Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 209 bits (531), Expect = 1e-58 Identities = 125/342 (36%), Positives = 194/342 (56%), Gaps = 21/342 (6%) Query: 4 LQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLD 63 +++R I K FG A+ + L+I GE + +GPSGCGK+TLLR+IAG+E D G +M + Sbjct: 3 IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62 Query: 64 GRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNL 123 G + T + +R + VFQ YAL+ HM+V+EN++F L++ ++ + +++ R+++L Sbjct: 63 GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRK--RVMDL 120 Query: 124 TQYLQ------RTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIA 177 +Q R P +LSGGQRQR+A+ RA+ PKV L DEP LD +R + R + Sbjct: 121 LSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLR 180 Query: 178 KLHRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTP 237 +LH ++ ++++VTHDQ EA+ +ADRVVV+ G IEQVG+P E+Y PA+ FV QF+G Sbjct: 181 RLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLG-- 238 Query: 238 QMNVVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATP--VGGQVDLIEALG 295 +NV + PAG A +RP +I + T ATP + +V ++ +G Sbjct: 239 NVNVFHSRVHGAWAEVARDDVPAGQEAVAF-IRPHDIDIDTV-ATPESLEAKVSYVQTIG 296 Query: 296 AETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHW 337 + V G V +R + L + A Q W Sbjct: 297 PLVRVEVIHQGELVEVELTRERQQV-------LGLTAGQQVW 331 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: 274 Number of extensions: 8 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: 360 Length adjustment: 29 Effective length of query: 321 Effective length of database: 331 Effective search space: 106251 Effective search space used: 106251 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 Apr 09 2024. 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