Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 148 bits (374), Expect = 1e-40 Identities = 93/247 (37%), Positives = 141/247 (57%), Gaps = 16/247 (6%) Query: 15 LLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILL 74 +L + ++ K++ EVL +LT+Q G T++G SG GKTT+LR + E+ GQILL Sbjct: 6 ILTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILL 65 Query: 75 DGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134 +G+ I ++ A+ R FQ + LFPHLT NV GL + Sbjct: 66 NGDDIA-------------RIPAEKRPF-NTVFQSYALFPHLTVFDNVAFGLKMAGVDVQ 111 Query: 135 DEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 194 D AV +A+ L V L E P QLSGGQ+QRVAIARA+ P ++L DE SALD + Sbjct: 112 DIAVRVADA-LAIVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYK 170 Query: 195 LVGEVLSVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 253 L ++ +K L G+T + VTH+ A +SD+I+ M+ G+ ++ G P+E++E P++ Sbjct: 171 LRQQMQLELKQLQRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRN 230 Query: 254 PRLAEFL 260 +A+F+ Sbjct: 231 LFVAQFI 237 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: 209 Number of extensions: 8 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: 265 Length of database: 369 Length adjustment: 27 Effective length of query: 238 Effective length of database: 342 Effective search space: 81396 Effective search space used: 81396 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: 48 (23.1 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