Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 6938805 Sama_2908 ABC transporter, ATP-binding/permease protein, putative (RefSeq)
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__SB2B:6938805 Length = 593 Score = 84.0 bits (206), Expect = 6e-21 Identities = 66/214 (30%), Positives = 109/214 (50%), Gaps = 10/214 (4%) Query: 18 IQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVFDDKDITDWQTAKI 77 ++AL E+S+HI GE V L+G +GAGK+TL L SG I DD DI + + Sbjct: 366 VRALDEISVHIRPGEKVALVGESGAGKSTLFQLLGRFYAPDSGTIYLDDTDIAN-ADLQA 424 Query: 78 MREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQ-----ERIKWVYELFPR-LHERR 131 +R A A+VP+ +F+ +V EN+ G A D+ + R E P H Sbjct: 425 LRRAFALVPQESVIFAD-SVLENVRYGKVDATLDEVKAACVAARAHDFIEAMPEGYHSYL 483 Query: 132 IQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLREQGMTIF 191 +R +SGG++Q +AI RA++++ +LLLDE + L + + + + ++ L G T Sbjct: 484 GERGVKLSGGQKQRIAIARAILASRPVLLLDEATSALDAVSERYVKEALDTL-ICGRTSL 542 Query: 192 LVEQNANQALKLADRGYVLENGHVVLSDTGDALL 225 ++ + ADR V++ G ++ + LL Sbjct: 543 IIAHRLATVIN-ADRILVMDKGKIIAQGSHTELL 575 Lambda K H 0.321 0.137 0.390 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: 301 Number of extensions: 14 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: 237 Length of database: 593 Length adjustment: 30 Effective length of query: 207 Effective length of database: 563 Effective search space: 116541 Effective search space used: 116541 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: 49 (23.5 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