Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Dino:3607124 Length = 338 Score = 347 bits (890), Expect = e-100 Identities = 184/338 (54%), Positives = 235/338 (69%), Gaps = 7/338 (2%) Query: 1 MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60 M +++ + K +G + L DINL +EDGEFVVFVGPSGCGKSTLLR ++GLE ++G I Sbjct: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 Query: 61 SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120 IGG+ VTT PA R +AMVFQSYALYPH++VRENM +K + R+AEA+R+ Sbjct: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120 Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180 L LEDYLDR+P +LSGGQRQRVAIGRA+V+ P +FLFDEPLSNLDA LR+ R+E+ LH Sbjct: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180 Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240 +QL A+MIYVTHDQ+EAMT+ADKIVVL GRIEQVG+PM+LY+ P +RFVAEFIG+PAMN Sbjct: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240 Query: 241 F----VPAQRLG-GNPGQFIGIRPEYARISPVGP--LAGEVIHVEKLGGDTNILVDMGED 293 V Q + F+G RPE+ I P G +A V E+LGG++ + + + Sbjct: 241 VFSSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLKGG 300 Query: 294 LTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQRI 331 AR+ G +T VG + F FDEAG+ I Sbjct: 301 GQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI 338 Lambda K H 0.320 0.137 0.391 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: 388 Number of extensions: 15 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: 331 Length of database: 338 Length adjustment: 28 Effective length of query: 303 Effective length of database: 310 Effective search space: 93930 Effective search space used: 93930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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