Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__PV4:5210736 Length = 241 Score = 143 bits (360), Expect = 5e-39 Identities = 90/239 (37%), Positives = 137/239 (57%), Gaps = 12/239 (5%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELD 63 +KI NL K F ++KGID + E V +GPSG GKST LR I LE+ + G I +D Sbjct: 2 IKISNLHKYFGDNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCINLLEQPTQGEIVID 61 Query: 64 GRDITE----VSPAKRDLAMVFQTYALYPHMSVRKNMSFA-LDLAGVAKAEVEKKVSEAA 118 G+ IT + ++ + MVFQ + L+PH +V++N++ A + L + +AE + SEA Sbjct: 62 GQSITAPDACIDKLRQKVGMVFQNFNLFPHKTVQQNITLAPVKLGLMTQAEAD---SEAM 118 Query: 119 RILE---LGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLE 175 R+L+ L P LSGGQ+QRVAI RA+ P++ LFDEP S LD + V L+ Sbjct: 119 RLLDQVGLSDKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPEM-VGDVLD 177 Query: 176 LLRLHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFL 234 +++ + TM+ VTH+ A ++D+V+ ++GG + + P L+ QP FL Sbjct: 178 VMKQLAQAGMTMVIVTHEMGFAKDVSDRVIFMDGGYVVESNVPALLFGQPQEPRTQAFL 236 Lambda K H 0.320 0.137 0.389 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: 189 Number of extensions: 14 Number of successful extensions: 5 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: 367 Length of database: 241 Length adjustment: 26 Effective length of query: 341 Effective length of database: 215 Effective search space: 73315 Effective search space used: 73315 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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