Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate BPHYT_RS16095 BPHYT_RS16095 sugar ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__BFirm:BPHYT_RS16095 Length = 369 Score = 296 bits (758), Expect = 6e-85 Identities = 166/363 (45%), Positives = 230/363 (63%), Gaps = 13/363 (3%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA++ LRN+ K Y + +++I L I +GEF++ VGPSGCGKSTLM IAGLE I+GG Sbjct: 1 MASVTLRNIRKAYDEN--EVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 + I V+ ++P R IAMVFQSYALYP M++ +N+ FGLK+ + +IDA V A Sbjct: 59 DLTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 K+L I+HLL+RKP QLSGGQ+QRVA+GRA+ R+PK++LFDEPLSNLDA LRV+MR E Sbjct: 119 KILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +H LKTT +YVTHDQ+EAMTL DK+ V+ G ++Q G+P +Y+ PAN+FVA FIGSP Sbjct: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPK 238 Query: 241 MNFVPLRLQ--RKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEG 298 MNF+ +Q DG + ++G+ + +A+ D+ V +G+RPE + + E Sbjct: 239 MNFMEGVVQSVTHDG-VTVRYETGETQ-RVAVEPAAVKQGDK-VTVGIRPEHLHVGMAE- 294 Query: 299 DSASSIRAEVQVTEPTGPDTLVFVQ--LNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLL 356 I A E G ++ + + + R+ P GET L P L Sbjct: 295 ---DGISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHL 351 Query: 357 FDA 359 FD+ Sbjct: 352 FDS 354 Lambda K H 0.318 0.135 0.382 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: 17 Number of successful extensions: 1 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: 369 Length adjustment: 30 Effective length of query: 356 Effective length of database: 339 Effective search space: 120684 Effective search space used: 120684 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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