Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 202051 SO2927 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__MR1:202051 Length = 253 Score = 142 bits (358), Expect = 7e-39 Identities = 92/231 (39%), Positives = 134/231 (58%), Gaps = 14/231 (6%) Query: 14 GSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANK 73 GS +LKG++L G+ ++I+G SGSGKST L + L+ P AG+I L+ E L + + Sbjct: 25 GSLTILKGINLDVKQGESVAILGPSGSGKSTLLGLLAALDTPTAGEIWLDGEALSPLNEE 84 Query: 74 DGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKAEAREKAELY 133 KAA KQ ++S +FQ F L +TA+EN+M P + G+ A +EKAE Sbjct: 85 Q---KAALRKQ------KVSFIFQSFMLVDTLTALENVM-LPAELAGVKNA--KEKAEAM 132 Query: 134 LAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLKVMQ 193 L +VG+SHR P +SGGEQQRVAIARA EP+V+ DEPT LD + ++ Sbjct: 133 LGRVGLSHRLTHLPKQLSGGEQQRVAIARAFICEPKVLFADEPTGNLDSVNGHKIADMLF 192 Query: 194 ALAQEGR-TMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 L QE T+++VTH++ A+ QLV + G ++E+ +P + N E Sbjct: 193 ELNQENHTTLILVTHDLQLAKRCQRQLV-MDNGHLQENEHPNALQSNSACE 242 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: 150 Number of extensions: 7 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: 254 Length of database: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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: 47 (22.7 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