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 GFF559 Psest_0564 urea ABC transporter, ATP-binding protein UrtD
Query= TCDB::P21629 (255 letters) >FitnessBrowser__psRCH2:GFF559 Length = 283 Score = 134 bits (337), Expect = 2e-36 Identities = 84/251 (33%), Positives = 144/251 (57%), Gaps = 12/251 (4%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 IL + + + F G A+ ++L + ++ +IGPNGAGKTT+ + +TG +PT G Sbjct: 42 ILSLEDINVSFDGFKALTDLSLYIGVGELRCIIGPNGAGKTTMMDVITGKTRPTSGSAWF 101 Query: 65 DGE--EIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPA 122 GE ++ + IA+ G+ R FQ +F+ ++ ENL +AQ + + A L + Sbjct: 102 -GETLDLTRMSEVDIAQAGIGRKFQKPTVFEALSVFENLELAQKT--DKSVWASLRAKLS 158 Query: 123 FRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182 + +R LE + L + +R AG L++GQ++ LEI +M P++L+LDEP A Sbjct: 159 GEQKDR-----IDEVLETIRLGQSRHRPAGLLSHGQKQFLEIGMLLMQSPQLLLLDEPVA 213 Query: 183 GLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIR 242 G+ ET+ L L +H +++++EHDM V +I+DH+ V++QG LA+G+ +Q++ Sbjct: 214 GMTDAETEFTAELFKSLARKH--SLMVVEHDMGFVETIADHVTVLHQGQVLAEGSLQQVQ 271 Query: 243 DNPDVIKAYLG 253 + VI+ YLG Sbjct: 272 ADERVIEVYLG 282 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: 176 Number of extensions: 10 Number of successful extensions: 4 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: 283 Length adjustment: 25 Effective length of query: 230 Effective length of database: 258 Effective search space: 59340 Effective search space used: 59340 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