Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 145 bits (367), Expect = 6e-40 Identities = 90/247 (36%), Positives = 134/247 (54%), Gaps = 21/247 (8%) Query: 21 KQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIVLDGESIGYD 80 K Y VL V L+++RG+ V L+G+SG+GKTTLL+ +N L E G I ++G + Sbjct: 9 KHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVA-- 66 Query: 81 DIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPKDEAVALAE 140 + +A R G FQ LFPH++ +NV L + +++ +P++E A Sbjct: 67 ----------AQPVAELRRRIGYVFQGIGLFPHMSVAENVAL-VPRLQGVPREERAARVA 115 Query: 141 KWLERVGL----LERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPELVGE 196 + L+ V L ERR P QLSGGQ QRV ARA+A P++ML DE ALDP E Sbjct: 116 ELLDLVALPADFAERR---PAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDE 172 Query: 197 VLNVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSPRLA 255 + + L E G+T L+VTH+M A ++D+++ + +GRI PP+ L PR+ Sbjct: 173 LGAAYRALHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIE 232 Query: 256 EFLKNTR 262 + R Sbjct: 233 AMIAVAR 239 Lambda K H 0.320 0.138 0.392 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: 146 Number of extensions: 6 Number of successful extensions: 4 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: 263 Length of database: 252 Length adjustment: 24 Effective length of query: 239 Effective length of database: 228 Effective search space: 54492 Effective search space used: 54492 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