Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Ga0059261_3668 Ga0059261_3668 ABC transporter
Query= reanno::Phaeo:GFF2754 (331 letters) >FitnessBrowser__Korea:Ga0059261_3668 Length = 201 Score = 125 bits (315), Expect = 7e-34 Identities = 72/191 (37%), Positives = 107/191 (56%), Gaps = 14/191 (7%) Query: 22 INLTVEDGE-FVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQTV------TTTPPAK 74 I+ +E GE +V GPSG GK+++L +++GL + G + +GG+T+ PP + Sbjct: 16 ISCRIEGGEGIIVLFGPSGVGKTSVLDMVAGLLEPDTGHVRVGGETLFDAAIGEDVPPER 75 Query: 75 RGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSLEDYLDRRPSEL 134 R VFQ L+PHLSVR N+ + ++AAR + LDR P L Sbjct: 76 RRAGYVFQDARLFPHLSVRANLLYGAGGDPSGLGDLAAR-------FDIAHLLDRWPRSL 128 Query: 135 SGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSASMIYVTHDQ 194 SGG+ +RVAIGRA++ +P+ L DEPLS+LD A R I RL + + ++ VTHD Sbjct: 129 SGGEARRVAIGRALLAKPRFLLLDEPLSSLDRARREEVTRVIERLRDEAALPILMVTHDP 188 Query: 195 IEAMTLADKIV 205 +EA L +I+ Sbjct: 189 VEAERLGQRII 199 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: 202 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: 201 Length adjustment: 24 Effective length of query: 307 Effective length of database: 177 Effective search space: 54339 Effective search space used: 54339 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: 47 (22.7 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