Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__psRCH2:GFF3990 Length = 334 Score = 226 bits (577), Expect = 5e-64 Identities = 127/324 (39%), Positives = 193/324 (59%), Gaps = 26/324 (8%) Query: 4 LQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLD 63 +++ I K FG+ +A+ I+L IQ GE + +GPSGCGK++LLR+IAGLE D GS++ Sbjct: 3 IEISHINKRFGQFQALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIVFH 62 Query: 64 GRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLA----KVDKQVIDEKVQNAAR 119 G D++ + R++ VFQ YAL+ HM+V+EN++F L++ + + VI EKV Sbjct: 63 GEDVSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHELLG 122 Query: 120 ILNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKL 179 ++ L R P++LSGGQRQR+A+ RA+ PKV L DEP LDA +R + R +A+L Sbjct: 123 LVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLARL 182 Query: 180 HRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQM 239 H D+ T+++VTHDQ EAM +ADR+VV+ G+IEQ+GTP E+Y PA++FV F+G Sbjct: 183 HEDVHLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLG---- 238 Query: 240 NVVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITV-RTTGATPVGGQVDLIEALGAET 298 ++L Q+ ++ RP + + R A + G+V I LGA T Sbjct: 239 ---DANRLQLDDQR------------SVLFRPHEVALSREAVAEHLAGEVRDIRPLGALT 283 Query: 299 LIYVTTPGGAQFVSRQ--NDRTDL 320 + + G A+ + + ND L Sbjct: 284 RVTLKVAGQAEPIEAEVGNDHASL 307 Lambda K H 0.320 0.137 0.388 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: 289 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: 350 Length of database: 334 Length adjustment: 29 Effective length of query: 321 Effective length of database: 305 Effective search space: 97905 Effective search space used: 97905 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