Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate BPHYT_RS35100 BPHYT_RS35100 ABC transporter substrate-binding protein
Query= CharProtDB::CH_018185 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS35100 Length = 263 Score = 228 bits (582), Expect = 7e-65 Identities = 112/255 (43%), Positives = 166/255 (65%), Gaps = 3/255 (1%) Query: 5 ALSLSLVLAFSSATAAFAAIPQKIRIGTDPTYAPFESKNAQGELVGFDIDLAKELCKRIN 64 ALS +L A + +T+AFA P +R+G DP+Y P ++K G GFD+DL E+CKRI+ Sbjct: 11 ALSTALSAALAFSTSAFAVEPTTLRLGIDPSYPPMDAKAPDGSFKGFDVDLGNEICKRIH 70 Query: 65 TQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDI 124 +C +VE +IP+L+A+KIDAI+SS++ITEKR+Q+I F+ KL+ SRL+ + S + Sbjct: 71 ARCQWVELEFSGMIPALQARKIDAILSSMAITEKREQQILFSSKLFQFKSRLIARQGSAL 130 Query: 125 QPTVASLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDE 184 +L GK++GV GT E + ++WAP G +V+Y+ QD +++DL GR+D A Sbjct: 131 AGGTNALAGKQIGVQSGTQFEGYALKNWAPLGAHVVAYKSQDEVFADLQNGRLDGALLGS 190 Query: 185 VAASEGFLKQPVGKDYKFGGPAVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGT 244 V A GFL+ P GK + F G + + G G+GLRK++ ++ ++N A A M DGT Sbjct: 191 VEADIGFLRTPAGKGFAFVGEPL---SMGDRGVGIGLRKDETAVQASINAAIASMLKDGT 247 Query: 245 YEKLAKKYFDFDVYG 259 Y ++AKKYFDFD YG Sbjct: 248 YAQIAKKYFDFDPYG 262 Lambda K H 0.316 0.133 0.372 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: 189 Number of extensions: 9 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: 260 Length of database: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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