Align Sugar ABC transporter permease (characterized, see rationale)
to candidate GFF2752 PGA1_c27950 ABC transporter permease protein
Query= uniprot:A0A161ZE72 (280 letters) >FitnessBrowser__Phaeo:GFF2752 Length = 280 Score = 130 bits (328), Expect = 2e-35 Identities = 82/267 (30%), Positives = 140/267 (52%), Gaps = 10/267 (3%) Query: 20 GVLLLY---AVFPFYYAIVTSLKPSSALFEVSYWIENPD-FS--NYAAVLNQASFLRAIG 73 G L+ Y A+FP + +V S K A+F + D FS Y VL Q F Sbjct: 17 GALITYTLIALFPVFVILVNSFKTRKAIFRDPLGLPTSDTFSLVGYQTVLKQGDFFLYFQ 76 Query: 74 NSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTV-LMMVLGVSMFPQVAVLSGLFEVIR 132 NS++V + + L L AA+AL +F+G + L + LG+ + ++ ++ + E++ Sbjct: 77 NSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTVA-ILELMV 135 Query: 133 ALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPL 192 GL NT ALIL YT LP V++L+ FM Q+ +L+ A +DG S + R++LPL Sbjct: 136 DTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIFFRLVLPL 195 Query: 193 LWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLMAASV 252 + PA+ T + I WN+ F L + +T+ + + G W +++A Sbjct: 196 VRPAMATVAVFNMIPIWNDLWFPLILAPAEETKTLTLGSQVFIG--QFVTDWNAVLSALS 253 Query: 253 VVTVPLVILVLIFQRRIVSGLTAGALK 279 + +P+++L +IF R+++ G+T+GA+K Sbjct: 254 MAILPVMVLYVIFSRQLIRGITSGAVK 280 Lambda K H 0.329 0.141 0.433 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: 184 Number of extensions: 8 Number of successful extensions: 4 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: 280 Length of database: 280 Length adjustment: 26 Effective length of query: 254 Effective length of database: 254 Effective search space: 64516 Effective search space used: 64516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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