Align ABC transporter (characterized, see rationale)
to candidate WP_012676168.1 PERMA_RS09515 ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >NCBI__GCF_000021565.1:WP_012676168.1 Length = 287 Score = 171 bits (432), Expect = 3e-47 Identities = 98/224 (43%), Positives = 144/224 (64%), Gaps = 16/224 (7%) Query: 8 NVNKQL---GGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDG 64 N+ K+L GG LR + L I GEFV G SG GK+T+LR+I+GL+ G + IDG Sbjct: 5 NIEKELLGDGGRFSLR-LDLHIKKGEFVTLFGRSGSGKTTVLRMISGLEKPDRGKIEIDG 63 Query: 65 R------RVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTA 118 + + DL P++R +G VFQ+YAL+P+M+V +NI F + D+ RE+ ++ Sbjct: 64 KVYFDSEKGIDLPPQKRNIGFVFQNYALFPNMTVLENILFAM-----DRPD-REKAIELL 117 Query: 119 QILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIAR 178 + + L+ L R P LSGGQ+QRVA+ RA+AREP ILL DEPLS LD S+R +++ EI R Sbjct: 118 KTVHLEDLKDRYPDTLSGGQQQRVAVARALAREPSILLLDEPLSALDFSIREKLQEEIKR 177 Query: 179 LHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELY 222 +H T I V+HD+ E L+D++V + GR+ + GSPR+++ Sbjct: 178 IHRVFNLTTILVSHDKTEVFKLSDRVVWIEKGRIIKEGSPRKVF 221 Lambda K H 0.320 0.137 0.394 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: 215 Number of extensions: 6 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: 381 Length of database: 287 Length adjustment: 28 Effective length of query: 353 Effective length of database: 259 Effective search space: 91427 Effective search space used: 91427 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: 49 (23.5 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