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_017618222.1 CDO52_RS18115 sugar ABC transporter substrate-binding protein
Query= TCDB::P25548 (354 letters) >NCBI__GCF_002263495.1:WP_017618222.1 Length = 369 Score = 167 bits (423), Expect = 4e-46 Identities = 114/355 (32%), Positives = 180/355 (50%), Gaps = 26/355 (7%) Query: 7 LMAACAI--GAASFAAPAFAQDKGSVGIAMPTKSSARWID-DGNNIVKQLQEAGYKTDLQ 63 L A C G A +D VG+ +P +AR+ D + L E K +L Sbjct: 15 LAAGCGTTTGGDGEGGTASVEDGFKVGLLLPESKTARYEKFDKPYFEEALTELCKKCELS 74 Query: 64 Y--ADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNS 121 Y AD + Q +Q E M+T+GV VLV+ ++D + + ++K A QG+ V+AYDRL Sbjct: 75 YQNADQETAKQQAQAEAMLTEGVDVLVLDAVDAESAAKIVKDAKGQGVPVVAYDRLA--Y 132 Query: 122 GDVSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVL 181 G V YY +FDN +VG +Q ++ + L ++ G I + GSP D NA F GA S+L Sbjct: 133 GGVDYYVSFDNRKVGEVQGKALIEALEKEETAGKGEIVMINGSPTDPNAADFKAGAHSIL 192 Query: 182 KPYIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSI 241 + G + T W P AQ M+ +++ D + V + DG++ Sbjct: 193 DNEAEIGA-----------EYDTPDWSPDRAQTEMEQAITSIGAD-DIVGVYAANDGMAQ 240 Query: 242 GIISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNA 301 G++++LK G LP ++GQDAE+ ++ IIAGEQY T++K R A+ M A Sbjct: 241 GVVAALKSAGV----DELPPITGQDAEIHGIQRIIAGEQYMTVYKAIRPEAETAAKMAVA 296 Query: 302 VMEGKE---PEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQL 353 G+E E+ T+ + V + LL P+ VT+EN ++ +V G+Y +++ Sbjct: 297 AATGEEYEGGEIGLTEVESGDGEKVQAVLLDPIPVTEENVEETVVSDGFYTIEEI 351 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: 351 Number of extensions: 26 Number of successful extensions: 5 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: 369 Length adjustment: 29 Effective length of query: 325 Effective length of database: 340 Effective search space: 110500 Effective search space used: 110500 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