Align D-xylose ABC transporter, permease protein (characterized)
to candidate SM_b20903 SM_b20903 sugar uptake ABC transporter permease
Query= CharProtDB::CH_024441 (393 letters) >FitnessBrowser__Smeli:SM_b20903 Length = 453 Score = 235 bits (600), Expect = 2e-66 Identities = 148/411 (36%), Positives = 227/411 (55%), Gaps = 42/411 (10%) Query: 25 LNLQVFVMIAAIIAIMLFFTWTT----DGAYLSARNVSNLLRQTAITGILAVGMVFVIIS 80 ++ ++ M+ A+I I L F T DG +L RN+ NL QT+ ++A GMV VI++ Sbjct: 42 IDTRLLGMVGALIIIWLGFQVMTGGLFDGLFLKPRNLWNLTVQTSSVAVMATGMVLVIVT 101 Query: 81 AEIDLSVGSMMGLLGGV-----AAICDVWLGWPLPLTIIVTLVLGLL----LGAWNGWWV 131 IDLSVGS++G G + A + +LG P T +TL G+ +GA +G + Sbjct: 102 RNIDLSVGSVLGFCGMIMGVLQAQVLPQYLGLGHPATWAITLACGIAVGGAIGALHGSII 161 Query: 132 AYRKVPSFIVTLAGMLAFRGILIGITNGTTVSPTSAAMSQIG---QSYLPASTGFIIGAL 188 A+ VP+FIVTL G+L +RG +T+G TV+P A +G + + A+ +I+G+L Sbjct: 162 AFLNVPAFIVTLGGLLVWRGATWFVTSGQTVAPMDATFRLMGGGTEGSIGATASWIVGSL 221 Query: 189 GLMAFVGWQWRGRMRRQALGLQSPASTAVVGRQALTAIIVLGAIWLLNDY---------- 238 +A VG R +R+ G A L +VLGA+ + N Y Sbjct: 222 ACIAIVGAILNSRKQRKRFGFPLRPVWAEYFLSILGCALVLGAVAVANHYYWPVNIARRY 281 Query: 239 ----------------RGVPTPVLLLTLLLLGGMFMATRTAFGRRIYAIGGNLEAARLSG 282 G+ PVL+ ++ + F+ATR FGR ++A+GGN EAA L+G Sbjct: 282 ADANGIAWPDGGLQISHGIAIPVLVAIVVGIVMTFIATRLRFGRYVFALGGNPEAAELAG 341 Query: 283 INVERTKLAVFAINGLMVAIAGLILSSRLGAGSPSAGNIAELDAIAACVIGGTSLAGGVG 342 I + +F + G++ AIA I ++RL A + + G + EL IAA VIGGTSLAGGVG Sbjct: 342 IKTRWVTVKIFTLMGVLCAIAAAISTARLNAATNAQGELDELYTIAAAVIGGTSLAGGVG 401 Query: 343 SVAGAVMGAFIMASLDNGMSMMDVPTFWQYIVKGAILLLAVWMDSATKRRS 393 ++AGA++GA +M SL +GM ++ + T +Q IV G +L+ AVW+D+ + R+ Sbjct: 402 TIAGAMIGALVMQSLQSGMVLLGIDTPFQRIVVGVVLVTAVWLDTVYRARA 452 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: 485 Number of extensions: 29 Number of successful extensions: 4 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: 453 Length adjustment: 32 Effective length of query: 361 Effective length of database: 421 Effective search space: 151981 Effective search space used: 151981 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