Align D-xylose ABC transporter, permease protein (characterized)
to candidate GFF2143 PS417_10930 D-xylose ABC transporter permease
Query= CharProtDB::CH_024441 (393 letters) >FitnessBrowser__WCS417:GFF2143 Length = 378 Score = 380 bits (976), Expect = e-110 Identities = 192/363 (52%), Positives = 261/363 (71%) Query: 28 QVFVMIAAIIAIMLFFTWTTDGAYLSARNVSNLLRQTAITGILAVGMVFVIISAEIDLSV 87 ++ ++ A+ I +FF+W T+G +L+ RN+SNLLRQ +ITGILA GMV VIIS EIDLSV Sbjct: 12 KMLALVIAVAVIWVFFSWQTEGGFLTPRNLSNLLRQMSITGILACGMVLVIISGEIDLSV 71 Query: 88 GSMMGLLGGVAAICDVWLGWPLPLTIIVTLVLGLLLGAWNGWWVAYRKVPSFIVTLAGML 147 GS++GLLGG+AAI DV PL + + + GL++G NG+ AY ++PSFIV L GML Sbjct: 72 GSLLGLLGGLAAILDVVYHIPLLANLSLVALCGLMIGLANGYMTAYLRIPSFIVGLGGML 131 Query: 148 AFRGILIGITNGTTVSPTSAAMSQIGQSYLPASTGFIIGALGLMAFVGWQWRGRMRRQAL 207 AFRGIL+GIT GTT++P S ++ +GQ YLP S G +G L V W+ R R Sbjct: 132 AFRGILLGITGGTTIAPVSPSLVYVGQGYLPHSVGIGLGVLLFSLTVFLTWKQRRNRALH 191 Query: 208 GLQSPASTAVVGRQALTAIIVLGAIWLLNDYRGVPTPVLLLTLLLLGGMFMATRTAFGRR 267 GL + + + R A+ ++ G + LN Y G+P PVLLL +LL ++ ++T FGRR Sbjct: 192 GLAAHSLVRDLVRVAVIGAVLAGFVTTLNSYDGIPVPVLLLLVLLGVFSYVTSQTVFGRR 251 Query: 268 IYAIGGNLEAARLSGINVERTKLAVFAINGLMVAIAGLILSSRLGAGSPSAGNIAELDAI 327 +YA+G N+EA RLSGINV+ KL +F I G+M A+AGL+ ++RL AGSPSAGN+ ELDAI Sbjct: 252 VYAVGSNMEATRLSGINVQAVKLWIFGIMGVMCALAGLVNTARLAAGSPSAGNMGELDAI 311 Query: 328 AACVIGGTSLAGGVGSVAGAVMGAFIMASLDNGMSMMDVPTFWQYIVKGAILLLAVWMDS 387 AAC IGGTS+ GG G+V GA++GA ++ SLDNGMSM+DV ++WQ IVKG+IL+LAVW+D Sbjct: 312 AACFIGGTSMRGGSGTVYGALLGALVITSLDNGMSMLDVDSYWQMIVKGSILVLAVWVDV 371 Query: 388 ATK 390 +T+ Sbjct: 372 STR 374 Lambda K H 0.325 0.138 0.415 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: 451 Number of extensions: 11 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: 393 Length of database: 378 Length adjustment: 30 Effective length of query: 363 Effective length of database: 348 Effective search space: 126324 Effective search space used: 126324 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.9 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