Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__HerbieS:HSERO_RS02210 Length = 372 Score = 300 bits (769), Expect = 3e-86 Identities = 171/368 (46%), Positives = 236/368 (64%), Gaps = 23/368 (6%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA + +RN+ K Y + +++I L+I+DGEF++ VGPSGCGKSTL+ IAGLE IS G Sbjct: 1 MAAVSIRNLAKRYDDN--EVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 + + ++ + R +AMVFQSYALYP MS+ DN+AFGLKI AEID V + Sbjct: 59 DLDIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 K+L I+HLL RKP LSGGQ+QRVA+GRA+ R+P ++LFDEPLSNLDA LRV+MR E Sbjct: 119 KILHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAK 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +H LKTT +YVTHDQIEAMTL DK+ V+ +G I+Q G+P+ +Y++PAN FVA FIGSP Sbjct: 179 LHDDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPK 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELP-LGMQDAGLE------DREVILGIRPEQIIL 293 MNFI DG + A+ G + +LP G+Q A ++ ++V LG+RPE + + Sbjct: 239 MNFI-------DGTVAAIQADG-VQVQLPGGGLQWAAVDGSTLQVGQKVTLGVRPEHLNI 290 Query: 294 ANGEANGLPTIRAEVQVTEPTGPDTLVFVNL--NDTKVCCRLAPDVAPAVGETLTLQFDP 351 A G+A ++A E G + ++ ++ + R+ + G L L DP Sbjct: 291 AQGQA----ALQARCTALELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADP 346 Query: 352 AKVLLFDA 359 A+ LF A Sbjct: 347 ARCHLFGA 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: 411 Number of extensions: 12 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: 372 Length adjustment: 30 Effective length of query: 356 Effective length of database: 342 Effective search space: 121752 Effective search space used: 121752 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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