Align ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized)
to candidate GFF726 PGA1_c07410 binding protein dependent transport system permease
Query= reanno::Smeli:SMc03062 (336 letters) >FitnessBrowser__Phaeo:GFF726 Length = 315 Score = 141 bits (356), Expect = 2e-38 Identities = 94/297 (31%), Positives = 156/297 (52%), Gaps = 17/297 (5%) Query: 40 GAVASRNLRIANSIRPWLFLAPALLALTLYLVYPVVQSVWLSLH---GRGGQNFVGLSNY 96 GA S R ++ PWLFLAP ++ Y+++P++QS LS + G G F+G+ NY Sbjct: 18 GASESWLRRNRQALAPWLFLAPGVIFFLFYVIFPILQSFNLSFYRWDGLGDPQFIGMENY 77 Query: 97 SWMINDGEFRQSIFNNFLWLLVVPALSTFFGLIIAALTDRIWWG-NIAKTLIFMPMAISF 155 +++D F S++NN WLL+ L+ GL IA ++ G + K+L F P IS Sbjct: 78 RELMDDRAFEVSLWNNLKWLLLY-LLAIPAGLFIALFLNQTVTGIRLYKSLFFFPFVISQ 136 Query: 156 VGAAVIWKFIYDYRAAGSEQIGLLNAIVVALGGEPQAWITLPFWNNFFLMVILIWIQTGF 215 V +++ + YD GLLN ++ +G P + P + +++ +W QT + Sbjct: 137 VVVGLVFSWFYD------PTFGLLNQVLAWVGLGPINVLGDPTLVTYGIIIAGLWPQTAY 190 Query: 216 AMVILSAALRGIPEETIEAAVIDGANGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDI 275 M++ L + E +EAA +DGA G ++ + +++PQ+ V + I L+ FD+ Sbjct: 191 CMILYLTGLNAVDPEQVEAARLDGAKGAKMLWYVIIPQLRPATFVAFVVTIIGALRSFDL 250 Query: 276 VLAMTNGQ--WQSQVLANLMFD-WMFRGGGDFGRGAAIAVV---IMILVVPIMIWNI 326 + MTNG S+VL+ MF+ + G G GAAIAVV IM+ + +W++ Sbjct: 251 ISIMTNGGPFGSSRVLSFYMFEKALSEYGFRMGYGAAIAVVLFLIMLCFIAYFLWSM 307 Lambda K H 0.330 0.142 0.466 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: 314 Number of extensions: 17 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: 336 Length of database: 315 Length adjustment: 28 Effective length of query: 308 Effective length of database: 287 Effective search space: 88396 Effective search space used: 88396 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