Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate GFF774 PGA1_c07880 alpha-glucoside transport system permease protein AglG
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__Phaeo:GFF774 Length = 382 Score = 559 bits (1441), Expect = e-164 Identities = 285/385 (74%), Positives = 326/385 (84%), Gaps = 3/385 (0%) Query: 1 MDNIAGSKSSLTWAVQLSVVGLVVLWLLPTFGLFVSSFRTVEQISSSGWWKAMFPSEQNL 60 M IAG K +L WA++LSVV LV LWL PT GL VSSFRT +QI++SGWW+AMFPSEQNL Sbjct: 1 MTVIAGEKPALIWALRLSVVLLVGLWLFPTLGLLVSSFRTSDQIATSGWWRAMFPSEQNL 60 Query: 61 TLRAADPDDFRMPQGDLFVVKGNLFEDEGISEAEISVWGTSSRDVAAYTAGETADLGDGE 120 TLR +P ++ +GD +V++G LF EG S +EIS WGTS+RD AAY G +A+L G Sbjct: 61 TLRT-NPPSAQVQEGDRYVIEGRLFA-EGTS-SEISAWGTSARDPAAYEPGISAELRRGG 117 Query: 121 TITVQSNGAYVWSGTDDQISGRGQRVFVTATTPPEFTFANYENMLLDPNNSEGMARAFFN 180 T+TV +GAY T++ RG RVFVTAT PPEFT NYE +L+ N+++ MA+AFFN Sbjct: 118 TLTVTEDGAYRLESTEEISGKRGPRVFVTATVPPEFTLENYETVLISGNSTDNMAKAFFN 177 Query: 181 TLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHNAI 240 TLTVTIPATIIPILVAAFAAYALAWMEFPGRALL+A IVGLLVVPLQLALIPLL HN I Sbjct: 178 TLTVTIPATIIPILVAAFAAYALAWMEFPGRALLVAAIVGLLVVPLQLALIPLLKFHNEI 237 Query: 241 GIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLSF 300 GIGKGY+G W+AHTGFG+PLAIYLLRNYMVG+PRDIIENA+VDGATDF IF +I+LPLSF Sbjct: 238 GIGKGYIGVWMAHTGFGLPLAIYLLRNYMVGIPRDIIENARVDGATDFLIFVRIILPLSF 297 Query: 301 PALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAAFVS 360 PALASFAIFQFLWTWNDLLVA VFLIDATG+TTVMT QIVELLGTRGGNWEILAT+AFVS Sbjct: 298 PALASFAIFQFLWTWNDLLVAMVFLIDATGETTVMTKQIVELLGTRGGNWEILATSAFVS 357 Query: 361 IAVPLLVFFSMQRFLVRGLLAGSVK 385 IAVPL VFF+MQ++LVRGLLAGSVK Sbjct: 358 IAVPLAVFFAMQKYLVRGLLAGSVK 382 Lambda K H 0.323 0.138 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: 521 Number of extensions: 15 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: 385 Length of database: 382 Length adjustment: 30 Effective length of query: 355 Effective length of database: 352 Effective search space: 124960 Effective search space used: 124960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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