Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate HSERO_RS00310 HSERO_RS00310 ABC transporter substrate-binding protein
Query= CharProtDB::CH_014295 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS00310 Length = 259 Score = 113 bits (283), Expect = 3e-30 Identities = 79/258 (30%), Positives = 127/258 (49%), Gaps = 8/258 (3%) Query: 1 MKKLVLSLSLVLAFSSATAAFAAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELC 60 +KKL+ + + LA S A A Q +G TY PFE + + ELVGFDIDL K + Sbjct: 3 LKKLLTTAASALALSCAAGTALAADQTYVVGAGGTYRPFEFETPKKELVGFDIDLIKAIS 62 Query: 61 KRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAK 120 + N + V P + + +L D I+S ++IT+KR Q + F+ + A+ V+ Sbjct: 63 QASNFKIQLVSTPWEGIFATLGQGDRDIIISGITITDKRAQMVDFSLPYFPAEQ--VIIT 120 Query: 121 NSDIQPT-VESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDA 179 N+D + T + LK +V V+ T + +E I + + +L G +DA Sbjct: 121 NADAKITSLSDLKKTQVAVVNSTAGDIVVSEELGKASTAIHRFDNTVLMLEELYRGGVDA 180 Query: 180 AFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEM 239 A D V + ++K K +K G S + FG+ ++K + EL + +N ++ Sbjct: 181 AVGD-VGVIKFYIKSHPEKKFKVVGDSKFVRQYFGI----AVKKGNKELLDKINAGLKKI 235 Query: 240 RADGTYEKLAKKYFDFDV 257 ADGTY K+ K +FD DV Sbjct: 236 VADGTYAKIYKTWFDGDV 253 Lambda K H 0.315 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: 133 Number of extensions: 6 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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