Align D-methionine ABC transporter membrane protein, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BPHYT_RS22540 BPHYT_RS22540 metal ABC transporter permease
Query= TCDB::Q9HT69 (225 letters) >FitnessBrowser__BFirm:BPHYT_RS22540 Length = 218 Score = 216 bits (551), Expect = 2e-61 Identities = 108/215 (50%), Positives = 150/215 (69%), Gaps = 5/215 (2%) Query: 16 EIWLASV-----DTFWMLGGSLLFTVVLGLPLGVLLFLTGPRQMFEQKAVYTLLSLVVNI 70 E+WL+ + DT M+G S ++G+PL ++L T +FE++AV + L +VN Sbjct: 3 ELWLSELADAIRDTIVMVGVSAFVAALIGIPLALVLVTTTRGGIFEKRAVNSTLGALVNA 62 Query: 71 LRSLPFIILLIVMIPLTVLITGTSLGVAGAIPPLVVGATPFFARLVETALREVDKGIIEA 130 RS PFIILL+ ++PLT L+ GT++GV AI PL + A PFFAR+ E +LREVD+G+IEA Sbjct: 63 FRSTPFIILLVALLPLTRLLIGTTIGVWAAIVPLSIAAIPFFARVAEVSLREVDRGLIEA 122 Query: 131 TQAMGASTRQIIWNALLPEARPGIIAAITVTAITLVSYTAMAGVVGAGGLGDLAIRFGYQ 190 QAMGA R IIW+ LLPEA PGI+ T+T + ++ +AMAG VGAGGLGDLAIR+GYQ Sbjct: 123 AQAMGAQRRHIIWHVLLPEALPGILGGFTITVVAMIGSSAMAGAVGAGGLGDLAIRYGYQ 182 Query: 191 RFQTDVMVVTVVMLLILVQILQTVGDKLVVHFSRK 225 RF T VMV +V+L+ +V +Q VGD+ V +++ Sbjct: 183 RFDTTVMVTVIVLLIAIVTAVQFVGDRFVRRLAQR 217 Lambda K H 0.329 0.143 0.419 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: 131 Number of extensions: 3 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: 225 Length of database: 218 Length adjustment: 22 Effective length of query: 203 Effective length of database: 196 Effective search space: 39788 Effective search space used: 39788 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 (21.8 bits) S2: 45 (21.9 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