Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate Ac3H11_2065 Maltose/maltodextrin ABC transporter, permease protein MalG
Query= reanno::WCS417:GFF4322 (281 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2065 Length = 289 Score = 344 bits (883), Expect = 1e-99 Identities = 174/289 (60%), Positives = 216/289 (74%), Gaps = 11/289 (3%) Query: 4 LASKPAI--SLSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGI 61 + +KP++ S+ R +YAVL LA +L+PL ML+TSFK E+I S +LL+ P + Sbjct: 1 MTAKPSLLPSVGRFLVYAVLALATAFFLLPLYAMLVTSFKYAEEIRSTSLLALPGSLNWS 60 Query: 62 GWVKAWAT---------VDGYFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFG 112 W AW + + +F NS+ + VPAVLIST GALNGYVLS W+F+GS FG Sbjct: 61 AWGTAWQSACTGVDCNGLRPFFMNSVAMAVPAVLISTVWGALNGYVLSLWKFRGSDALFG 120 Query: 113 LLLFGCFLPFQTVLLPASFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDAL 172 +LLFG F+PFQ VLLP S LG +GL+S+ TGLV VH + GLA TTLFFRNYY +IP L Sbjct: 121 MLLFGVFMPFQVVLLPMSQVLGWLGLSSSITGLVLVHCLAGLAGTTLFFRNYYAAIPKEL 180 Query: 173 IKAARLDGAGFFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVAL 232 + AAR+DGA FF IF +I+LP+STPI+MV LIWQFT IWNDFLFGVVFS DS+P+TV L Sbjct: 181 VNAARMDGASFFQIFWRIVLPLSTPIVMVTLIWQFTNIWNDFLFGVVFSGTDSKPVTVGL 240 Query: 233 NNLVNTSTGAKEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281 NNL NTS+ K YNVDMAAA+IAGLPT+++YV+AGK+FVRGLTAGAVKG Sbjct: 241 NNLANTSSSVKAYNVDMAAAIIAGLPTMVIYVLAGKFFVRGLTAGAVKG 289 Lambda K H 0.328 0.141 0.435 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: 308 Number of extensions: 10 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: 281 Length of database: 289 Length adjustment: 26 Effective length of query: 255 Effective length of database: 263 Effective search space: 67065 Effective search space used: 67065 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: 47 (22.7 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