Align Histidine transport system permease protein HisM (characterized)
to candidate BWI76_RS16800 BWI76_RS16800 amino acid ABC transporter permease
Query= SwissProt::P0AEU3 (238 letters) >FitnessBrowser__Koxy:BWI76_RS16800 Length = 254 Score = 111 bits (278), Expect = 1e-29 Identities = 76/250 (30%), Positives = 130/250 (52%), Gaps = 32/250 (12%) Query: 3 EILHEYWKPLLWTDGYRFTGVAITLWLLILSVVIGGVLALFLAIGRVSSNKY-------- 54 EI+ EY PL G +T+ I+ V++G + L L +GR++ ++ Sbjct: 7 EIIEEYG-PLF------MDGALMTIKCTIICVILGTLWGLTLGLGRMAKAEHGVWKYVLR 59 Query: 55 --IQFPIWLFTYIFRGTPLYVQLLVFYSGMYTLEI-----------VKGTEF---LNAFF 98 +QFP+ + FRGTPL+VQ++V + + L I + +F L + + Sbjct: 60 YLVQFPVRFYVSAFRGTPLFVQIMVVHFALVPLFINPRDGLLVTSGMMSADFARELRSNY 119 Query: 99 RSGLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAARAYGFSTFKMYRCIILPSALRI 158 + L+C ++A+TLN AY +EIF I+S+ G++EA+RA G +K R +ILP A R Sbjct: 120 GAFLSC-IVAITLNAGAYVSEIFRAGIQSIDKGQMEASRALGMPWWKTMRQVILPQAFRR 178 Query: 159 ALPAYSNEVILMLHSTALAFTATVPDLLKIARDINAATYQPFTAFGIAAVLYLIISYVLI 218 LP N I ++ ++LA + DL AR ++ A + + +++Y +I+++L Sbjct: 179 ILPPLGNNAIAIVKDSSLASAIGLADLAYAARTVSGAYATYWEPYLTISLVYWVITFLLA 238 Query: 219 SLFRRAEKRW 228 L R EKR+ Sbjct: 239 QLVNRLEKRF 248 Lambda K H 0.330 0.142 0.438 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: 150 Number of extensions: 10 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: 238 Length of database: 254 Length adjustment: 24 Effective length of query: 214 Effective length of database: 230 Effective search space: 49220 Effective search space used: 49220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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