Align AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate AZOBR_RS27130 AZOBR_RS27130 polyamine ABC transporter substrate-binding protein
Query= TCDB::O50181 (259 letters) >FitnessBrowser__azobra:AZOBR_RS27130 Length = 259 Score = 176 bits (446), Expect = 4e-49 Identities = 99/259 (38%), Positives = 145/259 (55%), Gaps = 6/259 (2%) Query: 1 MKKLALLGALALSVLSLPTFAADK----PVRIGIEAAYPPFSLKTPDGQLAGFDVDIGNA 56 MK+LAL A+ L L+ A + P+RI E AYPPF++ +PDG L G +V++ NA Sbjct: 1 MKRLALGLAMGLCALAAAVPTASRADGPPLRIATEGAYPPFNMTSPDGTLGGLEVELANA 60 Query: 57 LCEEMKVQCKWVEQEFDGLIPALKVRKIDAILSSMTITDERKRSVDFTNKYYNTPARFVM 116 LCE +K +C V Q++DG+IP L R+ DAI+++M IT ER +++ F+ Y PA FV Sbjct: 61 LCERIKRRCTLVAQDWDGIIPGLLSRRYDAIMATMNITPERAKAIAFSAPYMVVPAYFVA 120 Query: 117 KEGASLNDPKADLKGKKAGVLRGSTADRYASAELTPAGVEVVRYNSQQEANMDLVAGRLD 176 G ++ +A L GK G +T RY V + Y++ DL +GR+D Sbjct: 121 ATGGGIDGTEATLAGKSVGAQTSTTHYRYVEKHFGKT-VSLKNYDTASNLLADLKSGRID 179 Query: 177 AVVADSVNLEDGFLKTDAGKGYAFVGPQLTDAKYFGEGVGIAVRKGDSELAGKFNAAIDA 236 A + D ++K DA K VG L DA+ FG GVG+ +RK D++L F+AAI + Sbjct: 180 AAITTGATASD-WVKADASKSLQLVGKPLVDAEVFGPGVGVGLRKEDADLKAAFDAAIAS 238 Query: 237 LRANGKYKQIQDKYFSFDV 255 + +G +I KY F V Sbjct: 239 VVQDGTLARIAAKYVDFTV 257 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: 175 Number of extensions: 8 Number of successful extensions: 4 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: 259 Length adjustment: 24 Effective length of query: 235 Effective length of database: 235 Effective search space: 55225 Effective search space used: 55225 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