Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 199 bits (507), Expect = 6e-56 Identities = 122/324 (37%), Positives = 189/324 (58%), Gaps = 27/324 (8%) Query: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 M+ + I++++ Y L ++L + GE +GPSGCGK+TLL+ +AGL+ +S GRI Sbjct: 1 MSTLTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRI 60 Query: 61 EIGGRDVT---TVEPADR-DLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAE 116 I GR ++ T P++R ++ M+FQ YAL+PH+TV EN+ FG+K G + R+ R+ E Sbjct: 61 SINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVK--GLDKAARQARLGE 118 Query: 117 AARVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVEL 176 +++LE R P +LSGGQ+QRV+I RA+ P + L DEP SN+DAK+R +M VE+ Sbjct: 119 MLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEI 178 Query: 177 EGLHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGS 236 + KQ G + ++VTH + EA ADK+ + G I Q GS LY +P ++VAEF+G Sbjct: 179 REILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLGQ 238 Query: 237 PAMNVFSSDV----GLQDI--------SLDASAAFVG---CRPEHIEIVPDGDGHIAATV 281 +N S +V LQ + L +A + G RPE +++ D G T+ Sbjct: 239 --VNYLSCEVKDRARLQTLLGEVQSSSDLPKAAGYRGELLLRPEQLQMAGDEQGE--GTI 294 Query: 282 HVKERLGGESLLYLGLKGGGQIVA 305 + LG +L + + G +I+A Sbjct: 295 IARRFLG--NLCHYSILIGEEILA 316 Lambda K H 0.320 0.139 0.396 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: 299 Number of extensions: 17 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: 338 Length of database: 342 Length adjustment: 28 Effective length of query: 310 Effective length of database: 314 Effective search space: 97340 Effective search space used: 97340 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