Align D-methionine ABC transporter membrane protein, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate HSERO_RS07845 HSERO_RS07845 metal ABC transporter permease
Query= TCDB::Q9HT69 (225 letters) >FitnessBrowser__HerbieS:HSERO_RS07845 Length = 229 Score = 296 bits (757), Expect = 3e-85 Identities = 144/222 (64%), Positives = 185/222 (83%) Query: 4 FETMSFANIDWYEIWLASVDTFWMLGGSLLFTVVLGLPLGVLLFLTGPRQMFEQKAVYTL 63 F + + IDW E+ A+++T M GGSL FTV+LGLPLG+LLFLT RQ+ EQ+ +Y + Sbjct: 8 FSQIDLSVIDWGEVGDATLETLAMTGGSLFFTVLLGLPLGILLFLTNRRQLLEQRGLYLV 67 Query: 64 LSLVVNILRSLPFIILLIVMIPLTVLITGTSLGVAGAIPPLVVGATPFFARLVETALREV 123 LSLVVN+LRS+PF+ILLI++IP T+ + GTSLGV GAIPPLV+G PFFARL E+ LRE+ Sbjct: 68 LSLVVNVLRSVPFLILLIMLIPFTLWLVGTSLGVTGAIPPLVIGTAPFFARLTESVLREI 127 Query: 124 DKGIIEATQAMGASTRQIIWNALLPEARPGIIAAITVTAITLVSYTAMAGVVGAGGLGDL 183 D+GI+EA AMGA RQII+ ALLPEA PG++AA+T+TAITL+SY AM+GV+G GGLGDL Sbjct: 128 DRGILEACTAMGARRRQIIFGALLPEALPGLLAAVTITAITLMSYAAMSGVIGGGGLGDL 187 Query: 184 AIRFGYQRFQTDVMVVTVVMLLILVQILQTVGDKLVVHFSRK 225 AIR+GYQRFQT+VMVVTV +L++LVQ+LQ GD+LV+ F+RK Sbjct: 188 AIRYGYQRFQTEVMVVTVAILVVLVQLLQFFGDRLVLRFTRK 229 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: 163 Number of extensions: 2 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: 229 Length adjustment: 22 Effective length of query: 203 Effective length of database: 207 Effective search space: 42021 Effective search space used: 42021 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: 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