Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate AZOBR_RS00680 AZOBR_RS00680 ABC transporter permease
Query= uniprot:A0A1N7U128 (237 letters) >FitnessBrowser__azobra:AZOBR_RS00680 Length = 234 Score = 103 bits (258), Expect = 2e-27 Identities = 70/212 (33%), Positives = 109/212 (51%), Gaps = 2/212 (0%) Query: 17 GAGLSGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLL 76 G L G AMT+ + + + VLG A A++S ++ L EVYT + RG P + + Sbjct: 14 GQLLGGAAMTVAVSVSAFVLGLVFGSLGASAKLSRNLALTGVAEVYTTVVRGVPELLVIY 73 Query: 77 ICYTGLYSLEIVQDNALLNQFF--RNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIE 134 + + G + + + NA + +LA L + AY+ E+ GA++ +PHG+IE Sbjct: 74 LLFFGGSGAVMAVGRVFGYEGYIELNAFSIGVLAVGLISGAYSTEVIRGAVQAVPHGQIE 133 Query: 135 AARAYGLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDANA 194 AARA G+ W + ++VP LR ALP N L L T+L +A+I++V+ A Sbjct: 134 AARACGMSRWLILRRILVPQTLRYALPGLGNVWQLTLKDTALISVTALAEIMRVSHVAAG 193 Query: 195 ETFLTFQAFGIAALLYMLLSFALVGLFRLAER 226 T F + AA+LY+LL+ F AER Sbjct: 194 STRQPFLFYTTAAVLYLLLTTVSTVAFERAER 225 Lambda K H 0.332 0.143 0.443 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: 144 Number of extensions: 11 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: 237 Length of database: 234 Length adjustment: 23 Effective length of query: 214 Effective length of database: 211 Effective search space: 45154 Effective search space used: 45154 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 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