Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate YP_004144850.1 Mesci_5749 polar amino acid ABC transporter inner membrane subunit
Query= uniprot:A0A0H3PA28 (219 letters) >NCBI__GCF_000185905.1:YP_004144850.1 Length = 253 Score = 103 bits (258), Expect = 2e-27 Identities = 63/208 (30%), Positives = 115/208 (55%), Gaps = 6/208 (2%) Query: 13 LMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLWMLAA 72 + QGL+L++++++ + I + LA+ + +G ++ A I+I R TP L+ + Sbjct: 48 IAQGLWLSIQLSILSTAIGLAAAIPLAVARVHGSSFARIPAVFLIEIVRATPELMVIFWV 107 Query: 73 CFVLPVFFGQFPQAFW--GTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFGKFFT 130 F P GQ P W + S+ +S +AE+IR GL S+ KGQ+EAA S G + + Sbjct: 108 YFGAPAITGQ-PIDGWTAALVAMSIIAASYLAEVIRAGLYSVDKGQWEAAASTGLNNWQS 166 Query: 131 LFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTSFEEILAMI 190 +IILPQ ++PALLSQ++ K T+ ++ +G+ + ++ + S I ++ Sbjct: 167 FKWIILPQAISNMMPALLSQVIMLFKTTSLVSMVGVIDFFRAAQITNSNTFSPYAIYTLV 226 Query: 191 GVVAGIYFIICFSLSMLVRYYAKKTAYI 218 G+ YFIIC +LS++V+ + + + + Sbjct: 227 GIG---YFIICGTLSLVVKRWRGRVSAV 251 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: 137 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: 219 Length of database: 253 Length adjustment: 23 Effective length of query: 196 Effective length of database: 230 Effective search space: 45080 Effective search space used: 45080 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 24 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