Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate AO356_28580 AO356_28580 sugar ABC transporter permease
Query= reanno::psRCH2:GFF851 (296 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28580 Length = 280 Score = 109 bits (273), Expect = 6e-29 Identities = 70/213 (32%), Positives = 107/213 (50%), Gaps = 9/213 (4%) Query: 87 NSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPPVLSLVAIYALFDQ 146 NS+ +A L L LS T+AYA R++F G+ P+L +L MFP V L ++ + Sbjct: 74 NSLVVALCVVALALFLSLTAAYALGRVKFRGRGPVLMMVLGVSMFPQVAVLSGLFEVIRA 133 Query: 147 LGQH-VSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEAAIVDGATTWQAFFH 205 LG + SW + S+ ++ + +W + + + LEEAAI+DGA+ W Sbjct: 134 LGLYNTSWALILSY------TIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTR 187 Query: 206 ILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQYL--YPQNYLWGDF 263 +LLP+ P L +LAFI + E+ A + + T+ V P WG Sbjct: 188 VLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIALISGGSPHELPWGLL 247 Query: 264 AAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 296 AA+VL +P+ + L Q+ IV GLTAG +KG Sbjct: 248 MAASVLVTVPLVILVLIFQRRIVSGLTAGALKG 280 Lambda K H 0.327 0.139 0.433 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: 241 Number of extensions: 12 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: 296 Length of database: 280 Length adjustment: 26 Effective length of query: 270 Effective length of database: 254 Effective search space: 68580 Effective search space used: 68580 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 (21.7 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