Align ABC transporter related (characterized, see rationale)
to candidate WP_076482473.1 BW971_RS17350 amino acid ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_900156495.1:WP_076482473.1 Length = 250 Score = 244 bits (624), Expect = 1e-69 Identities = 130/240 (54%), Positives = 173/240 (72%), Gaps = 1/240 (0%) Query: 16 KSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLAGEELKMK 75 KSFG VLKGISL+ +G+V ++G SGSGKSTFLRC+N LE+ G + + + + + Sbjct: 9 KSFGALQVLKGISLEVERGEVTCLIGPSGSGKSTFLRCVNHLESVTAGRLYVDDDLIGYR 68 Query: 76 RRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSRAESVEEA 135 +G GKL + R +GMVFQ+FNL+ H T L+N+IE P++V+ RA +VE Sbjct: 69 EKG-GKLYELSAKDAAAQRRDIGMVFQHFNLFPHRTALDNIIEAPIQVKGVVRARAVERG 127 Query: 136 EALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPELVGEVLR 195 + LL +VGLA+K YPA LSGGQQQRVAIARALAM PK+MLFDEPTSALDPELVG+VL Sbjct: 128 KDLLDQVGLADKASAYPAQLSGGQQQRVAIARALAMDPKLMLFDEPTSALDPELVGDVLA 187 Query: 196 VMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSDRFRQFVS 255 VMR+LA++G TM+VVTHEMGFAR V+++++F+ G+V G P EV + +R + F+S Sbjct: 188 VMRNLAKDGMTMVVVTHEMGFAREVADQLVFMDAGKVVEKGDPREVLNSPQHERTQSFLS 247 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: 187 Number of extensions: 5 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: 263 Length of database: 250 Length adjustment: 24 Effective length of query: 239 Effective length of database: 226 Effective search space: 54014 Effective search space used: 54014 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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