Align Histidine transport system permease protein HisM (characterized)
to candidate H281DRAFT_06475 H281DRAFT_06475 amino acid ABC transporter membrane protein 2, PAAT family
Query= SwissProt::P0A2I7 (235 letters) >FitnessBrowser__Burk376:H281DRAFT_06475 Length = 237 Score = 317 bits (813), Expect = 1e-91 Identities = 149/233 (63%), Positives = 194/233 (83%) Query: 1 MIEIIQEYWKSLLWTDGYRFTGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIW 60 MI+I+ ++W++ L+ DG R +G+A+TLWLL++SV +G LA+ LAV RVS +++ P+ Sbjct: 1 MIDILNQFWRAFLYWDGQRISGLAVTLWLLVASVGIGFCLAIPLAVARVSKKRWLSTPVR 60 Query: 61 LFTYIFRGTPLYVQLLVFYSGMYTLEIVKGTDLLNAFFRSGLNCTVLALTLNTCAYTTEI 120 L+TY+FRGTPLYVQLL+ Y+GMY+LE V+ LL+AFFRSG +C +LA LNTCAYTTEI Sbjct: 61 LYTYVFRGTPLYVQLLLIYTGMYSLEFVRSHQLLDAFFRSGFHCAILAFALNTCAYTTEI 120 Query: 121 FAGAIRSVPHGEIEAARAYGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTA 180 FAGAIRS HGE+EAARAYG S F MYR I++PSALR ALP YSNEVILMLH+T +AFTA Sbjct: 121 FAGAIRSTSHGEVEAARAYGMSWFTMYRRIVIPSALRRALPLYSNEVILMLHATTVAFTA 180 Query: 181 TVPDLLKIARDINSATYQPFTAFGIAAVLYLLISYVLISLFRRAERRWLQHVS 233 TVPD+LK+ARD NSATYQ F AFG+AA++YL++S+ L++LFRRAER WL +++ Sbjct: 181 TVPDILKVARDANSATYQSFDAFGLAALIYLVVSFALVALFRRAERHWLGYLA 233 Lambda K H 0.330 0.141 0.429 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: 236 Number of extensions: 9 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: 235 Length of database: 237 Length adjustment: 23 Effective length of query: 212 Effective length of database: 214 Effective search space: 45368 Effective search space used: 45368 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