Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_012050591.1 SWIT_RS22335 ATP-binding cassette domain-containing protein
Query= reanno::Phaeo:GFF2754 (331 letters) >NCBI__GCF_000016765.1:WP_012050591.1 Length = 211 Score = 122 bits (306), Expect = 8e-33 Identities = 76/182 (41%), Positives = 106/182 (58%), Gaps = 9/182 (4%) Query: 35 VGPSGCGKSTLLRVISGLEDATAGEISIGGQT----VTTTPPAKRGIAMVFQSYALYPHL 90 +GPSG GK+++LR ++GLE AG I + G+ T PP +R + VFQ L PHL Sbjct: 32 LGPSGSGKTSILRALAGLE-RIAGTIIVDGEVWQDGATFLPPERRRVGYVFQGAGLLPHL 90 Query: 91 SVRENMALALKQERQPKEEIAARVAEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVR 150 SV N+A A ER+ AR A +R + LDRRP+ LSGG+ QR I RA++ Sbjct: 91 SVAANLAYA---ERRAGPGRFARDAIVART-GIAPLLDRRPASLSGGEAQRAGIARALLG 146 Query: 151 EPKLFLFDEPLSNLDAALRMNTRLEIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDG 210 +P+L L DEPLS LD R + + L +++ + +VTHD EA LA + + LRDG Sbjct: 147 QPRLLLLDEPLSALDTDARADLLDWLDDLLAEIAIPVFHVTHDHAEAARLAARTIRLRDG 206 Query: 211 RI 212 R+ Sbjct: 207 RV 208 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: 180 Number of extensions: 8 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: 211 Length adjustment: 25 Effective length of query: 306 Effective length of database: 186 Effective search space: 56916 Effective search space used: 56916 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 Apr 09 2024. 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