Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate Echvi_3112 Echvi_3112 ABC-type hemin transport system, ATPase component
Query= uniprot:A0A159ZWL6 (233 letters) >FitnessBrowser__Cola:Echvi_3112 Length = 271 Score = 100 bits (248), Expect = 4e-26 Identities = 74/239 (30%), Positives = 126/239 (52%), Gaps = 13/239 (5%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 M+ EN+ K L V++++ GE++T++G NGAGKSTLL L G +G I Sbjct: 2 MISAENIHFCIQKRPILDQVDLQIYPGEVLTILGPNGAGKSTLLKLLSGENTCDTGKIS- 60 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQ-MDKVLHL 119 + + L+ Q + K AV+P+ V TVEE +A+G D +Q M++V+ + Sbjct: 61 INQVLLQQLKPRQLAKYRAVMPQHSSVNFPYTVEEIIALGKLAHDPHSSSDQLMEEVMDI 120 Query: 120 --FPRLKERFTQRGGTMSGGEQQMLAIGRALM----SKP--KLLLLDEPSLGLAPIIIQQ 171 L+ER + +SGGE+Q + + RAL+ KP + LLLDEP+ + Q Sbjct: 121 TGTAALRERMIK---GLSGGERQRVHLARALLQIWEDKPYARYLLLDEPTSSMDIAQQHQ 177 Query: 172 IFDIIEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAY 230 + ++ LR+ + V + + N A + +D+ ++++G+VV G A++T K+ Y Sbjct: 178 VLRLLRFLRQRNIGVLTILHDLNLAAQYSDKVMLMKDGKVVGFGPTSAIMTATKLSHVY 236 Lambda K H 0.320 0.137 0.381 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: 134 Number of extensions: 11 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: 233 Length of database: 271 Length adjustment: 24 Effective length of query: 209 Effective length of database: 247 Effective search space: 51623 Effective search space used: 51623 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: 46 (22.3 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