Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate 207829 DVU2342 amino acid ABC transporter, periplasmic amino acid-binding protein
Query= CharProtDB::CH_002441 (302 letters) >MicrobesOnline__882:207829 Length = 270 Score = 146 bits (368), Expect = 6e-40 Identities = 93/262 (35%), Positives = 141/262 (53%), Gaps = 14/262 (5%) Query: 10 ILALALSAGLAQADDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQK-VVGYSQD 68 +L LAL+ GL AA A LD+I + G +V G ++S VPF + D K +VG+ D Sbjct: 4 LLLLALTLGLVLT--AAVAHAGKLDEIKQRGTLVCGVKDSVVPFGFIDETSKQLVGFDVD 61 Query: 69 YSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSD 128 I + KL +VK + TS RIP+L G+ D + T+ ER FS Sbjct: 62 ICQFIADRAGVKL-----EVKTV--TSATRIPMLTQGSVDLVAATMTHKFERDDVIDFSI 114 Query: 129 TIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHG 188 T F G RLL KKGG IK A+LK K V G+TSE K + + + ++S ++ Sbjct: 115 TYFDAGQRLLVKKGGGIKSAADLKGKKVATVKGSTSE----KNMKAAQPDCVVVSFDEYP 170 Query: 189 DSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKL 248 +F L+ G+A A D+ +L G + +PD W+IVG + E YG L ++D +F+ Sbjct: 171 QAFLALKQGKAEAVTTDEPILVGLKNSDPEPDKWDIVGDFIASEPYGLGLVENDSKFRDF 230 Query: 249 MDDTIAQVQTSGEAEKWFDKWF 270 ++ ++A++ T+G +K +DKWF Sbjct: 231 VNKSLAEMWTTGAYQKSYDKWF 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: 189 Number of extensions: 11 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: 270 Length adjustment: 26 Effective length of query: 276 Effective length of database: 244 Effective search space: 67344 Effective search space used: 67344 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