Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS05190 HSERO_RS05190 sugar ABC transporter substrate-binding protein
Query= TCDB::P25548 (354 letters) >FitnessBrowser__HerbieS:HSERO_RS05190 Length = 357 Score = 543 bits (1400), Expect = e-159 Identities = 275/355 (77%), Positives = 310/355 (87%), Gaps = 1/355 (0%) Query: 1 MKSIISLMA-ACAIGAASFAAPAFAQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYK 59 +KS++S +A + S +A AQ K VG+AMPTKSSARWI DGNN+VK L+E GY+ Sbjct: 3 IKSVLSGIALGLGVTLMSISAQVSAQSKQLVGVAMPTKSSARWIADGNNMVKVLKEKGYQ 62 Query: 60 TDLQYADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIR 119 TDLQYA+DDIPNQLSQIENM+TKG KVLVIA+IDGTTL+DVL++A ++G+KVIAYDRLIR Sbjct: 63 TDLQYAEDDIPNQLSQIENMLTKGAKVLVIAAIDGTTLTDVLQKAADKGVKVIAYDRLIR 122 Query: 120 NSGDVSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMS 179 S +V YYATFDNFQVGVLQA S+ LGLK+GKGPFNIELFGGS DDNNAFFFY+GAMS Sbjct: 123 GSKNVDYYATFDNFQVGVLQAQSLEKALGLKEGKGPFNIELFGGSSDDNNAFFFYNGAMS 182 Query: 180 VLKPYIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGL 239 VLKPYIDSGKLVV+S QMGMDKV TLRWDPATAQARMDNLLSAYYT+AKV+AVLSPYDGL Sbjct: 183 VLKPYIDSGKLVVRSKQMGMDKVATLRWDPATAQARMDNLLSAYYTNAKVNAVLSPYDGL 242 Query: 240 SIGIISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMV 299 SIGI+SSL+GVGYGT QP P VSGQDAEVPSVKSII GEQYSTIFKDTRELAKVTV MV Sbjct: 243 SIGILSSLRGVGYGTPQQPFPYVSGQDAEVPSVKSIIRGEQYSTIFKDTRELAKVTVGMV 302 Query: 300 NAVMEGKEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQLK 354 +AV+ GK+P++NDTKTY NGVKVVPSYLLKPV V K N+K+VLV GYY E QLK Sbjct: 303 DAVLGGKQPQINDTKTYNNGVKVVPSYLLKPVVVDKSNWKEVLVGSGYYTEAQLK 357 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: 543 Number of extensions: 14 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: 357 Length adjustment: 29 Effective length of query: 325 Effective length of database: 328 Effective search space: 106600 Effective search space used: 106600 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