Align ABC transporter for D-Glucosamine, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_05870 H281DRAFT_05870 amino acid ABC transporter substrate-binding protein, PAAT family
Query= reanno::pseudo5_N2C3_1:AO356_00480 (282 letters) >FitnessBrowser__Burk376:H281DRAFT_05870 Length = 283 Score = 110 bits (274), Expect = 5e-29 Identities = 88/254 (34%), Positives = 124/254 (48%), Gaps = 15/254 (5%) Query: 19 TAAMGVAQAAD-SKLDSVLQRGKLIVGTGSTNAPWHFQGADGKLQGFDIDIARMVAKGLF 77 T G A AA S L +VLQRG L VG T AP+ F DG G+D+D+A+ +AK + Sbjct: 33 TPEQGPAAAAPASTLQAVLQRGTLRVGDCLTFAPFGFYDKDGNADGYDVDLAKELAKQM- 91 Query: 78 NDPEKVEFVVQSSDARIPNLLTDKVDMSCQFITVTASRAQQVAFTLPYYREGVGLLLPAN 137 K+E V +S RIPNL T KVD+ T RA+ V FT PY +L+ + Sbjct: 92 --GVKLEVVNTTSANRIPNLQTAKVDVVFCNFTRNLERAKVVEFTSPYVVASEAMLVKKS 149 Query: 138 SKYKEIEDLKAAGDDVTVAVLQ-NVYAEELVHQALPKAKVDQYDSVDLMYQAVNSGRADA 196 S + +D+ T+A ++ + +E+ +P K+ +YDS AV G+ADA Sbjct: 150 SGIQSAKDMNGR----TIATVKGSTNGDEVRSMGIP-VKIQEYDSSQAAILAVKQGQADA 204 Query: 197 AATDQSSVKYLMVQNPGRYRSPAYAWSPQTY-ACAVKRGDQDWLNFVNTTLHEAMTGVEF 255 D + + Y +P A P Y A VK GDQ WLN++N L Sbjct: 205 MIEDNNFLAYQAKLDP-ELTVTNEALVPLEYNAFGVKAGDQAWLNYLNLFLFNINAS--- 260 Query: 256 PTYAASFKQWFGVE 269 A +K+WFGV+ Sbjct: 261 KLNAQLYKKWFGVD 274 Lambda K H 0.319 0.132 0.390 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: 184 Number of extensions: 10 Number of successful extensions: 4 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: 282 Length of database: 283 Length adjustment: 26 Effective length of query: 256 Effective length of database: 257 Effective search space: 65792 Effective search space used: 65792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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