Align D-xylose ABC transporter, permease protein (characterized)
to candidate HSERO_RS22470 HSERO_RS22470 D-xylose ABC transporter permease
Query= CharProtDB::CH_024441 (393 letters) >FitnessBrowser__HerbieS:HSERO_RS22470 Length = 377 Score = 373 bits (958), Expect = e-108 Identities = 198/368 (53%), Positives = 261/368 (70%), Gaps = 10/368 (2%) Query: 28 QVFVMIAAIIAIMLFFTWTTDGAYLSARNVSNLLRQTAITGILAVGMVFVIISAEIDLSV 87 ++ ++ AI I FF++ TDG +++ RN+SNLLRQ ++TGILA GMV VII+ EIDLSV Sbjct: 12 KIIALLIAIAIIWGFFSFMTDGGFVTPRNLSNLLRQMSVTGILACGMVLVIIAGEIDLSV 71 Query: 88 GSMMGLLGGVAAICDVWLGWPLPLTIIVTLVLGLLLGAWNGWWVAYRKVPSFIVTLAGML 147 GS++GLLGG+AA+ DV PL L +++ L GL LG NG+ AY +PSFIV L GML Sbjct: 72 GSLLGLLGGLAALLDVSHHLPLALNLVLALGFGLALGLLNGYLTAYLGIPSFIVGLGGML 131 Query: 148 AFRGILIGITNGTTVSPTSAAMSQIGQSYLPASTGFIIGALGLMAFVGWQWRGRMRRQAL 207 AFRGIL+GIT G T++P S M +GQ YLP G +G + V W R+ R Sbjct: 132 AFRGILLGITGGLTIAPVSDNMVYLGQGYLPPQMGVALGIALFVLAVALTWMSRVNRSRH 191 Query: 208 GLQSPASTAVVGRQALTAIIVLGAIWL-----LNDYRGVPTPVLLLTLLLLGGMFMATRT 262 GL A + R AL ++V+GA+ L LN Y G+P PVLLL LL +++T+T Sbjct: 192 GL----PLAALWRDAL-KVVVIGAVLLAFVRTLNSYDGIPVPVLLLLALLGLFSYVSTQT 246 Query: 263 AFGRRIYAIGGNLEAARLSGINVERTKLAVFAINGLMVAIAGLILSSRLGAGSPSAGNIA 322 FGRRIY++G N+EA RLSG+NV+ KL VF I G+M A+AGL+ ++RL AGSPSAGN+ Sbjct: 247 VFGRRIYSVGSNMEATRLSGVNVQAVKLWVFGIMGVMCALAGLVNTARLAAGSPSAGNMG 306 Query: 323 ELDAIAACVIGGTSLAGGVGSVAGAVMGAFIMASLDNGMSMMDVPTFWQYIVKGAILLLA 382 ELDAIAAC IGGTS+ GG G++ GA++GA +MASLDNGMSM+DV T+WQ IVKG+IL+LA Sbjct: 307 ELDAIAACFIGGTSMRGGSGTIYGALIGALVMASLDNGMSMLDVGTYWQMIVKGSILVLA 366 Query: 383 VWMDSATK 390 VW+D +T+ Sbjct: 367 VWVDVSTR 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: 377 Length adjustment: 30 Effective length of query: 363 Effective length of database: 347 Effective search space: 125961 Effective search space used: 125961 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