Align AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate WP_015933040.1 MNOD_RS31675 transporter substrate-binding domain-containing protein
Query= TCDB::O50181 (259 letters) >NCBI__GCF_000022085.1:WP_015933040.1 Length = 256 Score = 134 bits (338), Expect = 1e-36 Identities = 91/258 (35%), Positives = 133/258 (51%), Gaps = 12/258 (4%) Query: 1 MKKLALLGALALSVLSLPTFAAD--KPVRIGIEAAYPPFSLKTPDGQLAGFDVDIGNALC 58 + +L +L +LA S P AA PVRI E PPF+ DG+ AGF+VD+ ALC Sbjct: 5 LSRLLVLVSLAAS----PVQAAPLPDPVRIATEGGNPPFNY-VEDGKPAGFEVDLAEALC 59 Query: 59 EEMKVQCKWVEQEFDGLIPALKVRKIDAILSSMTITDERKRSVDFTNKYYNTPARFVMKE 118 + + C+ V ++DG+I L+ + DAI++S+ IT +R+ + F+ YY P+ ++ + Sbjct: 60 KAAGLTCRIVLHQWDGIIRGLEGAEYDAIMASLAITPKRRSRISFSRSYYRIPSSYMARR 119 Query: 119 GASLN--DPKADLKGKKAGVLRGSTADRYASAELTPAGVEVVRYNSQQEANMDLVAGRLD 176 DP A LKG+ G S Y A A ++ ++S ++A DL GRLD Sbjct: 120 DDQTGPLDPAA-LKGRAVGAAAHSPQLAYLEARAPEA--DIRSFDSVKDAGYDLRLGRLD 176 Query: 177 AVVADSVNLEDGFLKTDAGKGYAFVGPQLTDAKYFGEGVGIAVRKGDSELAGKFNAAIDA 236 V+ D L + D VG GEGVGI +RKGD L F+ AI A Sbjct: 177 LVLGDKRELTEILALPDGAACCRLVGDVPPGDPLLGEGVGIGLRKGDDALREAFDRAIAA 236 Query: 237 LRANGKYKQIQDKYFSFD 254 + A+G Y +I+ KY FD Sbjct: 237 VIADGTYDRIRAKYLPFD 254 Lambda K H 0.316 0.135 0.381 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: 184 Number of extensions: 9 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: 259 Length of database: 256 Length adjustment: 24 Effective length of query: 235 Effective length of database: 232 Effective search space: 54520 Effective search space used: 54520 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 (21.6 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