Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >FitnessBrowser__Dino:3606890 Length = 432 Score = 98.2 bits (243), Expect = 2e-25 Identities = 62/205 (30%), Positives = 111/205 (54%), Gaps = 18/205 (8%) Query: 30 LLAIVLGT---LIGLVAGLVLTYGRTW----MRAPFRFYVDLIRGTPVFVL-----VLAC 77 ++ +LGT + L G+ L GR ++ +++ IRG P+ L V+ Sbjct: 226 MINFILGTSGIALSLPLGIALALGRQSNLPIIKGVCVVFIEFIRGVPLITLLFVASVMLA 285 Query: 78 FYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQSLG 137 +++ P + + ++ +TLF +++AE +RG L ALPRGQ EA ++GL ++QS+ Sbjct: 286 YFLPPGTSFDL--VLRVIIMITLFASAYIAEAIRGGLAALPRGQYEAGDSLGLDYWQSMR 343 Query: 138 YVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYL---- 193 ++LPQAL+ +P+ VN + + K +TL+S+I + ++L Q I + Y Sbjct: 344 LIILPQALKISIPSIVNIAIGLFKDTTLVSIISMFDMLGMIQGPILSSTEWFGVYWELLG 403 Query: 194 FAGFLFFIINYAIELLGRHIEKRVA 218 FAG LFF+ Y I + +E+++A Sbjct: 404 FAGVLFFVFCYGISQYSQWLERQLA 428 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: 313 Number of extensions: 19 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: 432 Length adjustment: 27 Effective length of query: 193 Effective length of database: 405 Effective search space: 78165 Effective search space used: 78165 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: 48 (23.1 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