Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__WCS417:GFF2270 Length = 342 Score = 256 bits (653), Expect = 8e-73 Identities = 142/334 (42%), Positives = 202/334 (60%), Gaps = 5/334 (1%) Query: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 MA+LQL + K +G A+ DL +++GEF+ +GPSGCGK+T L++IAG + GG + Sbjct: 1 MAFLQLNALSKRYGAVDAVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGGQI 60 Query: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 +LDGRDIT + R L +VFQSYAL+PHMSV +N++F LK+ KV I KV+ + Sbjct: 61 LLDGRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVLEL 120 Query: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 + L + R P+ELSGGQRQRVA+ RA+V P V L DEPLSNLDA LR + + EI ++ Sbjct: 121 VRLAPHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180 Query: 181 RDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMN 240 +G TT+ VTHDQ EA++++DRVVV++ G + Q+ P +LY+ P +F++ F+G + Sbjct: 181 CAVGITTLMVTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVGKANLL 240 Query: 241 VVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVDLIEALGAETLI 300 D L P + +G + LRPE I + G+ + G+V G++ L Sbjct: 241 PGDYDLLGSPQVRH----ESGDGELTLSLRPEKIQLVDAGSGRLQGKVLDSYFFGSQWLY 296 Query: 301 YVTTPGGAQFVSRQND-RTDLRVGDAVSLDIDAS 333 + T G V R ND L G AV LD AS Sbjct: 297 RIHTSLGEITVVRSNDGSAPLGYGAAVGLDWQAS 330 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: 291 Number of extensions: 14 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: 342 Length adjustment: 29 Effective length of query: 321 Effective length of database: 313 Effective search space: 100473 Effective search space used: 100473 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