Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized)
to candidate AZOBR_RS08665 AZOBR_RS08665 amino acid ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4772 (223 letters) >FitnessBrowser__azobra:AZOBR_RS08665 Length = 367 Score = 119 bits (297), Expect = 1e-31 Identities = 75/208 (36%), Positives = 114/208 (54%), Gaps = 7/208 (3%) Query: 15 LWNGMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPLLLVITWF 74 LW G+ +TL L +G+ +LAL R S + I+ Y+ R +PL+ ++ F Sbjct: 156 LWGGLPLTLMLSVVGLSVAFPASVLLALGRRSQLPAIRVISVTYIELIRGVPLISLL--F 213 Query: 75 YLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGM 134 +V F L TG + +AF+MF AAY E +R G+Q+IPKGQ AA ALG+ Sbjct: 214 MASVMFPLFLPTGVN--FDKLLRAQIAFIMFAAAYMAEAIRGGLQAIPKGQYEAADALGL 271 Query: 135 SYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRAS-GDIIGRS- 192 +Y Q M IILPQA P L+ I F+DTSLV +GL D L ++A+ D R Sbjct: 272 NYWQAMGKIILPQALAISIPPLVNTFISFFKDTSLVIIIGLYDLLGTAKAALSDPAWRGF 331 Query: 193 -NEFLIFAGLVYFIISFAASQLVKRLQK 219 E +F G++Y++ ++ S+ ++L++ Sbjct: 332 YREAYLFIGVIYWVFCYSMSKYSQKLER 359 Lambda K H 0.332 0.144 0.428 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: 214 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: 223 Length of database: 367 Length adjustment: 26 Effective length of query: 197 Effective length of database: 341 Effective search space: 67177 Effective search space used: 67177 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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