Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate 8502446 DvMF_3152 extracellular solute-binding protein family 3 (RefSeq)
Query= CharProtDB::CH_002441 (302 letters) >FitnessBrowser__Miya:8502446 Length = 271 Score = 148 bits (374), Expect = 1e-40 Identities = 92/262 (35%), Positives = 135/262 (51%), Gaps = 16/262 (6%) Query: 10 ILALALSAGLAQADDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQK-VVGYSQD 68 +LA+AL L A ++ I G +V G ++S+VPF Y D Q K +VG+ D Sbjct: 6 LLAVALCVVLT----GTMAHAGKIEDIKARGALVCGVKDSTVPFGYIDEQSKQIVGFDID 61 Query: 69 YSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSD 128 A+ + + KL +L +TS RIP+L G+ D + T+ ER FS Sbjct: 62 ICKAVADKLGVKL-------ELKTVTSATRIPMLTQGSVDMVAATMTHKFERDDVIDFSI 114 Query: 129 TIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHG 188 T F+ G +LL KKGG +K A+LK K V G+TSE + E ++S ++ Sbjct: 115 TYFMDGQKLLVKKGGGVKSAADLKGKKVATAKGSTSEKNIKAAQPEAT----VVSFDEYP 170 Query: 189 DSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKL 248 +F L+ G+A A D +L G R +PD WEIVG S E YG L ++D +F+ L Sbjct: 171 QAFLALKQGKAEAVTTDSTILLGLRNSDPEPDKWEIVGDYISPEPYGLGLAENDSKFRDL 230 Query: 249 MDDTIAQVQTSGEAEKWFDKWF 270 ++ T+ + SGE K +DKWF Sbjct: 231 VNRTLVDLWNSGEYVKLYDKWF 252 Lambda K H 0.314 0.130 0.366 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: 173 Number of extensions: 9 Number of successful extensions: 3 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: 302 Length of database: 271 Length adjustment: 26 Effective length of query: 276 Effective length of database: 245 Effective search space: 67620 Effective search space used: 67620 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 (22.0 bits) S2: 47 (22.7 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