Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS31425 BPHYT_RS31425 arginine ABC transporter ATP-binding protein
Query= uniprot:Q88GX0 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS31425 Length = 233 Score = 274 bits (700), Expect = 1e-78 Identities = 139/241 (57%), Positives = 175/241 (72%), Gaps = 8/241 (3%) Query: 20 LIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQV 79 +I + ++K YG VL D + GE +V+CGPSGSGKSTLI+ +N LE Q G I V Sbjct: 1 MIELNNVSKWYGGNRVLNDCTASIARGEVVVICGPSGSGKSTLIKSVNGLEAVQSGQIVV 60 Query: 80 DGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMY 139 DGID+ A + +++R+ +GMVFQHF LFPH+SV N +LA +V G +R A ERAR+ Sbjct: 61 DGIDVTAKRADLSRLRARVGMVFQHFELFPHLSVQRNLMLAQMNVLGRARDKAAERARLL 120 Query: 140 LSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLV 199 L +VG+ HKYP+QLSGGQQQRVAIARAL M P MLFDEPTSALDPEMV EVLDV Sbjct: 121 LLRVGLSGHEHKYPAQLSGGQQQRVAIARALSMDPVAMLFDEPTSALDPEMVNEVLDV-- 178 Query: 200 QLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAFLAQIL 259 MTMLCVTHEMGFA++VA+RVLF++ G I+ED + FF +PR+ERA+ FL++IL Sbjct: 179 ------MTMLCVTHEMGFAKRVADRVLFMDRGVIVEDDTREAFFERPRSERARDFLSRIL 232 Query: 260 H 260 H Sbjct: 233 H 233 Lambda K H 0.322 0.137 0.395 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: 205 Number of extensions: 4 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: 260 Length of database: 233 Length adjustment: 24 Effective length of query: 236 Effective length of database: 209 Effective search space: 49324 Effective search space used: 49324 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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