Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_038017589.1 HA49_RS11785 maltose/maltodextrin ABC transporter ATP-binding protein MalK
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_000757425.2:WP_038017589.1 Length = 369 Score = 294 bits (753), Expect = 2e-84 Identities = 164/360 (45%), Positives = 231/360 (64%), Gaps = 10/360 (2%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA++ L V K+YG + ++I L I+EGEF++LVGPSGCGKST++ IAGLE IT G Sbjct: 1 MASVSLDGVYKSYGETVIS--RDITLEIEEGEFVVLVGPSGCGKSTILRMIAGLEDITAG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 + I Q ++ P DR I MVFQSYALYP ++V EN+ FGLK+ +++I V +VA Sbjct: 59 ELKIAGQRMNETPPADRGIGMVFQSYALYPHLTVAENMSFGLKLAGTKKSEIAQRVNQVA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++LQ+ HLL+R+P LSGGQ+QRVA+GR L P ++L DEPLSNLDA LRV+MR E+ Sbjct: 119 EVLQLAHLLDRRPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +H+RLK T +YVTHDQ+EAMTL DK+ V+ G I Q G P +Y+ PAN+FVA FIGSP Sbjct: 179 LHKRLKRTMIYVTHDQVEAMTLADKIVVLDAGQIAQIGKPLALYHYPANRFVAGFIGSPK 238 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 MNF+P++ + R V + + R L + + ++ LG+RPE ++ GD+ Sbjct: 239 MNFLPVKATAAEARRVEVELPNRQRIWLMVEGHDI-TPGSNLSLGIRPEHLL----PGDA 293 Query: 301 AS-SIRAEVQVTEPTGPDTLVFVQLNDTK--VCCRLAPDVAPQVGETLTLQFDPSKVLLF 357 A ++ EVQV E G +T + +Q+ + + R V + G T T+ P + LF Sbjct: 294 AEVTLSGEVQVAERLGNETQIHIQIPAIRQNLVYRQNDVVLAEEGATFTIGLPPHRCHLF 353 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: 360 Number of extensions: 14 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 24 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