Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate Pf6N2E2_3857 Arginine ABC transporter, permease protein ArtQ
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3857 Length = 231 Score = 131 bits (329), Expect = 1e-35 Identities = 80/212 (37%), Positives = 121/212 (57%), Gaps = 11/212 (5%) Query: 17 LLAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLILLI 76 L AG + ++LAL ++ +G V+GLL A A S ++ L+ L Y T++R P L+ +LLI Sbjct: 12 LAAGALMTVKLALTALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVRGIPELLWVLLI 71 Query: 77 YFA----LPSLG-------IRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLREAGL 125 YF L +LG + LD + +I L L GAY TEVFRG +L+IPKG REAG+ Sbjct: 72 YFGTVNLLRALGEYFGNPDLTLDAFAAGVIALGLCFGAYATEVFRGAILAIPKGHREAGV 131 Query: 126 AIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESY 185 A+GL +W++ + +P M R LP L N F+ L KDT+L + I + E+ +A S Sbjct: 132 ALGLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIMRHAEIGVTVSK 191 Query: 186 RVIETWLVTTALYVAACYLIAMLLRYLEQRLA 217 + ++V +Y+ L + + LE+R A Sbjct: 192 QPFTFYMVAAFMYLGLTVLAMIGMHLLERRAA 223 Lambda K H 0.329 0.143 0.416 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: 160 Number of extensions: 9 Number of successful extensions: 2 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: 220 Length of database: 231 Length adjustment: 22 Effective length of query: 198 Effective length of database: 209 Effective search space: 41382 Effective search space used: 41382 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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