Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate 3609758 Dshi_3141 ABC transporter related (RefSeq)
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Dino:3609758 Length = 352 Score = 294 bits (752), Expect = 3e-84 Identities = 169/366 (46%), Positives = 234/366 (63%), Gaps = 17/366 (4%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA + L+++ K +G + + N L +++ EFL+L+GPSGCGK+T M IAGLE T G Sbjct: 1 MAEVILKDLTKRWGDFVG--VDNQSLHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 I IGD+ V+ PKDRD+AMVFQ+Y LYP M++ ENI + L++R + +A+I V R A Sbjct: 59 EIWIGDRMVNDDLPKDRDVAMVFQNYGLYPHMTIFENIAYPLRVRGVDKAEIPPRVQRAA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 + +++ L+RKP LSGGQ+QRVA+ RA+ R+PK++L DEPLSNLDAKLRV MR E+K Sbjct: 119 EQVELTKFLHRKPKALSGGQRQRVALARAIVRKPKVFLMDEPLSNLDAKLRVTMRAELKH 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 + + L+ TTVYVTHDQIEAMTL D+VAVMK G+IQQ GTP EIYN+PAN FVA FIGSP Sbjct: 179 LSRELQITTVYVTHDQIEAMTLADRVAVMKHGVIQQLGTPDEIYNDPANLFVAGFIGSPA 238 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIML-AAGEGD 299 MN + ++ DG V +G R + A ILG+R + + + AG+GD Sbjct: 239 MNLINGSVE--DGMFVT---TGGTRLVKVPSPDRA-----RAILGVRADDMQVHEAGQGD 288 Query: 300 SASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDA 359 I + E TG TL+ VQ +V R + + + + + + + LFD Sbjct: 289 ----IDVTIYAFENTGESTLLTVQWGKQRVIARGDRHLRKEQDDVVGISLNTDHLYLFDP 344 Query: 360 NTGERL 365 +T ER+ Sbjct: 345 DTEERI 350 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: 375 Number of extensions: 17 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: 352 Length adjustment: 30 Effective length of query: 356 Effective length of database: 322 Effective search space: 114632 Effective search space used: 114632 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