Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__psRCH2:GFF3990 Length = 334 Score = 209 bits (531), Expect = 1e-58 Identities = 126/321 (39%), Positives = 176/321 (54%), Gaps = 34/321 (10%) Query: 3 ALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILI 62 ++EI +I KR+G+ + L I++ ++SGE + LLG SGCGK++LL IIAGL P G I+ Sbjct: 2 SIEISHINKRFGQFQALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIVF 61 Query: 63 GERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMR----RVPQAEHDKAVRDTA 118 V +DR++ VFQ YAL+ +++V N+ FGL M+ R +A + V + Sbjct: 62 HGEDVSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHELL 121 Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178 L+Q++ L DR P QLSGGQRQR+A+ RAL P+V L DEP LDAK+R E+R L R Sbjct: 122 GLVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLAR 181 Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238 LH+ + T V+VTHDQ EAM +A RI VM G IEQ+ P EVY PA+ +V F+G Sbjct: 182 LHEDVHLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLGD-- 239 Query: 239 MNILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTA 298 AN L+++ VL RP + L+ + A+ L Sbjct: 240 ---------ANRLQLDDQRSVL-------------------FRPHEVALSREAVAEHLAG 271 Query: 299 SVEVVELTGPELVTTATVGSQ 319 V + G T V Q Sbjct: 272 EVRDIRPLGALTRVTLKVAGQ 292 Lambda K H 0.320 0.136 0.385 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: 279 Number of extensions: 12 Number of successful extensions: 2 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: 360 Length of database: 334 Length adjustment: 29 Effective length of query: 331 Effective length of database: 305 Effective search space: 100955 Effective search space used: 100955 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: 49 (23.5 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