Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3433 (232 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 112 bits (281), Expect = 5e-30 Identities = 65/207 (31%), Positives = 108/207 (52%), Gaps = 9/207 (4%) Query: 18 GLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRGTPMLVQLFLIYYG 77 G TTL L +S GL+ L R ++ VV +A + +VIRGTP+LVQ+ +Y+ Sbjct: 55 GARTTLWLTLISGSVGLVLGTGAALARTARWAVVRWAASFYIWVIRGTPLLVQILFVYFA 114 Query: 78 LAQFEAVRESFLWPWLSSATFCAC-LAFAINTSAYTAEIIAGSLRATPNGEIEAAKAMGM 136 L L P L+ F A LA +N AY AE I L A P G+ EAAKA+G+ Sbjct: 115 LP--------VLVPGLNLPDFAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTEAAKALGL 166 Query: 137 SRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQFYLPFE 196 R+ ++ ++ P A + +LP + + +L+ +SLA + ++++T + + + P Sbjct: 167 GRMHVFFDVVFPQAFKISLPPLVSNFVALLKDSSLAYAIGVVELTNVGNRIQSATFQPIA 226 Query: 197 AYITAGVFYLCLTFILVRLFKMAEHRW 223 T + YL LT ++ ++ E+R+ Sbjct: 227 TLSTVAITYLLLTTLVTQISNAVEYRF 253 Lambda K H 0.330 0.140 0.427 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: 133 Number of extensions: 5 Number of successful extensions: 2 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: 232 Length of database: 260 Length adjustment: 24 Effective length of query: 208 Effective length of database: 236 Effective search space: 49088 Effective search space used: 49088 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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