Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate AZOBR_RS31240 AZOBR_RS31240 sugar ABC transporter substrate-binding protein
Query= TCDB::P25548 (354 letters) >FitnessBrowser__azobra:AZOBR_RS31240 Length = 358 Score = 522 bits (1344), Expect = e-153 Identities = 262/355 (73%), Positives = 301/355 (84%), Gaps = 3/355 (0%) Query: 3 SIISLMAACAIGAASF---AAPAFAQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYK 59 S + +A A+G + AAP AQDK +VGIAMPTKSSARWIDDGNN+VKQ Q GYK Sbjct: 4 SFTTTLAGMAVGVLALTVAAAPTLAQDKPTVGIAMPTKSSARWIDDGNNMVKQFQAKGYK 63 Query: 60 TDLQYADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIR 119 TDLQYA+DDIPNQL+QIE MV K KVLVIA+IDGTTL+DVL+QA ++G+KVIAYDRLIR Sbjct: 64 TDLQYAEDDIPNQLAQIETMVAKNSKVLVIAAIDGTTLTDVLQQAKDRGVKVIAYDRLIR 123 Query: 120 NSGDVSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMS 179 S +V YYATFDNFQVGVLQ + I D LGLKDGKGPFNIELFGGSPDDNNA+FFY+GAMS Sbjct: 124 GSENVDYYATFDNFQVGVLQGSYIVDALGLKDGKGPFNIELFGGSPDDNNAYFFYNGAMS 183 Query: 180 VLKPYIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGL 239 VL+P+IDSGKL V SGQ+GMDKV TLRWD ATAQARMDNLLSA+Y + +VDAVLSPYDG+ Sbjct: 184 VLQPHIDSGKLKVGSGQVGMDKVSTLRWDGATAQARMDNLLSAFYGNRRVDAVLSPYDGI 243 Query: 240 SIGIISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMV 299 SIGIISSLKGVGYG+ QP+PVV+GQDAEVPS+KSI+AGEQ +T+FKDTRELA+VTV MV Sbjct: 244 SIGIISSLKGVGYGSPSQPMPVVTGQDAEVPSIKSILAGEQRATVFKDTRELARVTVEMV 303 Query: 300 NAVMEGKEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQLK 354 +AV+ G P VNDTKTY+NG KVVP+YLLKPV+V N+K LV GYY E Q K Sbjct: 304 DAVLGGGTPPVNDTKTYDNGKKVVPAYLLKPVSVDASNWKSTLVGSGYYTEAQFK 358 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: 535 Number of extensions: 16 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: 354 Length of database: 358 Length adjustment: 29 Effective length of query: 325 Effective length of database: 329 Effective search space: 106925 Effective search space used: 106925 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 Apr 09 2024. 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