Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_008509253.1 BIBO1_RS15350 D-xylose ABC transporter substrate-binding protein
Query= TCDB::P25548 (354 letters) >NCBI__GCF_000182725.1:WP_008509253.1 Length = 339 Score = 174 bits (442), Expect = 2e-48 Identities = 113/342 (33%), Positives = 175/342 (51%), Gaps = 21/342 (6%) Query: 9 AACAIGAASFAAPAFAQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYKTDLQYADDD 68 AA IGA + + + +G ++ RW D + + ++ G K ++Q AD + Sbjct: 14 AALGIGAMGATPASASPEHPVIGFSIDDLRVERWARDRDYFIAAAEKLGAKVNVQSADGN 73 Query: 69 IPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNSGDVSYYA 128 Q+ Q+EN++++GV +VI ++ V+ A GIKV++YDRLI N+ D+ Y Sbjct: 74 EEKQVKQVENLISQGVDAIVIVPMNSKVFDAVVADAKASGIKVLSYDRLILNA-DIDAYI 132 Query: 129 TFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVLKPYIDSG 188 +FDN +VG +QA ++ K N L GGSP DNNA G LK +DSG Sbjct: 133 SFDNERVGFMQAQAVL------KAKPEGNYYLLGGSPTDNNAKLLRAGQEKALKEAVDSG 186 Query: 189 KLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSIGIISSLK 248 K+ + Q W P A + M+N L+A T K+DAV++ DG + G I +L Sbjct: 187 KVKIVGSQW------VKEWSPTEALSIMENALTA--TQNKIDAVVASNDGTAGGAIQALA 238 Query: 249 GVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNAVMEGKEP 308 G K VSGQD+++ +VK ++ G Q T++K + +A+ + ++ ++P Sbjct: 239 AQGLAGK----TAVSGQDSDLAAVKRLVDGTQTVTVYKPLKLIAEEAAKLTVQLVRDEKP 294 Query: 309 EVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKE 350 E N NG K V + LL P AVTK+N + DG Y KE Sbjct: 295 EFNG--KINNGSKDVDTLLLTPTAVTKDNIDIYIKDGFYTKE 334 Lambda K H 0.314 0.133 0.372 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: 329 Number of extensions: 17 Number of successful extensions: 6 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: 354 Length of database: 339 Length adjustment: 29 Effective length of query: 325 Effective length of database: 310 Effective search space: 100750 Effective search space used: 100750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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