Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 158 bits (399), Expect = 2e-43 Identities = 98/248 (39%), Positives = 144/248 (58%), Gaps = 15/248 (6%) Query: 14 ALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIL 73 A LE+ D+ ++YG V+ G+ ++ G + L+G SG GKTTLLRC+ E+ G I Sbjct: 2 AHLELADVMQRYGAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSIA 61 Query: 74 LDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLH 133 LDGE + R K+ + R + GM FQ + LFPHLT N+ G LK K Sbjct: 62 LDGELVS---------RPGFKLAPEQRRI-GMVFQDYALFPHLTVADNIAFG-LKTKGGE 110 Query: 134 KDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDP 193 + + V L+ VGL + + YP +LSGGQQQRVA+ARA+A P L+L DE S LD Sbjct: 111 RQQRVA---AMLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDV 167 Query: 194 ELVGEV-LSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQ 252 +L + L V + L + G T +LVTH+ AF ++D+I M++GRI++ P L+ +P Sbjct: 168 DLRERLSLEVREILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPA 227 Query: 253 SPRLAEFL 260 + +A+F+ Sbjct: 228 NRFVADFV 235 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: 224 Number of extensions: 14 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: 356 Length adjustment: 27 Effective length of query: 238 Effective length of database: 329 Effective search space: 78302 Effective search space used: 78302 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 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