Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__ANA3:7026373 Length = 349 Score = 187 bits (476), Expect = 3e-52 Identities = 113/300 (37%), Positives = 178/300 (59%), Gaps = 17/300 (5%) Query: 2 ATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGA 61 +TL L V+ Y LK ++L++ +GE L L+GPSGCGK+TL+ +AGL+ I+ G Sbjct: 3 STLNLHQVHSDYQG--QQVLKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGE 60 Query: 62 IMIGDQDVSG----MSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVA 117 I I + VSG + + R I M+FQ YAL+P ++V ENI FG + K+ A A + Sbjct: 61 IQINGKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFG--VAKLTPAQRKARLD 118 Query: 118 RVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTE 177 + L+++E L R P +LSGGQQQRV++ RALA P++ L DEP SN+DA++R M E Sbjct: 119 DMLALVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAE 178 Query: 178 MKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIG 237 ++ + ++ + V+VTH + EA D +A+ G+I Q G + +Y P +++VA F+G Sbjct: 179 IRSILKQRNVSAVFVTHSKDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLG 238 Query: 238 SPPMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGE 297 S N++P + DG V + G+ R L+ + A + + LRP+Q+ L+A + Sbjct: 239 SG--NYLPAEV--IDGHSV-VTPIGELRSLTPLSQSHA----FNGQVFLRPQQLALSADD 289 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: 282 Number of extensions: 15 Number of successful extensions: 3 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: 349 Length adjustment: 30 Effective length of query: 356 Effective length of database: 319 Effective search space: 113564 Effective search space used: 113564 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: 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