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_011426401.1 RHE_RS16200 sugar ABC transporter substrate-binding protein
Query= TCDB::P25548 (354 letters) >NCBI__GCF_000092045.1:WP_011426401.1 Length = 354 Score = 615 bits (1585), Expect = 0.0 Identities = 312/354 (88%), Positives = 328/354 (92%) Query: 1 MKSIISLMAACAIGAASFAAPAFAQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYKT 60 MKSIISLMAA A G ASF APA A DKG+VGIAMPTK+SARWIDDGNNIVKQLQ AGY T Sbjct: 1 MKSIISLMAAAAFGVASFVAPAMAADKGTVGIAMPTKASARWIDDGNNIVKQLQAAGYGT 60 Query: 61 DLQYADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRN 120 DLQY DDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVL++A + GIKVIAYDRLIR+ Sbjct: 61 DLQYGDDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLQKAHDAGIKVIAYDRLIRD 120 Query: 121 SGDVSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSV 180 S +V YYATFDNFQVGVLQA SI D LGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSV Sbjct: 121 SANVDYYATFDNFQVGVLQANSIVDGLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSV 180 Query: 181 LKPYIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLS 240 L+PYIDSGKLVVKSGQ GMDKVGTLRWDPATAQARMDNLLSA YTDAKVDAVLSPYDGLS Sbjct: 181 LQPYIDSGKLVVKSGQTGMDKVGTLRWDPATAQARMDNLLSANYTDAKVDAVLSPYDGLS 240 Query: 241 IGIISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVN 300 IGIISSLKGVGYGT QPLP+V+GQDAE+PSVKSIIAGEQ+STIFKDTRELAKVTV MV+ Sbjct: 241 IGIISSLKGVGYGTAAQPLPIVTGQDAEIPSVKSIIAGEQHSTIFKDTRELAKVTVAMVD 300 Query: 301 AVMEGKEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQLK 354 AVM GKEPEVNDTKTY+NGVKVVPSYLLKPVAV K NYKQ+LVD GYY ED+LK Sbjct: 301 AVMSGKEPEVNDTKTYDNGVKVVPSYLLKPVAVDKTNYKQILVDSGYYTEDKLK 354 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: 612 Number of extensions: 20 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: 354 Length adjustment: 29 Effective length of query: 325 Effective length of database: 325 Effective search space: 105625 Effective search space used: 105625 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