Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate HSERO_RS14705 HSERO_RS14705 ABC transporter
Query= TCDB::P21629 (255 letters) >FitnessBrowser__HerbieS:HSERO_RS14705 Length = 253 Score = 233 bits (594), Expect = 3e-66 Identities = 111/250 (44%), Positives = 169/250 (67%), Gaps = 1/250 (0%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 +L+++ ++ FGGL + GVN V + ++ +IGPNGAGKTTVFN +TG + + G IR Sbjct: 2 LLQLNDISKNFGGLQVLQGVNFNVRQGEIFGLIGPNGAGKTTVFNLITGLLRASSGSIRF 61 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 + ++I + HKI +G+ RTFQN+R+FKEMT +EN++V H HLN + L FR Sbjct: 62 NDDDIGAVAPHKITERGIARTFQNIRVFKEMTLLENVVVGMHDHLNYGVASMLLNLGGFR 121 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 +E+EA E A L V L A+ A +L+YG+QR+LE AR + T+P++L+LDEP AG+ Sbjct: 122 NAEKEARERALELLSWVRLDHKAHMLADSLSYGEQRKLEFARALATKPKLLLLDEPVAGM 181 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 NP E +L + I ++ + T+ +IEHDM+ VM + + I V+N G +A+GTP+QI++N Sbjct: 182 NPAEKTELMSEIVNIK-QRGFTIFMIEHDMRFVMGLCERIAVLNFGKIIAEGTPDQIKNN 240 Query: 245 PDVIKAYLGE 254 +VI+AYLG+ Sbjct: 241 QEVIEAYLGK 250 Lambda K H 0.320 0.137 0.391 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: 192 Number of extensions: 7 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: 255 Length of database: 253 Length adjustment: 24 Effective length of query: 231 Effective length of database: 229 Effective search space: 52899 Effective search space used: 52899 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 (21.8 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