Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_110804296.1 C8J30_RS02695 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_003217355.1:WP_110804296.1 Length = 358 Score = 155 bits (393), Expect = 9e-43 Identities = 93/247 (37%), Positives = 140/247 (56%), Gaps = 16/247 (6%) Query: 15 LLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILL 74 ++E +HK YG L+G+ T++ G +L+G SG GKTTLLR + E+ G +L+ Sbjct: 1 MIEFDRVHKYYGDYHALRGITATIREGEFFSLLGPSGCGKTTLLRTIAGFEDISSGSVLI 60 Query: 75 DGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134 DG +H E V R T M FQ + +FPHL+ QNV GL + + Sbjct: 61 DG-------------KHMEDVPPNKRP-TNMVFQSYAIFPHLSVGQNVGFGLRRDPRSEA 106 Query: 135 DEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 194 ++A + E+ LE VGL LSGGQ+QRVA+ARA+ + P ++L DE SALD + Sbjct: 107 EKAKAV-EEALEMVGLKGYGARAAHALSGGQRQRVALARALILKPKVLLLDEPLSALDKK 165 Query: 195 LVGEV-LSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 253 + ++ + +IK E G+T +LVTH+ A +SD+I M +G I + P+ L+ RP S Sbjct: 166 IREQMQIELIKLQREVGITFVLVTHDQEEALVMSDRIAVMFEGEIAQLADPETLYRRPAS 225 Query: 254 PRLAEFL 260 R+A+F+ Sbjct: 226 RRVADFI 232 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: 212 Number of extensions: 9 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: 358 Length adjustment: 27 Effective length of query: 238 Effective length of database: 331 Effective search space: 78778 Effective search space used: 78778 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 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