Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__Keio:15248 Length = 378 Score = 117 bits (293), Expect = 3e-31 Identities = 78/252 (30%), Positives = 129/252 (51%), Gaps = 20/252 (7%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 ++++ + F G + + LT+ + + L+GP+G GKTTV + G G I+L Sbjct: 17 LVQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIML 76 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124 D E I +P + + V FQ+ LF MT EN+ F + KTPA Sbjct: 77 DNEDITHVPAEN---RYVNTVFQSYALFPHMTVFENVA----------FGLRMQKTPAAE 123 Query: 125 KSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 + R ME L V L FA R L+ GQQ+R+ IAR ++ +PR+L+LDE + L Sbjct: 124 ITPR-VMEA----LRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSAL 178 Query: 185 NPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRDN 244 + K + ++ + L+ + +T + + HD + +++SD IVV+ G DGTP +I + Sbjct: 179 DYKLRKQMQNELKALQRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEE 238 Query: 245 PE--VIKAYLGE 254 P+ + ++GE Sbjct: 239 PKNLFVAGFIGE 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: 227 Number of extensions: 15 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: 378 Length adjustment: 27 Effective length of query: 228 Effective length of database: 351 Effective search space: 80028 Effective search space used: 80028 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