Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 331 bits (848), Expect = 2e-95 Identities = 172/359 (47%), Positives = 236/359 (65%), Gaps = 3/359 (0%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA + L + K Y G + I +GE L+LVGPSGCGK+TL+ IAGLE+I+GG Sbjct: 1 MAKVRLDKLRKVYPNGHVGVAE-ASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGG 59 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 + IG++ V+ ++PKDRDIAMVFQ+YALYP M+V EN+ FGLK+R P+A+I+ VA A Sbjct: 60 TLSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAA 119 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++L++E L+ +P LSGGQ+QRVA+GRAL R PK++L DEPLSNLDAKLR+ MR E+ Sbjct: 120 RMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIAR 179 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +HQRLK T VYVTHDQIEAMTLG ++ V+ G+IQQ TP +Y+ PAN FVA F+GSP Sbjct: 180 IHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPA 239 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 MN + L R G +A+ EL DRD+++GLRPE ++L A + Sbjct: 240 MNLLRGILYRDGGWKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDLLLCADAAGA 299 Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDA 359 A + A+++V EP G + + ++ + + R+ P P G TL F P ++ FDA Sbjct: 300 A--LAAQLEVVEPVGNEVFLNLRHGELALVSRMPPRELPAPGSTLHFGFAPERLHFFDA 356 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: 399 Number of extensions: 15 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: 364 Length adjustment: 30 Effective length of query: 356 Effective length of database: 334 Effective search space: 118904 Effective search space used: 118904 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