Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate AO356_18220 AO356_18220 amino acid ABC transporter permease
Query= uniprot:A0A0H3PA28 (219 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18220 Length = 223 Score = 105 bits (262), Expect = 7e-28 Identities = 71/211 (33%), Positives = 113/211 (53%), Gaps = 10/211 (4%) Query: 13 LMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLL----W 68 L G+ +TLK+ + I+ GT LA+ + ++L +A Y++ FR+ PLLL + Sbjct: 15 LWNGMVMTLKLMAMGVVGGIILGTILALMRLSHNKLISNIAGAYVNYFRSIPLLLVITWF 74 Query: 69 MLAACFVLPVFFGQ-FPQAFWGT--IGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGF 125 LA FVL G+ P +G+ + F ++ ++ EI+R G+ SIPKGQ AA + G Sbjct: 75 YLAVPFVLRWITGEDTPIGAFGSCVVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGM 134 Query: 126 GKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTSFEE 185 T+ IILPQ FRK+ P LL Q + +DT+ + +G+ + S+ + E Sbjct: 135 NYGQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNASRANGDIIGRSNE 194 Query: 186 ILAMIGVVAGIYFIICFSLSMLVRYYAKKTA 216 L + G+V YF I F+ S+LV+ K+ A Sbjct: 195 FLIVAGLV---YFTISFAASLLVKRLQKRFA 222 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: 10 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: 223 Length adjustment: 22 Effective length of query: 197 Effective length of database: 201 Effective search space: 39597 Effective search space used: 39597 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: 45 (21.9 bits)
This GapMind analysis is from Apr 09 2024. 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