Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate BWI76_RS07590 BWI76_RS07590 glutamate ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__Koxy:BWI76_RS07590 Length = 253 Score = 253 bits (645), Expect = 4e-72 Identities = 124/249 (49%), Positives = 185/249 (74%), Gaps = 2/249 (0%) Query: 16 LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75 + ++++ KQ+ +EVL+ ++LT+++G VV+++GSSGSGK+TLLRC+N LE+ G+I + Sbjct: 7 VSVKNVSKQFDNVEVLRDINLTVEKGTVVSILGSSGSGKSTLLRCMNWLEQPDRGEIRIS 66 Query: 76 GESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHKD 135 G+ +G E NG+ + H + +++ R GM FQ FNL+PHLT QNV+ LL VK + +D Sbjct: 67 GQRLGIDEHNGRAMSHRQ--LSKIRERVGMVFQSFNLWPHLTVQQNVSEALLHVKGMKRD 124 Query: 136 EAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPEL 195 EA +A + LE+VG+ + D YP LSGGQ+QRVAIAR++AM+P ++LFDE TSALDPEL Sbjct: 125 EAKAIAMQQLEKVGMAHKADVYPITLSGGQKQRVAIARSLAMSPEVILFDEPTSALDPEL 184 Query: 196 VGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSPR 255 V EVL V+K LA +G TM++VTHEM FA +VSD++VF+ +G + E+ PP++ F P S R Sbjct: 185 VNEVLGVMKALAAEGYTMVVVTHEMDFARQVSDEVVFLEKGLLIEKAPPEKFFSNPDSER 244 Query: 256 LAEFLKNTR 264 + +FL+ +R Sbjct: 245 VRQFLQGSR 253 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: 206 Number of extensions: 9 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: 253 Length adjustment: 24 Effective length of query: 241 Effective length of database: 229 Effective search space: 55189 Effective search space used: 55189 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