Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate YP_425186.1 Rru_A0094 binding-protein dependent transport system inner membrane protein
Query= reanno::WCS417:GFF4322 (281 letters) >NCBI__GCF_000013085.1:YP_425186.1 Length = 312 Score = 350 bits (899), Expect = e-101 Identities = 173/277 (62%), Positives = 214/277 (77%), Gaps = 9/277 (3%) Query: 14 RIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGIGWVKAW------ 67 RI +YAVL+L L YL+PL VMLLTS KT +DI +G+L++ P +T W+KAW Sbjct: 36 RIGLYAVLVLFALYYLLPLFVMLLTSVKTLDDIRAGSLIALPRTLTFEPWLKAWDSACVG 95 Query: 68 ---ATVDGYFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQT 124 A + YF NS+ + VPAV IST +GALNGY L+ WRF GSQL F L+LFGCF+PFQ Sbjct: 96 VQCAGLKPYFLNSLLLVVPAVAISTVLGALNGYALTKWRFPGSQLIFALMLFGCFIPFQV 155 Query: 125 VLLPASFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAGFF 184 VLLP + LG GLA + GL+ VHVVYGL+FTTLFFRN+Y+++PD L++AA +DGAGFF Sbjct: 156 VLLPMARVLGLAGLAGSIQGLILVHVVYGLSFTTLFFRNFYMTVPDELVRAATIDGAGFF 215 Query: 185 TIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTGAKE 244 IF I+LPMS PII+V +IWQFTQI+NDFLFGV F+ QP+TVALNNLV +STG KE Sbjct: 216 RIFFSILLPMSPPIIVVTIIWQFTQIYNDFLFGVSFTVSGGQPVTVALNNLVASSTGVKE 275 Query: 245 YNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281 YNVDMAAA++ LPTL+VY +AGKYF+RGL+AGAVKG Sbjct: 276 YNVDMAAAILTALPTLVVYAVAGKYFIRGLSAGAVKG 312 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: 272 Number of extensions: 5 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: 312 Length adjustment: 26 Effective length of query: 255 Effective length of database: 286 Effective search space: 72930 Effective search space used: 72930 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