Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate GFF2690 PGA1_c27320 putative sugar ABC transporter, ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Phaeo:GFF2690 Length = 349 Score = 298 bits (764), Expect = 1e-85 Identities = 167/368 (45%), Positives = 227/368 (61%), Gaps = 22/368 (5%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA +ELRN++K +G+ + + N +L+I + EFL+L+GPSGCGK+T M IAGLE+ + G Sbjct: 1 MAQIELRNISKRWGSFVG--VDNFDLTIADKEFLVLLGPSGCGKTTTMRMIAGLESASEG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 I++ V+ + PKDRD+AMVFQSYALYP M+V ENI F LK+R + D +V R + Sbjct: 59 DILVDGNRVNELEPKDRDVAMVFQSYALYPNMNVYENIRFPLKVRGVDAKTHDEKVRRAS 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +++++ L+RKP +LSGGQ+QRVA+ RA+ R P ++L DEPLSNLDAKLRV R ++K Sbjct: 119 AMVELDEFLHRKPAELSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRAQIKN 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 + L TT+YVTHDQIEAMTL D+V VM G++QQ G+P EIY+ PAN FVASFIGSP Sbjct: 179 LSHELAVTTIYVTHDQIEAMTLADRVVVMNKGVVQQVGSPTEIYDRPANAFVASFIGSPA 238 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRD--VILGLRPEQIMLAAGEG 298 MN + L GR A +T AGL +D V LG R E A Sbjct: 239 MNLMEGGL--SGGRFT------------AQHTDIAGLSGQDGPVTLGFRAED----ASVV 280 Query: 299 DSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFD 358 DS I A + E G T+V V++ V + ++ + +++ LFD Sbjct: 281 DSGGQINAPIYTMELLGDATMVTVRIGGVLVSVKADKTFRAEIDDMVSIHVPTDHCHLFD 340 Query: 359 ANTGERLG 366 TG RLG Sbjct: 341 TQTGARLG 348 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: 344 Number of extensions: 15 Number of successful extensions: 4 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