Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__psRCH2:GFF4241 Length = 335 Score = 166 bits (419), Expect = 8e-46 Identities = 101/251 (40%), Positives = 137/251 (54%), Gaps = 14/251 (5%) Query: 15 LLEIRDLHKQYGP----LEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGG 70 ++E +HK Y + L+ L + G V LIG SG+GK+TLLR +N LEE GG Sbjct: 1 MIEFHQVHKTYRTGGRDVPALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGG 60 Query: 71 QILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVK 130 +IL++GE + + +G R + R GM FQ FNL T NV + L Sbjct: 61 RILVNGEDVTALDADGLR---------RFRQRVGMIFQHFNLLMSKTVADNVAMPLRLAG 111 Query: 131 KLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSA 190 + E LERVGL E YP QLSGGQ+QRV IARA+A PS++L DE TSA Sbjct: 112 IRSRREIDARVAALLERVGLKEHARKYPAQLSGGQKQRVGIARALATEPSILLCDEATSA 171 Query: 191 LDPELVGEVLSVIKGL-AEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFE 249 LDP+ VL ++ + E +T++L+THEM V D++ M+ G I EQGP E+F Sbjct: 172 LDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVFL 231 Query: 250 RPQSPRLAEFL 260 P+ P F+ Sbjct: 232 HPKHPTTQRFV 242 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: 213 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: 335 Length adjustment: 26 Effective length of query: 239 Effective length of database: 309 Effective search space: 73851 Effective search space used: 73851 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