Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_091526344.1 BM253_RS16085 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_900115115.1:WP_091526344.1 Length = 304 Score = 94.4 bits (233), Expect = 3e-24 Identities = 70/223 (31%), Positives = 107/223 (47%), Gaps = 23/223 (10%) Query: 21 LNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLY-QPDTGTFELDGKPYSPSAPHEVAK 79 L+ V I + IYG +GPNGAGK+T +ITGL + + G L GKP P ++ Sbjct: 19 LDKVSIQVPEKSIYGFLGPNGAGKSTTIRLITGLLGEQNPGQISLFGKPLEEQLPFAFSQ 78 Query: 80 AGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAREEEAAIREKSQKLLD 139 G + L+G +T LE++ F K +E+ E +LD Sbjct: 79 IGCI--IETPTLYGHLTGLEHLK---------------FVAKLQNTDESKFNE----VLD 117 Query: 140 FVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMNATEKLGLRELLVKI 199 VG+ ++ S G ++RL IA AL DP+LL LDEP G++ + +R LL K+ Sbjct: 118 LVGLDHAKNIKSKKYSLGMKQRLSIAMALINDPKLLILDEPVNGLDPQGIIEMRLLLQKL 177 Query: 200 QAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQ 241 E G TI + H + + LC + +L G +G +D++ Sbjct: 178 NREKGITIFISSHILAEVEKLCTHVGILYNGILQFQGTMSDLK 220 Lambda K H 0.320 0.138 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: 178 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 255 Length of database: 304 Length adjustment: 25 Effective length of query: 230 Effective length of database: 279 Effective search space: 64170 Effective search space used: 64170 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: 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