Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Ac3H11_610 L-arabinose-binding periplasmic protein precursor AraF (TC 3.A.1.2.2)
Query= TCDB::P25548 (354 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_610 Length = 356 Score = 541 bits (1395), Expect = e-159 Identities = 272/353 (77%), Positives = 306/353 (86%), Gaps = 3/353 (0%) Query: 2 KSIISLMAACAIGAASFAAPAFAQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYKTD 61 K++++ MA AIGA S A+ AQDKG++GI+MPTKSSARWI DG+N+VK L+E GYKTD Sbjct: 7 KAVLASMALTAIGATSVAS---AQDKGAIGISMPTKSSARWIADGDNMVKVLKERGYKTD 63 Query: 62 LQYADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNS 121 LQYADDDIPNQL+QIENM+TKG KVLVIASIDGTTLS L+ A ++G+KVIAYDRLI+ S Sbjct: 64 LQYADDDIPNQLAQIENMITKGAKVLVIASIDGTTLSKALQNAADKGVKVIAYDRLIKGS 123 Query: 122 GDVSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVL 181 +V YYATFDNFQVGVLQATSI DKLGLK GKGPFNIELFGGSPDDNNAFFFYDGAMSVL Sbjct: 124 KNVDYYATFDNFQVGVLQATSIVDKLGLKQGKGPFNIELFGGSPDDNNAFFFYDGAMSVL 183 Query: 182 KPYIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSI 241 +PYIDSGKLVV+S Q GM+KVGTLRWD + AQARMDNLLSAYY KV AVLSPYDG+SI Sbjct: 184 QPYIDSGKLVVRSKQTGMNKVGTLRWDGSVAQARMDNLLSAYYGKDKVHAVLSPYDGISI 243 Query: 242 GIISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNA 301 GI+SSLKGVGY T QP PVVSGQDAEVPS+KSI+ GEQ ST+FKDTRELAKV NMV+A Sbjct: 244 GILSSLKGVGYCTAQQPCPVVSGQDAEVPSIKSILKGEQSSTVFKDTRELAKVAANMVDA 303 Query: 302 VMEGKEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQLK 354 V+ GK+PE+NDTKTY NGVKVVPSYLLKPVAV N+ VLV GYYKE Q+K Sbjct: 304 VLTGKQPEINDTKTYNNGVKVVPSYLLKPVAVDSSNWNAVLVGSGYYKESQIK 356 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: 549 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: 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 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