Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_000942251.1 HK29_RS01475 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >NCBI__GCF_000382825.1:WP_000942251.1 Length = 254 Score = 230 bits (587), Expect = 2e-65 Identities = 119/246 (48%), Positives = 172/246 (69%), Gaps = 7/246 (2%) Query: 13 LLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIVL 72 +L + + K +G +VL+ V+L + +G+VV ++G SGSGKTT LRC+N LE+ G++ L Sbjct: 1 MLQVEHIAKTFGERQVLEDVNLQVNQGDVVVILGPSGSGKTTFLRCLNHLEKADSGRLTL 60 Query: 73 DGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPK 132 G++ YD + +K I R T FQ +NLF + TAL+N+ GL+ +K+PK Sbjct: 61 AGKT--YD-----LAKLSKKDILEIRQKTAFVFQHYNLFANKTALENILEGLIVARKVPK 113 Query: 133 DEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 192 +EA+ AE LE+VGLL +D++P QLSGGQQQR+ IARAIA+ P ++L DE TSALDPE Sbjct: 114 EEALKRAESALEKVGLLAYKDYYPSQLSGGQQQRIGIARAIAVKPEVILLDEPTSALDPE 173 Query: 193 LVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 252 LVG+VL+V+K LA +G+TM++VTHEM FA +V++ ++FM+ GRI E+ P + F RPQ Sbjct: 174 LVGDVLDVLKQLAGEGVTMVVVTHEMGFARDVANHVIFMDGGRIVEENNPHDFFSRPQEE 233 Query: 253 RLAEFL 258 R +FL Sbjct: 234 RTKQFL 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: 181 Number of extensions: 11 Number of successful extensions: 2 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: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 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 24 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