Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate WP_068168721.1 HTA01S_RS07505 ABC transporter permease subunit
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >NCBI__GCF_001592305.1:WP_068168721.1 Length = 226 Score = 122 bits (305), Expect = 7e-33 Identities = 72/216 (33%), Positives = 118/216 (54%), Gaps = 7/216 (3%) Query: 8 LHELWVARDTLWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRG 67 + +LW+ L G +VQ +L ++V+G +GLV GRT +R R L+RG Sbjct: 1 MDDLWLYAGQLLQGAWVTVQLALSSLVVGLALGLVLAAGSLSGRTLLRRAVRLCTGLLRG 60 Query: 68 TPVFVLVLACFYMAPAL-------GWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRG 120 P F++VL C++ L +I F AGV L++ ++ +E+ RG+ A+PRG Sbjct: 61 IPEFLIVLVCYFGLSNLINNHLDGAVEISPFAAGVFALSIVFAAYASEVFRGSFAAIPRG 120 Query: 121 QMEASQAIGLTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQ 180 Q+EA+QA GLT Q+ V LPQA R LP+ N ++K ++L+SV+G+ +LL + Sbjct: 121 QIEAAQAFGLTATQTFFAVRLPQAWRIALPSLGNLWQSLLKDTSLVSVVGLEDLLKKSNM 180 Query: 181 IIARTFMTLEFYLFAGFLFFIINYAIELLGRHIEKR 216 T F+L A ++F+ +A + + +E+R Sbjct: 181 AAQATHQPFLFFLAAATVYFVFLHASQPVFAWLERR 216 Lambda K H 0.330 0.142 0.443 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: 166 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: 220 Length of database: 226 Length adjustment: 22 Effective length of query: 198 Effective length of database: 204 Effective search space: 40392 Effective search space used: 40392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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