search space used: 69445 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: 48 (23.1 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