Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate RR42_RS02585 RR42_RS02585 amino acid ABC transporter permease
Query= uniprot:A0A0H3PA28 (219 letters) >FitnessBrowser__Cup4G11:RR42_RS02585 Length = 227 Score = 112 bits (279), Expect = 7e-30 Identities = 71/219 (32%), Positives = 120/219 (54%), Gaps = 11/219 (5%) Query: 6 NAQNIEFLMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPL 65 NA ++ L +G+ ++LKI + ++ IV+GT LA+ + +L + A Y+ IFR+ PL Sbjct: 11 NATTLDVLGEGMLVSLKITVTAVVVGIVWGTILAMMRLSSVKLLNWFAQGYVTIFRSIPL 70 Query: 66 LLWMLAACFVLPVFFGQ---FPQAF-----WGTIGFSLYTSSVMAEIIRGGLNSIPKGQF 117 ++ +L ++P + QA I F+L+ ++ +EIIR G+ S+ +GQ Sbjct: 71 VMVLLWFFLIIPQLLQKAFNLSQASDLRMTSALIAFALFEAAYYSEIIRAGIQSVSRGQM 130 Query: 118 EAAYSQGFGKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTIL 177 AA + G ++ +ILPQ FR ++P LL+Q + +DT+ + +A+ + I Sbjct: 131 FAAQAMGMTYGQSMRLVILPQAFRNMVPLLLTQGIILFQDTSLVYVSALADFFGQAYGIG 190 Query: 178 AKLTSFEEILAMIGVVAGIYFIICFSLSMLVRYYAKKTA 216 + E+L G+V YFIICFS S+LV+ Y KK A Sbjct: 191 ERDGRIVEMLLFAGLV---YFIICFSASLLVKRYQKKVA 226 Lambda K H 0.331 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: 152 Number of extensions: 6 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: 219 Length of database: 227 Length adjustment: 22 Effective length of query: 197 Effective length of database: 205 Effective search space: 40385 Effective search space used: 40385 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: 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