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_011782434.1 MVAN_RS26615 sugar ABC transporter substrate-binding protein
Query= TCDB::P25548 (354 letters) >NCBI__GCF_000015305.1:WP_011782434.1 Length = 356 Score = 159 bits (402), Expect = 1e-43 Identities = 113/346 (32%), Positives = 168/346 (48%), Gaps = 25/346 (7%) Query: 8 MAACAIGAASFAAPAFAQDKGSVGIAMP-TKSSARW-IDDGNNIVKQLQEAGYKTDLQYA 65 + AC + S + A + G VG+ +P TKSS RW D + Q AG +Q A Sbjct: 19 LTACGSNSDSGSTEARS---GKVGVILPDTKSSVRWETKDRPALAAAFQNAGVDYTIQNA 75 Query: 66 DDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNSGDVS 125 + + + M+ GV VL I ++D + + + ++A QG+K I YDRL G Sbjct: 76 EGSADTMATIADGMIADGVTVLAIVNLDSDSGASIQQKAASQGVKTIDYDRLTLG-GSAD 134 Query: 126 YYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVLKPYI 185 Y +FDN VG LQ + D LG + P N+ GSP DNNA F GA SV + Sbjct: 135 VYVSFDNNVVGELQGQGLVDCLGGR----PANVVFLNGSPTDNNATLFSSGAHSV----V 186 Query: 186 DSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSIGIIS 245 D+ + G+ + WD A + L +A D +VD V + DGL+ +IS Sbjct: 187 DATPSITIVGEQAVPD-----WDNDKAVTIFEQLYTA--ADGRVDGVYAANDGLAGSVIS 239 Query: 246 SLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNAVMEG 305 L+ K V+GQDA V +++I+AG Q T++K E A + A+ G Sbjct: 240 ILEK----NKRAGQVPVTGQDATVEGLQNILAGTQCMTVYKSATEEANALAEVAIALANG 295 Query: 306 KEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKED 351 ++P+ T + G + VPS LL P ++TK+N V DGG K++ Sbjct: 296 EQPQTTSTSRDDTGGRDVPSVLLTPKSITKDNINVVFDDGGQSKDE 341 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: 355 Number of extensions: 26 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: 354 Length of database: 356 Length adjustment: 29 Effective length of query: 325 Effective length of database: 327 Effective search space: 106275 Effective search space used: 106275 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