Align AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate 8500830 DvMF_1571 extracellular solute-binding protein family 3 (RefSeq)
Query= TCDB::O50181 (259 letters) >FitnessBrowser__Miya:8500830 Length = 249 Score = 122 bits (305), Expect = 9e-33 Identities = 88/251 (35%), Positives = 138/251 (54%), Gaps = 14/251 (5%) Query: 6 LLGALALSVLSLPTFA-ADKPVRIGIEAAYPPFSLKTPDGQLAGFDVDIGNALCEEMKVQ 64 L+ ALAL VL+L A A+K GI+A YPPF+ G+ AGFDV+ + + ++M + Sbjct: 7 LVAALAL-VLALGGVAFAEKTYINGIDANYPPFAYVDKSGKPAGFDVESMDWIAKKMGFK 65 Query: 65 CKWVEQEFDGLIPALKVRKIDAILSSMTITDERKRSVDFTNKYYNTPARFVMKEGASLND 124 ++DG+IP L +KID + S M+IT+ER++ V+F+N Y+N F+ K+G++LN Sbjct: 66 VTHQPMDWDGIIPNLLAKKIDMVCSGMSITEERRQKVNFSNPYWNVKQVFIAKKGSTLNT 125 Query: 125 PKADLKGK-KAGVLRGSTADR--YASAELTPAGVEVVRYNSQQEANMDLVAGRLDAVVAD 181 + LKGK K GV RG++ E G ++ Y+S A D++ GR+DA D Sbjct: 126 DQI-LKGKVKLGVQRGTSEAEALQKDKEAKGYGYDLRFYDSAPLAIEDVLNGRIDAATMD 184 Query: 182 SVNLEDGFLKTDAGKGYAFVGPQLTDAKYFGEGVGIAVRKGDSELAGKFNAAIDALRANG 241 ++ +D A KG A Q+ E G+A RK D+EL N L A+ Sbjct: 185 NLPADDA-----AAKGKAI---QVVGVYGDSEDFGVATRKEDAELLKMINDGYKLLMADP 236 Query: 242 KYKQIQDKYFS 252 ++Q++ K+ + Sbjct: 237 YWEQLKQKHLA 247 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: 145 Number of extensions: 7 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: 249 Length adjustment: 24 Effective length of query: 235 Effective length of database: 225 Effective search space: 52875 Effective search space used: 52875 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 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