Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 352022 BT2494 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Btheta:352022 Length = 238 Score = 141 bits (355), Expect = 1e-38 Identities = 80/228 (35%), Positives = 135/228 (59%), Gaps = 14/228 (6%) Query: 4 LEVQDLHKRYGSH---EVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKI 60 +++ D++K Y + VLKG++L G+ +SI+G+SGSGKST L + +L+ G Sbjct: 2 IKLTDINKTYNNGAPLHVLKGINLDIQRGEFVSIMGASGSGKSTLLNILGILDNYDTGDY 61 Query: 61 LLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLG 120 LNN +K ++ K + + +FQ FNL S A+EN+ P+ G Sbjct: 62 YLNNVLIK---------DLSETKAAEYRNRMIGFIFQSFNLISFKDAVENVA-LPLFYQG 111 Query: 121 MSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSAL 180 +S+ + A YL+++G+ P MSGG++QRVAIARAL +P+++L DEPT AL Sbjct: 112 VSRKKRNALALEYLDRLGLKEWAHHMPNEMSGGQKQRVAIARALITQPQIILADEPTGAL 171 Query: 181 DPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVE 228 D + +V+++++ L + G T+VVVTHE G A + +++++ + G++E Sbjct: 172 DSKTSVEVMQILKDLHRMGMTIVVVTHESGVANQ-TDKIIHIKDGIIE 218 Lambda K H 0.317 0.131 0.366 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: 168 Number of extensions: 13 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: 238 Length adjustment: 24 Effective length of query: 230 Effective length of database: 214 Effective search space: 49220 Effective search space used: 49220 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