Align ABC transporter related (characterized, see rationale)
to candidate WP_053938863.1 WG78_RS16125 amino acid ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_001294205.1:WP_053938863.1 Length = 246 Score = 243 bits (619), Expect = 4e-69 Identities = 123/242 (50%), Positives = 173/242 (71%), Gaps = 12/242 (4%) Query: 14 IHKSFG-DHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLAGEEL 72 ++K +G DHHVLK ISL+ QG+V+ + G SGSGKST +R +N LE +DG + + G ++ Sbjct: 7 VNKWYGRDHHVLKNISLEVKQGEVVVVCGPSGSGKSTLIRTINQLEPVNDGEIWVDGVQV 66 Query: 73 KMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSRAESV 132 R ++R+R ++G VFQ+FNL+ H++VL+N+ P++V+K S+A++ Sbjct: 67 N-----------HPRTNINRLREEVGFVFQHFNLYPHLSVLQNITLAPVKVRKMSQADAD 115 Query: 133 EEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPELVGE 192 + LL +VGL+ KR YP+ LSGGQQQRVAIAR LAM PKVMLFDEPTSALDPE++GE Sbjct: 116 QRGMELLERVGLSNKRDAYPSQLSGGQQQRVAIARGLAMQPKVMLFDEPTSALDPEMIGE 175 Query: 193 VLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSDRFRQ 252 VL+VM++LAE G TM+VVTHEMGFAR V++RV+FL G++ P + F + DR +Q Sbjct: 176 VLKVMQNLAESGMTMMVVTHEMGFAREVADRVVFLDHGEILEQAAPAQFFNNPQCDRAQQ 235 Query: 253 FV 254 F+ Sbjct: 236 FL 237 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: 207 Number of extensions: 8 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: 246 Length adjustment: 24 Effective length of query: 239 Effective length of database: 222 Effective search space: 53058 Effective search space used: 53058 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