Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF776 PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Phaeo:GFF776 Length = 363 Score = 296 bits (757), Expect = 8e-85 Identities = 171/361 (47%), Positives = 227/361 (62%), Gaps = 11/361 (3%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA L+L NV KTYG G+ + L++I L I GE ++ VGPSGCGKSTL+ IAGLE ISGG Sbjct: 1 MANLKLTNVAKTYGGGV-EVLRDINLDIKQGELIVFVGPSGCGKSTLLRMIAGLERISGG 59 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 + +D+A ++ + P R IAMVFQSYALYP M+VRDN+AF LKI K EID + R + Sbjct: 60 TLEIDNAVMNDIPPAQRGIAMVFQSYALYPHMTVRDNMAFALKIAKKSKDEIDAAIDRAA 119 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 K+LQ+E L R P LSGGQ+QRVA+GR++ R PK+YLFDEPLSNLDA LRV R E+ Sbjct: 120 KILQLEPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQ 179 Query: 181 MHQRL-KTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSP 239 + + + +T +YVTHDQ+EAMTL ++ V+ D I Q GTP D+Y P N FVA FIGSP Sbjct: 180 LKEAMPDSTMIYVTHDQVEAMTLASRIVVLADKGIAQVGTPLDLYQRPENEFVAQFIGSP 239 Query: 240 PMNFIPLRLQRKDGRLLALLDSG-QARCELPLGMQDAGLEDREVILGIRPEQIILANGEA 298 MN IP + R L SG + E+P D GL V +G+RPE ++ E Sbjct: 240 AMNLIPGTVVATGPRTTVRLTSGEEVVAEIPTTDADQGL---AVNVGVRPEDLV---EEG 293 Query: 299 NGLPTIRAEVQVTEPTGPDTLVFVNLNDTK--VCCRLAPDVAPAVGETLTLQFDPAKVLL 356 G I + V + E G T++++ + K + +L G ++ L DPA++ L Sbjct: 294 TGGALIDSRVDIVEALGEVTVLYIAAGEGKDPLIAKLPGIHKGLRGSSVRLYADPARLHL 353 Query: 357 F 357 F Sbjct: 354 F 354 Lambda K H 0.319 0.138 0.393 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: 392 Number of extensions: 20 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: 386 Length of database: 363 Length adjustment: 30 Effective length of query: 356 Effective length of database: 333 Effective search space: 118548 Effective search space used: 118548 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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