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 Pf1N1B4_691 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::P21629 (255 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_691 Length = 351 Score = 127 bits (318), Expect = 4e-34 Identities = 76/240 (31%), Positives = 128/240 (53%), Gaps = 18/240 (7%) Query: 6 LEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLD 65 L + + +G AV VNL + E ++V +GP+G GKTT+ + G TGG IRLD Sbjct: 4 LILENVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLTGGEIRLD 63 Query: 66 GEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRR 125 GE+I P H+ + FQ++ LF MT EN+ A K + Sbjct: 64 GEDIGHTPAHQ---RNFGMVFQSLALFPHMTVGENI-------------AYPLKLRGVSK 107 Query: 126 SEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLN 185 ++++A LE + L E +R L+ GQ++R+ IAR + +RP+IL+LDEP + L+ Sbjct: 108 ADQQAR--VVELLELIQLQEMIDRPVAKLSGGQRQRVAIARAIASRPKILLLDEPLSALD 165 Query: 186 PKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNP 245 K + ++ I +L+ N+T +++ HD + M+++D +VV+ + G+P +I +P Sbjct: 166 AKLRESMQVEIRQLQQRLNITTIMVTHDQREAMTMADIVVVLGEHRVQQVGSPIEIYRHP 225 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: 204 Number of extensions: 10 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: 255 Length of database: 351 Length adjustment: 27 Effective length of query: 228 Effective length of database: 324 Effective search space: 73872 Effective search space used: 73872 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: 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