Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >MicrobesOnline__882:209225 Length = 354 Score = 168 bits (426), Expect = 2e-46 Identities = 112/320 (35%), Positives = 162/320 (50%), Gaps = 34/320 (10%) Query: 4 LQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLD 63 L + G+ + + ++LT GE + VGPSG GK+TLLR IAGL+A D G++ Sbjct: 3 LAVEGLGRTLAGREVLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIR-- 60 Query: 64 GRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARIL-- 121 +T + +VFQ Y L+PH+SV+EN++F + V + E+V R Sbjct: 61 ---VTPPQGHGGGVVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAFRL 117 Query: 122 ---NLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAK 178 +L R P +LS GQRQRVA+ RA+V P V L DEP +NLD LRG+ + Sbjct: 118 DTDDLAHMASRYPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRD 177 Query: 179 LHRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQ 238 + R G T+ VTHD EA + DR+ V+ G + Q+ PL++Y PA++ A+F+G Sbjct: 178 VVRRFGVATVTVTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLG--- 234 Query: 239 MNVVPVDKLPQPVQQ-----QAPAAPAGAAVGAIGL---RPENITVRTTGATPV------ 284 PV L + ++ PAA A GL RPE + VR P Sbjct: 235 ----PVTVLDETTRRTLGIDTPPAAATACADTMQGLRLYRPEALAVRPWADGPAVLVSAR 290 Query: 285 -GGQVD--LIEALGAETLIY 301 GQV L++ G E L++ Sbjct: 291 FTGQVMQLLLDVEGQELLVH 310 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: 276 Number of extensions: 11 Number of successful extensions: 3 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: 354 Length adjustment: 29 Effective length of query: 321 Effective length of database: 325 Effective search space: 104325 Effective search space used: 104325 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