Align ABC transporter related (characterized, see rationale)
to candidate 5210215 Shew_2658 ABC transporter-related protein (RefSeq)
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__PV4:5210215 Length = 227 Score = 136 bits (342), Expect = 4e-37 Identities = 82/213 (38%), Positives = 128/213 (60%), Gaps = 12/213 (5%) Query: 24 LKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLAGEELKMKRRGDGKLQ 83 +K + L QG+ ++I+G SGSGK+T L + +++P G+V + GE++ Sbjct: 23 VKSLDLTIAQGEFVAIMGPSGSGKTTLLNMIGGIDSPSSGAVFIDGEDIT---------H 73 Query: 84 PSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSRAESVEEAEALLAKVG 143 S++ + R +G +FQ+++L +T LEN +E M++Q S AE + A ALLA+VG Sbjct: 74 LSEQALIAFRRDHVGFIFQDYSLLPVLTALEN-VEFVMQLQGHSEAECRDRAMALLAQVG 132 Query: 144 LAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPELVGEVLRVMRSLAE- 202 LA ++ PA LSGGQQQRVA+ARALA P+ ++ DEPT+ LD + E+L +M+SL E Sbjct: 133 LAAQQDKIPAKLSGGQQQRVAVARALAPRPRFVMADEPTANLDAKSTAELLDIMQSLNEQ 192 Query: 203 EGRTMLVVTHEMGFARHVSNRVMFLHQGQVEAD 235 EG T + TH+ + RV+ G++ D Sbjct: 193 EGTTFIFSTHDPRVIAR-AKRVIVFEDGRLVED 224 Lambda K H 0.318 0.133 0.377 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: 9 Number of successful extensions: 3 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: 263 Length of database: 227 Length adjustment: 24 Effective length of query: 239 Effective length of database: 203 Effective search space: 48517 Effective search space used: 48517 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 (21.7 bits) S2: 46 (22.3 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