Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate Pf6N2E2_1800 putative ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1800 Length = 254 Score = 253 bits (647), Expect = 2e-72 Identities = 132/252 (52%), Positives = 178/252 (70%) Query: 13 QALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQI 72 +++++ L+K Y LK +++ +++G V+ +IG SGSGK+TLLRCVN LE+ G + Sbjct: 2 RSIVKAVSLNKYYDQFHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGL 61 Query: 73 LLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKL 132 +DGE +GY V K +E IA+ R TGM FQ+FNLFPH+T LQN+ G +V K Sbjct: 62 WVDGELVGYRIVGNKLHELNETQIARQRLSTGMVFQRFNLFPHMTVLQNIIEGPCQVLKR 121 Query: 133 HKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 192 EA A + L RVGL ++R+ YP +LSGGQQQRVAIARA+AM P LMLFDE TSALD Sbjct: 122 SPKEANEEALELLARVGLADKRNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSALD 181 Query: 193 PELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQ 252 PELVGEVLSV++ LA+ GMTM++VTHE+ FA EVS+++VFM+ G+I E G P+E+ PQ Sbjct: 182 PELVGEVLSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDGGQIVEAGSPEEILISPQ 241 Query: 253 SPRLAEFLKNTR 264 +PR F+ R Sbjct: 242 NPRTQSFISAVR 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: 201 Number of extensions: 8 Number of successful extensions: 1 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: 254 Length adjustment: 24 Effective length of query: 241 Effective length of database: 230 Effective search space: 55430 Effective search space used: 55430 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