Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate HSERO_RS17560 HSERO_RS17560 glutamate/aspartate transporter permease GltK
Query= uniprot:A0A0H3PA28 (219 letters) >FitnessBrowser__HerbieS:HSERO_RS17560 Length = 227 Score = 115 bits (288), Expect = 7e-31 Identities = 70/215 (32%), Positives = 120/215 (55%), Gaps = 11/215 (5%) Query: 10 IEFLMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLWM 69 + L GL ++LKI L + +V+GT LA+ + ++ AA Y+++FR+ PL++ + Sbjct: 15 LRVLGDGLLVSLKITLVAIVFGMVWGTLLAMMRLSRHSPLQWFAAGYVNLFRSIPLVMVL 74 Query: 70 LAACFVLPVF----FGQFP----QAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAY 121 L ++P FG P + + F+L+ ++ AEIIR G+NS+ +GQ AAY Sbjct: 75 LWFFLIVPQLLQKLFGLSPANDLRMTSALVAFALFEAAYYAEIIRAGINSVSRGQMAAAY 134 Query: 122 SQGFGKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLT 181 + G + +ILPQ FR ++P LL+Q + +DT+ + +A+ + +I + Sbjct: 135 ALGLTYPQAMGMVILPQAFRNMVPLLLTQGIVLFQDTSLVYVSALADFFGRAYSIGER-- 192 Query: 182 SFEEILAMIGVVAGIYFIICFSLSMLVRYYAKKTA 216 I+ M+ V +YFIICFS+S++V+ Y KK A Sbjct: 193 -NGRIIEMLFVAGAVYFIICFSMSLMVKRYRKKVA 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: 164 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: 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