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:
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