Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF247 PGA1_c02590 putative high-affinity branched-chain amino acid transport system permease protein LivH
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__Phaeo:GFF247 Length = 291 Score = 149 bits (377), Expect = 6e-41 Identities = 98/297 (32%), Positives = 154/297 (51%), Gaps = 10/297 (3%) Query: 5 VQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGL 64 VQ L++GL G +YGL+A+G+ ++Y +NFA GD MLG F V L LT+ L Sbjct: 4 VQLLVSGLANGCVYGLIALGFVLIYKATEAVNFAQGDFMMLGAF----VTLGLTNA-EYL 58 Query: 65 PVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQG 124 + L L +A +M L + ++ V R L G + A +I I + + F G Sbjct: 59 HLPFWLAAPLSIA-IMAGL-GYLLDLVILRHLFGQNQTAVVILTIALGFVIRFFAGAIWG 116 Query: 125 PRNKPIP-PMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQDR 183 + + P+ Q + + L + II++T +L + RT LG A +A Q++ Sbjct: 117 HEPQTLESPLALGDVQLAGVVLGLADLAIIIVTVLLTWSLYQFFQRTKLGLAMQAASQNQ 176 Query: 184 KMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLGGI 243 A +G+ V + + + + A AAVAG ++ G N G G+KAF AAV+GG Sbjct: 177 MAAYFMGIPVKRVQGLIWGLSGATAAVAGILFASK-GAIDPNAGLL-GIKAFAAAVIGGF 234 Query: 244 GSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300 GSLPGA+ GGL++G+IE + Y Y +A + +L VL+F+P G+ + +KV Sbjct: 235 GSLPGALAGGLIVGVIEPFAARYLAAGYSQIAPYVLLLAVLVFRPHGLFSQVRTKKV 291 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: 277 Number of extensions: 16 Number of successful extensions: 3 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: 291 Length adjustment: 26 Effective length of query: 274 Effective length of database: 265 Effective search space: 72610 Effective search space used: 72610 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 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