Align Histidine transport system permease protein HisM (characterized)
to candidate RR42_RS29655 RR42_RS29655 amino acid ABC transporter permease
Query= SwissProt::P0AEU3 (238 letters) >FitnessBrowser__Cup4G11:RR42_RS29655 Length = 237 Score = 308 bits (790), Expect = 5e-89 Identities = 143/232 (61%), Positives = 190/232 (81%) Query: 1 MIEILHEYWKPLLWTDGYRFTGVAITLWLLILSVVIGGVLALFLAIGRVSSNKYIQFPIW 60 MI+IL+++W+ L+ DG F+G+A+TLWLL S+ IG +LA+ LA+ R+S NK++ +W Sbjct: 1 MIDILNQFWRAFLYWDGQGFSGLAVTLWLLDASLFIGFILAVPLAVARISKNKFLSVAVW 60 Query: 61 LFTYIFRGTPLYVQLLVFYSGMYTLEIVKGTEFLNAFFRSGLNCTVLALTLNTCAYTTEI 120 +TY+FRGTPLYVQLL+ Y+G+Y E V+ TE L+A FRSG C+++A LNTCAYTTEI Sbjct: 61 CYTYVFRGTPLYVQLLLIYTGLYGFEFVRSTEVLSAVFRSGYYCSIIAFALNTCAYTTEI 120 Query: 121 FAGAIRSVPHGEIEAARAYGFSTFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTA 180 FAGA+R+ HGEIEAARAYG S F MYR I++PSALR +LP Y NEVILMLH+T++AFTA Sbjct: 121 FAGAMRTTNHGEIEAARAYGMSWFTMYRRIVIPSALRRSLPQYGNEVILMLHATSVAFTA 180 Query: 181 TVPDLLKIARDINAATYQPFTAFGIAAVLYLIISYVLISLFRRAEKRWLQHV 232 TVPD+LK+ARD NAATYQ F +FGIAA+LYL +S+ L++LFR+AE+RWL ++ Sbjct: 181 TVPDILKVARDANAATYQSFQSFGIAALLYLAVSFALVALFRQAEQRWLAYL 232 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: 226 Number of extensions: 6 Number of successful extensions: 1 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: 237 Length adjustment: 23 Effective length of query: 215 Effective length of database: 214 Effective search space: 46010 Effective search space used: 46010 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