Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 317 bits (811), Expect = 4e-91 Identities = 175/368 (47%), Positives = 241/368 (65%), Gaps = 25/368 (6%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA + L +V K Y G+ + + + KI+DGEF++LVGPSGCGKSTL+ IAGLE I+ G Sbjct: 1 MAQVTLNSVRKVYPNGV-EAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEG 59 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 + + D ++ + P DRDIAMVFQ+YALYP M+VR NIA+GLK RK P AEI ++VA + Sbjct: 60 TLEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAA 119 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 K+L +E L RKP QLSGGQ+QRVAMGRA+ R P ++LFDEPLSNLDAKLR +MR E+K Sbjct: 120 KMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKA 179 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 + +RL T++YVTHDQ+EAMT+ D++ V+ G I+Q GTP +IY+NPA++FVASF+G+PP Sbjct: 180 LQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPP 239 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLE---DREVILGIRPEQI-ILANG 296 MN + A + +GQ LP G+ L+ V LGIRPE + ++A G Sbjct: 240 MNLLD-----------ATIANGQV--TLPDGVSMGALDTSAQGAVKLGIRPEDVQLVAEG 286 Query: 297 EANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLL 356 + +V++ E G L+ L + D+ P T + DPA + L Sbjct: 287 ------GLAIDVELIEELGAHRLLHGKLGGQPFTIHVLKDI-PVDPGTHQISVDPAAICL 339 Query: 357 FDAKTGER 364 FDA++G+R Sbjct: 340 FDAESGQR 347 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: 414 Number of extensions: 18 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: 348 Length adjustment: 30 Effective length of query: 356 Effective length of database: 318 Effective search space: 113208 Effective search space used: 113208 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: 49 (23.5 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