Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 271 bits (694), Expect = 2e-77 Identities = 157/351 (44%), Positives = 209/351 (59%), Gaps = 18/351 (5%) Query: 4 LQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLD 63 +++ G++ +G HR +K I L I+ GEF F+GPSGCGK+TLLRLIAG G++ + Sbjct: 19 VRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIG 78 Query: 64 GRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNL 123 GRDI+ P+ KRD+ MVFQSYAL+PHM+V N++F L+ +V + I+ +V A ++ L Sbjct: 79 GRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGL 138 Query: 124 TQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLHRDL 183 R P +LSGGQ+QRVA+ R IV PKV L DEPLSNLDA LR Q R E+ L R L Sbjct: 139 KHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKL 198 Query: 184 GATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQM---N 240 G TTI+VTHDQ EA T+ DR+ V+ DGI++QVGTP ELYD PAN FVA F+GT + Sbjct: 199 GLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGTANVLEGQ 258 Query: 241 VVPVD-----KLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVDLI---- 291 V VD + V P A G + RP+N+ +R G P G V L+ Sbjct: 259 VRAVDGGTAFVMGGGVPIPLPHGVEPGAAGKLMFRPQNLFIRQDGGPPRAGHVRLMGVVR 318 Query: 292 --EALGAETLIYVTTPGGAQF---VSRQNDRTDLRVGDAVSLDIDASQAHW 337 E LGA ++ Y GG Q Q L ++LD+ A +A + Sbjct: 319 HREFLGA-SIRYAVDIGGQQVQVDAPHQAGDALLPTDTPITLDLAADKARF 368 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: 366 Number of extensions: 13 Number of successful extensions: 1 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: 371 Length adjustment: 29 Effective length of query: 321 Effective length of database: 342 Effective search space: 109782 Effective search space used: 109782 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