Align D-xylose ABC transporter, permease protein (characterized)
to candidate WP_110804518.1 C8J30_RS04455 sugar ABC transporter permease
Query= CharProtDB::CH_024441 (393 letters) >NCBI__GCF_003217355.1:WP_110804518.1 Length = 429 Score = 235 bits (599), Expect = 2e-66 Identities = 143/405 (35%), Positives = 221/405 (54%), Gaps = 36/405 (8%) Query: 25 LNLQVFVMIAAIIAIMLFFTWTTDGAYLSARNVSNLLRQTAITGILAVGMVFVIISAEID 84 L+ ++ MI A + I L F TDG +L+ RN+ NL QT I+A GMVFVI++ ID Sbjct: 21 LDTRLLGMIGAFVVICLVFNVITDGRFLTPRNIFNLSIQTVSVAIMATGMVFVIVTRHID 80 Query: 85 LSVGSMMGLLGGVAAICDVWL-------GWPL--PLTIIVTLVLGLLLGAWNGWWVAYRK 135 LSVG+++ + V + V L G PL PLT++ L+ G +GA NGW V Y++ Sbjct: 81 LSVGAVLAICSSVMGVMQVQLLPQLFGIGHPLVMPLTVLAGLLTGAAIGALNGWLVGYQR 140 Query: 136 VPSFIVTLAGMLAFRGILIGITNGTTVSPTSAAMSQIG--QSYLPASTGFIIGALGLMAF 193 +P+FIVTL G+L +R + +T+G TV P G + + ++ + + + + Sbjct: 141 IPAFIVTLGGLLIWRNVGWYLTDGQTVGPLDQTFMLFGGVEGTVGSALSWGLAIVFSVLA 200 Query: 194 VGWQWRGRMRRQALGLQSPASTAVVGRQALTAIIVLGAIWLLN----------------- 236 V WR R + A A + +LG + +LN Sbjct: 201 VFGLWRARQAKIHHEFPVKPLWAEGALMATSVAAILGFVAILNSYAIPVGRLKREFESRG 260 Query: 237 --------DYRGVPTPVLLLTLLLLGGMFMATRTAFGRRIYAIGGNLEAARLSGINVERT 288 DY G+P VL+L ++++ +A +T GR I+A GGN +AA LSGIN Sbjct: 261 EVMPEGYVDYFGLPISVLMLVVIVVVMTLVARKTRLGRYIFAAGGNPDAAELSGINTRML 320 Query: 289 KLAVFAINGLMVAIAGLILSSRLGAGSPSAGNIAELDAIAACVIGGTSLAGGVGSVAGAV 348 + +F + G++ AI+ ++ +RL + G++ EL IAA VIGGT+LAGG+G++ GAV Sbjct: 321 TVKIFTLMGVLCAISAMVAQARLANHTNDIGSLDELRVIAAAVIGGTALAGGIGTIYGAV 380 Query: 349 MGAFIMASLDNGMSMMDVPTFWQYIVKGAILLLAVWMDSATKRRS 393 +GA IM SL +GM+M+ V +Q IV G +L+LAVW+D ++R+ Sbjct: 381 LGAVIMQSLQSGMAMVGVDAPFQNIVVGGVLVLAVWIDIQYRKRT 425 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: 415 Number of extensions: 20 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: 393 Length of database: 429 Length adjustment: 31 Effective length of query: 362 Effective length of database: 398 Effective search space: 144076 Effective search space used: 144076 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 24 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