Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate AO353_12000 AO353_12000 amino acid transporter
Query= reanno::pseudo5_N2C3_1:AO356_09895 (257 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12000 Length = 257 Score = 486 bits (1250), Expect = e-142 Identities = 249/257 (96%), Positives = 256/257 (99%) Query: 1 MAQATPALEIRNLHKRYGQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPN 60 MA+ATPALEIRNLHKRYG+LEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENP+ Sbjct: 1 MAEATPALEIRNLHKRYGKLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPH 60 Query: 61 QGQILVAGEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPR 120 QGQILVAGEELKLK AKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPR Sbjct: 61 QGQILVAGEELKLKPAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPR 120 Query: 121 RVLGQSKAEAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEP 180 RVLGQSK+EA+EVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEP Sbjct: 121 RVLGQSKSEAIEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEP 180 Query: 181 TSALDPEMVQEVLSVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQV 240 TSALDPEMVQEVL+VIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGL+EEQGSPQQV Sbjct: 181 TSALDPEMVQEVLNVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGLIEEQGSPQQV 240 Query: 241 FENPLSARCKQFMSSNR 257 FENPLSARCKQFMSSNR Sbjct: 241 FENPLSARCKQFMSSNR 257 Lambda K H 0.317 0.132 0.363 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: 307 Number of extensions: 1 Number of successful extensions: 1 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: 257 Length of database: 257 Length adjustment: 24 Effective length of query: 233 Effective length of database: 233 Effective search space: 54289 Effective search space used: 54289 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 Apr 09 2024. 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