Align ABC transporter for D-glucosamine, periplasmic substrate-binding component (characterized)
to candidate AZOBR_RS15685 AZOBR_RS15685 ABC transporter substrate-binding protein
Query= reanno::pseudo3_N2E3:AO353_21710 (282 letters) >FitnessBrowser__azobra:AZOBR_RS15685 Length = 266 Score = 104 bits (259), Expect = 2e-27 Identities = 82/269 (30%), Positives = 125/269 (46%), Gaps = 14/269 (5%) Query: 3 RRLSLFTACVFLFAATASAVGIAQAADSRLDNVLKRGHLIVGTGSTNAPWHFQGADGKLQ 62 RRL++ A V + AA A AV AA +D + +G L +G P+ ADGK Sbjct: 7 RRLAV--AGVMMAAAVALAV---PAAAQTVDEIKSKGKLTIGMLVDFPPFGITTADGKPD 61 Query: 63 GFDIDIGRMVAKGLFNDPSKVEFVVQSSDARIPNLLTDKVDMSCQFITVTASRAQQVAFT 122 G+D D+ +++ K + VE V + RIP LLT+KVD+ + +T +RA+QV F+ Sbjct: 62 GYDADVAKLLGKHM---GVPVEIVPVTGPNRIPYLLTNKVDLLVASLGITPARAEQVQFS 118 Query: 123 LPYYREGVGLLLPANSKYKEIEDLKAAGDSVTVAVLQNVYAEELVHQALPKAKVDQYDSV 182 PY +GL+ PAN+K KE +L V A Q+ L A A++ ++D Sbjct: 119 EPYAAIEIGLVAPANTKIKEAAELSGKRIGVARASTQD---NALTAVAPKDARIMRFDDD 175 Query: 183 DLMYQAVNSGRADTAATDQSSVKYLMVQNPGRYRSPTYAWSPQTYACAVKRGDQDWLNFV 242 QA+ SG+ D K + P + + Q A+++G L +V Sbjct: 176 ASAVQAMLSGQVDALGLSNVVTKEIKKLAPQANYEMKFVLNRQVQGIAMRKGQDALLKWV 235 Query: 243 NTVLHEAMTGVEFPTYAASFKQWFGVDLP 271 N + A + E K+W G DLP Sbjct: 236 NEFIETAKSNGELNEV---HKKWLGTDLP 261 Lambda K H 0.319 0.133 0.394 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: 135 Number of extensions: 7 Number of successful extensions: 2 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: 266 Length adjustment: 25 Effective length of query: 257 Effective length of database: 241 Effective search space: 61937 Effective search space used: 61937 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