Align AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate WP_043917276.1 jaqu_RS02050 transporter substrate-binding domain-containing protein
Query= TCDB::O50181 (259 letters) >NCBI__GCF_000877395.1:WP_043917276.1 Length = 252 Score = 195 bits (496), Expect = 7e-55 Identities = 110/258 (42%), Positives = 161/258 (62%), Gaps = 8/258 (3%) Query: 1 MKKLALLGALALSVLSLPTFAADKPVRIGIEA-AYPPFSLKTPDGQLAGFDVDIGNALCE 59 MKK+ L A A ++ AA V+IGI A AYPPF+ K G G++++I +A+C Sbjct: 1 MKKIVTLAAAA----AISATAATADVKIGISAEAYPPFAEKDAAGNWVGWEMEIIDAVCA 56 Query: 60 EMKVQCKWVEQEFDGLIPALKVRKIDAILSSMTITDERKRSVDFTNKYYNTPARFVMKEG 119 M+ +C+ V +DG+IPAL ++DAI++SM+IT+ER R++DF++KYYNTPA V + Sbjct: 57 AMEEECEVVPVAWDGIIPALLSGRMDAIMASMSITEERMRTIDFSDKYYNTPAVIVAAKD 116 Query: 120 ASLNDPKADLKGKKAGVLRGSTADRYASAELTPAGVEVVRYNSQQEANMDLVAGRLDAVV 179 + ++ A L GK GV + Y E+ Y + E N DLVAGR+DAVV Sbjct: 117 SEISGDPASLDGKIVGVQVSTIHANYVEKHFEEQ-AEMKVYQTFDEHNQDLVAGRVDAVV 175 Query: 180 ADSVNLEDGFLKTDAGKGYAFVGPQLTDAKYFGEGVGIAVRKGDSELAGKFNAAIDALRA 239 DS+ +D FL +DAG+ Y G +L D + FG GVG+ +R+G+ EL +FNAAI +R Sbjct: 176 GDSLAFQD-FLSSDAGQAYEVKG-ELNDEEVFGPGVGVGLRQGEDELKERFNAAIRQIRE 233 Query: 240 NGKYKQIQDKYFSFDVYG 257 +G Y +I ++YF FD+YG Sbjct: 234 DGTYDEISNRYFDFDIYG 251 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: 218 Number of extensions: 10 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: 252 Length adjustment: 24 Effective length of query: 235 Effective length of database: 228 Effective search space: 53580 Effective search space used: 53580 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 Sep 24 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