Align ABC transporter related (characterized, see rationale)
to candidate BPHYT_RS05495 BPHYT_RS05495 histidine ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__BFirm:BPHYT_RS05495 Length = 259 Score = 317 bits (813), Expect = 1e-91 Identities = 160/248 (64%), Positives = 197/248 (79%), Gaps = 1/248 (0%) Query: 9 LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68 L V +HK +GD+ VLKG+SL A+ GDVIS++G+SGSGKST LRC+N LE P+ G + + Sbjct: 8 LFVDELHKQYGDNEVLKGVSLKANAGDVISVIGSSGSGKSTMLRCINFLEQPNSGRIFVD 67 Query: 69 GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSR 128 GEE++ + +G L+ SD +Q+ RVR++L MVFQ+FNLWSHM VLEN+IE P+ V R Sbjct: 68 GEEVRTQIGKNGALRVSDPKQLQRVRTRLSMVFQHFNLWSHMNVLENIIEAPVNVLGLKR 127 Query: 129 AESVEEAEALLAKVGLAEK-RGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDP 187 E+ + A L KVGLA + YP+HLSGGQQQRVAIARALAMHP VMLFDEPTSALDP Sbjct: 128 KEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMHPDVMLFDEPTSALDP 187 Query: 188 ELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKS 247 ELVGEVL+VM++LAEEGRTM+VVTHEM FAR+VSN VMFLHQG+VE +G PDEVF KS Sbjct: 188 ELVGEVLKVMQTLAEEGRTMIVVTHEMAFARNVSNHVMFLHQGRVEEEGHPDEVFRNTKS 247 Query: 248 DRFRQFVS 255 DR +QF+S Sbjct: 248 DRLKQFLS 255 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: 242 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: 259 Length adjustment: 25 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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 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