Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate GFF2245 HP15_2195 amino acid ABC transporter, permease protein
Query= uniprot:A0A0H3PA28 (219 letters) >FitnessBrowser__Marino:GFF2245 Length = 395 Score = 72.0 bits (175), Expect = 1e-17 Identities = 41/131 (31%), Positives = 69/131 (52%), Gaps = 4/131 (3%) Query: 86 AFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFGKFFTLFYIILPQTFRKIIP 145 A W I SLYT+S +AEI+R G+ S+ KGQ EA+ + G TL +++PQ R IIP Sbjct: 265 ALW--IALSLYTASFIAEIVRSGILSVSKGQTEASKALGLPNGLTLRLVVIPQAMRVIIP 322 Query: 146 ALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTSFEEILAMIGVVAGIYFIICFSLS 205 L SQ + VK+++ +G +L + + L + + ++ + +Y I +S Sbjct: 323 PLTSQYLNLVKNSSLATAIGYPDLV--AVFMGTTLNQTGQAVEVVAITMAVYLTISLLIS 380 Query: 206 MLVRYYAKKTA 216 + + Y + A Sbjct: 381 LFMNIYNRAVA 391 Score = 32.0 bits (71), Expect = 2e-05 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 4/66 (6%) Query: 16 GLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLL----WMLA 71 GL TL ++ + + + G + + + + L +A YI++ RN PLLL W A Sbjct: 89 GLTNTLLVSAMGVVAATILGFIIGVARLSSNWLVAKMALVYIEVIRNIPLLLQIFFWYFA 148 Query: 72 ACFVLP 77 LP Sbjct: 149 VLSNLP 154 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: 219 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 219 Length of database: 395 Length adjustment: 26 Effective length of query: 193 Effective length of database: 369 Effective search space: 71217 Effective search space used: 71217 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: 48 (23.1 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