Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate H281DRAFT_02631 H281DRAFT_02631 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__Burk376:H281DRAFT_02631 Length = 300 Score = 130 bits (326), Expect = 5e-35 Identities = 77/261 (29%), Positives = 140/261 (53%), Gaps = 6/261 (2%) Query: 40 IIWTFILSFTNSSFMPSYKWVGLQQYMRLMDNDRWWVASKNLALFGGMFISISLVLGVFL 99 I + LSF N M ++GL Y+ L D +++A KN L +F ++ LG+ Sbjct: 46 IFSSIALSFYNWDGMTPRTFIGLANYVELFHADTFYLALKN-NLIWLVFFLLAPPLGLLF 104 Query: 100 AVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWL 159 A+ L+Q+I+ +++++ P LS +V G + W +P GL K++ G + L Sbjct: 105 ALYLNQQIKGMRVVKSLFFAPFVLSGVVVGLVFSWFYDPAFGLLKLI-----VGHGIPVL 159 Query: 160 VDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSL 219 D V + +V AA+W + + M ++L GL ++ ++ AA+++GA ++ ++LP L Sbjct: 160 GDPRTVTFGIVFAALWPQTPYCMVLYLTGLTSINPEVVEAARMEGAKGWSLLWHVILPQL 219 Query: 220 RPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAML 279 RP F A ++ A++SFDL++ M+ GGP SS + A +MY + G ++ A++ Sbjct: 220 RPATFMAVVLTVIGALRSFDLISVMSGGGPFDSSTVLAYYMYDQAIKYYREGYSASIAVV 279 Query: 280 MLGAVLTILVPYLYSELRGKR 300 + +L +V +L LR +R Sbjct: 280 LFAIMLVYIVFHLRRMLREER 300 Lambda K H 0.329 0.141 0.448 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: 249 Number of extensions: 16 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: 302 Length of database: 300 Length adjustment: 27 Effective length of query: 275 Effective length of database: 273 Effective search space: 75075 Effective search space used: 75075 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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