Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 120 bits (301), Expect = 2e-32 Identities = 69/215 (32%), Positives = 115/215 (53%), Gaps = 3/215 (1%) Query: 7 PVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGT 66 P+ + GA T+ +T S +G V+G + R + VV + Y+ IRGT Sbjct: 44 PIGSNAQAFSDGARTTLWLTLISGSVGLVLGTGAALAR-TARWAVVRWAASFYIWVIRGT 102 Query: 67 PLLVQLFILFFGLPQF--GILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAAR 124 PLLVQ+ ++F LP G+ LP F V+ LG+ GAY +E +R + ++ +GQ EAA+ Sbjct: 103 PLLVQILFVYFALPVLVPGLNLPDFAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTEAAK 162 Query: 125 SIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSY 184 ++G+ VV PQA +PPL + F+AL+K+S+L + + +L + G +I S ++ Sbjct: 163 ALGLGRMHVFFDVVFPQAFKISLPPLVSNFVALLKDSSLAYAIGVVELTNVGNRIQSATF 222 Query: 185 RSLEVYLAIAVVYFILTGATTLVLRRIELRLRAGG 219 + + +A+ Y +LT T + +E R G Sbjct: 223 QPIATLSTVAITYLLLTTLVTQISNAVEYRFDVEG 257 Lambda K H 0.328 0.143 0.412 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: 154 Number of extensions: 6 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: 222 Length of database: 260 Length adjustment: 23 Effective length of query: 199 Effective length of database: 237 Effective search space: 47163 Effective search space used: 47163 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 (21.8 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