Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_011383782.1 AMB_RS06945 phosphate ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >NCBI__GCF_000009985.1:WP_011383782.1 Length = 259 Score = 137 bits (344), Expect = 3e-37 Identities = 93/246 (37%), Positives = 131/246 (53%), Gaps = 16/246 (6%) Query: 14 LDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIMLD 73 + RGL YG + L +DL + G V LIG SG GK+T LRC+N + + M+D Sbjct: 12 ISARGLNVHYGEKQALHDIDLDIPAGEVTALIGPSGCGKSTFLRCINRMND------MVD 65 Query: 74 GESI-GYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPK 132 G + G +DG V + + RA GM FQ+ N FP + NV G ++ L + Sbjct: 66 GAKVTGSLTLDGSDVYDRSLDVVQLRARVGMVFQKPNPFPK-SIYDNVAYG-PRIHGLAR 123 Query: 133 DEAV--ALAEKWLERVGLL----ERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVT 186 D+A + LE+ GLL R LSGGQQQR+ IARAIA+ P ++L DE Sbjct: 124 DQAELDEIVMNSLEKAGLLAEVESRLSESGTGLSGGQQQRLCIARAIAVAPEVILMDEPC 183 Query: 187 SALDPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 246 SALDP +V +I L D T+++VTH M+ A VS + F + G++ E G +E+F Sbjct: 184 SALDPIATAKVEELIDEL-RDNYTIVIVTHSMQQAARVSQRTAFFHLGKLIEVGGTEEIF 242 Query: 247 ERPQSP 252 P+ P Sbjct: 243 TNPKEP 248 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: 162 Number of extensions: 10 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: 259 Length adjustment: 25 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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