Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate PfGW456L13_878 amino acid ABC transporter, permease protein
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_878 Length = 222 Score = 132 bits (332), Expect = 5e-36 Identities = 74/219 (33%), Positives = 119/219 (54%) Query: 1 MNYQLNFAAVWRDFDTLLAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVY 60 M YQ +F V + D LL G LEL + +G +G++ A R + +VY Sbjct: 1 MAYQFDFLPVVNNTDLLLRGALFTLELTAIGAVLGVGLGIVGALVRAWNIRPFAGIFAVY 60 Query: 61 VTVIRNTPILVLILLIYFALPSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGL 120 V +IRNTP LV + I+F LPSLG+++ + + ++ + + GAY TE+ R G+ +IP+G Sbjct: 61 VELIRNTPFLVQLFFIFFGLPSLGVQISEWQAAVLAMVINLGAYSTEIIRAGIQAIPRGQ 120 Query: 121 REAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKI 180 EA A+ + ++ +V + L V PALS+ I + +++ + IA EL++ A I Sbjct: 121 LEAAAALAMTRFEAFRHVVLLPALGKVWPALSSQIIIVMLGSAVCSQIATEELSFAANFI 180 Query: 181 NVESYRVIETWLVTTALYVAACYLIAMLLRYLEQRLAIR 219 ++R ET+ +TT LY+ LI LL +L R R Sbjct: 181 QSRNFRAFETYALTTLLYLCMALLIRQLLNWLGHRFIAR 219 Lambda K H 0.329 0.143 0.416 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: 135 Number of extensions: 4 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: 220 Length of database: 222 Length adjustment: 22 Effective length of query: 198 Effective length of database: 200 Effective search space: 39600 Effective search space used: 39600 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: 45 (21.9 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