Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_051302387.1 A3GO_RS0114430 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000428045.1:WP_051302387.1 Length = 307 Score = 114 bits (286), Expect = 2e-30 Identities = 94/312 (30%), Positives = 144/312 (46%), Gaps = 33/312 (10%) Query: 3 YFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFA 62 +F + + GL G +Y LVA+G+ +++ G+ NFA G A+++F LT + Sbjct: 15 FFFEVAIGGLLSGVMYSLVALGFVLIFKASGVFNFAQG---------AMVLFSALTLVGL 65 Query: 63 ---GLP----VAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITL 115 GLP V V LLVMLV+A+ IERV R L + + IG++ L Sbjct: 66 NEMGLPMWLSVIVTLLVMLVLAI--------AIERVVLRSLVNQEHIILFMATIGIAYFL 117 Query: 116 SNFIQVTQGPRNKPIPPMVSS---VYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTAL 172 F Q G K + S Y G I ++ +I VI +L+ + T + Sbjct: 118 DGFGQTIWGSEVKNLDIGFSQEPGFYFDGLILINDFDLIAAVIAGILVIVLALFFQYTRI 177 Query: 173 GRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGV 232 GRA RA D + A +G+ + I + + +A VAG M+ GV F+ + Sbjct: 178 GRALRAVADDHQAALSVGIPLKHIWVIVWAVAGIVALVAGIMWGSKLGV-QFSLALI-AL 235 Query: 233 KAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTI----AYKDVATFAILAFVLIFKP 288 KA +LGG S+PGA+ GGLLIG E L + +D + + L+F+P Sbjct: 236 KALPVLILGGFTSVPGAIIGGLLIGAGEKLAEVFIAPMIGGGIEDWFAYMLALAFLVFRP 295 Query: 289 TGILGRPEVEKV 300 G+ G +E+V Sbjct: 296 QGLFGEKIIERV 307 Lambda K H 0.329 0.143 0.421 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: 291 Number of extensions: 20 Number of successful extensions: 6 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: 300 Length of database: 307 Length adjustment: 27 Effective length of query: 273 Effective length of database: 280 Effective search space: 76440 Effective search space used: 76440 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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