Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate AZOBR_RS00690 AZOBR_RS00690 ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__azobra:AZOBR_RS00690 Length = 268 Score = 267 bits (682), Expect = 2e-76 Identities = 141/252 (55%), Positives = 187/252 (74%), Gaps = 2/252 (0%) Query: 10 NASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQG 69 NA +A+L + ++HK++GPLEVLKGV LT + G+V+TLIGSSGSGK+TLLRC+NMLE Sbjct: 10 NAPEAVL-VENVHKRFGPLEVLKGVSLTAREGDVITLIGSSGSGKSTLLRCINMLEVPDE 68 Query: 70 GQILLDGESIGYHEVNG-KRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLK 128 G+I++ GE+IG + G + V + + + R GM FQ FNL+ H+T L+NV + Sbjct: 69 GRIVIGGEAIGLKKARGGQTVPADSRQVDRIRTRLGMVFQSFNLWTHMTILENVIEAPVH 128 Query: 129 VKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVT 188 V + K EAV A K L++VG+L + + YP QLSGGQQQR AIARA+AM P +MLFDE T Sbjct: 129 VLGVPKAEAVDRARKLLDKVGILAKAESYPVQLSGGQQQRAAIARALAMQPKVMLFDEPT 188 Query: 189 SALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 248 SALDPELVGEVL VI+ LAE+G TM+LVTHEM FA EV+ ++VF++QGRIEE+GPP + Sbjct: 189 SALDPELVGEVLLVIRQLAEEGNTMILVTHEMGFAREVASEVVFLHQGRIEERGPPDRVL 248 Query: 249 ERPQSPRLAEFL 260 P+S R+ +FL Sbjct: 249 VNPESDRVRQFL 260 Lambda K H 0.319 0.135 0.379 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: 223 Number of extensions: 7 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: 265 Length of database: 268 Length adjustment: 25 Effective length of query: 240 Effective length of database: 243 Effective search space: 58320 Effective search space used: 58320 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