Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_043769602.1 U743_RS15750 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >NCBI__GCF_000733765.1:WP_043769602.1 Length = 231 Score = 135 bits (341), Expect = 6e-37 Identities = 84/219 (38%), Positives = 126/219 (57%), Gaps = 14/219 (6%) Query: 17 EVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANKDGA 76 ++L+GV L A G+ +SI+G+SGSGK+T L + L+ P +G++LLN + + + A Sbjct: 22 DILRGVELDVAPGESVSILGTSGSGKTTLLALLAGLDTPTSGRVLLNGRDTSAMDEEARA 81 Query: 77 LKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKAEAREKAELYLAK 136 AD + VFQ F+L + TA+EN+M P + G A AR A LA+ Sbjct: 82 AARADT---------VGFVFQSFHLLAGFTALENVM-LPAELAGRHDAAAR--AADALAR 129 Query: 137 VGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLKVMQALA 196 VG++ R YP +SGGEQQRVA+ARA P ++ DEPT +LD +++++ AL Sbjct: 130 VGLAQRHGHYPHQLSGGEQQRVALARAWVTRPAILFADEPTGSLDAATGAQIIELLFALN 189 Query: 197 QE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPR 234 QE G T+V+VTH+ A +L L G++E+ PR Sbjct: 190 QESGTTLVLVTHDHQLAGRCGRRL-HLADGLLEQIATPR 227 Lambda K H 0.317 0.131 0.364 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: 132 Number of extensions: 7 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: 254 Length of database: 231 Length adjustment: 23 Effective length of query: 231 Effective length of database: 208 Effective search space: 48048 Effective search space used: 48048 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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