Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 5210215 Shew_2658 ABC transporter-related protein (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__PV4:5210215 Length = 227 Score = 129 bits (323), Expect = 7e-35 Identities = 79/232 (34%), Positives = 132/232 (56%), Gaps = 16/232 (6%) Query: 4 LEVQDLHKRYGSHE-----VLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAG 58 + +Q L K Y +K + L A G+ ++I+G SGSGK+T L I ++ P +G Sbjct: 3 IAIQALTKIYNPESDFPVAAVKSLDLTIAQGEFVAIMGPSGSGKTTLLNMIGGIDSPSSG 62 Query: 59 KILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHV 118 + ++ E++ ++ + AL A R + +FQ ++L +TA+EN+ E + + Sbjct: 63 AVFIDGEDITHLSEQ--ALIAF-------RRDHVGFIFQDYSLLPVLTALENV-EFVMQL 112 Query: 119 LGMSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178 G S+AE R++A LA+VG++ ++D P +SGG+QQRVA+ARALA P ++ DEPT+ Sbjct: 113 QGHSEAECRDRAMALLAQVGLAAQQDKIPAKLSGGQQQRVAVARALAPRPRFVMADEPTA 172 Query: 179 ALDPELVGDVLKVMQAL-AQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEE 229 LD + ++L +MQ+L QEG T + TH+ +VF +VE+ Sbjct: 173 NLDAKSTAELLDIMQSLNEQEGTTFIFSTHDPRVIARAKRVIVFEDGRLVED 224 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: 115 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: 227 Length adjustment: 23 Effective length of query: 231 Effective length of database: 204 Effective search space: 47124 Effective search space used: 47124 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 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