Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate H281DRAFT_02375 H281DRAFT_02375 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__Burk376:H281DRAFT_02375 Length = 259 Score = 177 bits (449), Expect = 2e-49 Identities = 101/254 (39%), Positives = 152/254 (59%), Gaps = 13/254 (5%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 IL+ L+ F G +AVNGV L V+ + ALIGPNGAGKTT FN LT F +PT G I+ Sbjct: 7 ILETRGLTREFKGFIAVNGVNLRVRRGSIHALIGPNGAGKTTCFNLLTKFLEPTAGQIVF 66 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124 +GE I IAR+G++R+FQ +F +TA++N+ I R L T F F Sbjct: 67 NGEDITNERPAQIARRGIIRSFQISAVFPHLTALQNVRIGLQRSLGTAFH--------FW 118 Query: 125 KSEREAMEYAEYWLD---KVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 KSER + + +D +V LT+FA+ L+YG++R LEIA + P +++LDEP Sbjct: 119 KSERTLRQLDDRAMDLLTQVGLTDFADVLTVELSYGRKRALEIATTLAMEPELMLLDEPT 178 Query: 182 AGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQI 241 G+ ++ + + ALI + T+L++EH+M ++ ISD I V+ +G LA+G+ ++ Sbjct: 179 QGMGHEDVDRVTALI--KKVSSGRTILMVEHNMNVIAGISDTITVLQRGEVLAEGSYAEV 236 Query: 242 RDNPEVIKAYLGEA 255 NP V++AY+G A Sbjct: 237 SKNPLVMQAYMGSA 250 Lambda K H 0.321 0.138 0.398 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: 169 Number of extensions: 11 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: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 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