Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 17627 b3566 D-xylose transporter subunit (NCBI)
Query= TCDB::P25548 (354 letters) >FitnessBrowser__Keio:17627 Length = 330 Score = 205 bits (521), Expect = 2e-57 Identities = 128/324 (39%), Positives = 184/324 (56%), Gaps = 21/324 (6%) Query: 30 VGIAMPTKSSARWIDDGNNIVKQLQEAGYKTDLQYADDDIPNQLSQIENMVTKGVKVLVI 89 +G+A+ RW D + VK+ + G K +Q A+ + Q+SQIENM+ +GV VLVI Sbjct: 28 IGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVI 87 Query: 90 ASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNSGDVSYYATFDNFQVGVLQATSITDKLGL 149 +G LS+V+K+A ++GIKV+AYDR+I N D+ +Y +FDN +VG LQA ++ D + Sbjct: 88 IPYNGQVLSNVVKEAKQEGIKVLAYDRMI-NDADIDFYISFDNEKVGELQAKALVDIV-- 144 Query: 150 KDGKGPFNIELFGGSPDDNNAFFFYDGAMSVLKPYIDSGKLVVKSGQMGMDKVGTLRWDP 209 N L GGSP DNNA F G M VLKPY+DSGK+ V G +D W P Sbjct: 145 ----PQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKV-VGDQWVD-----GWLP 194 Query: 210 ATAQARMDNLLSAYYTDAKVDAVLSPYDGLSIGIISSLKGVGYGTKDQPLPVVSGQDAEV 269 A M+N L+A + K+DAV++ D + G I +L G K +SGQDA++ Sbjct: 195 ENALKIMENALTA--NNNKIDAVVASNDATAGGAIQALSAQGLSGK----VAISGQDADL 248 Query: 270 PSVKSIIAGEQYSTIFKDTRELAKVTVNMVNAVMEGKEPEVNDTKTYENGVKVVPSYLLK 329 +K I AG Q T++K LA + + G+EP+ + T NG+K VPS LL Sbjct: 249 AGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKAD--TTLNNGLKDVPSRLLT 306 Query: 330 PVAVTKENYKQVLVDGGYYKEDQL 353 P+ V K N K ++ G++KE +L Sbjct: 307 PIDVNKNNIKDTVIKDGFHKESEL 330 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: 326 Number of extensions: 17 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: 330 Length adjustment: 29 Effective length of query: 325 Effective length of database: 301 Effective search space: 97825 Effective search space used: 97825 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 17 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