Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_042119961.1 RHE_RS26930 carbohydrate ABC transporter permease
Query= reanno::psRCH2:GFF851 (296 letters) >NCBI__GCF_000092045.1:WP_042119961.1 Length = 271 Score = 115 bits (287), Expect = 1e-30 Identities = 71/213 (33%), Positives = 118/213 (55%), Gaps = 9/213 (4%) Query: 83 LWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPPVLSLVAIYA 142 L+LWNS+ + +++L L++ + Y AR++ A I+ +I +M P + L+ ++ Sbjct: 68 LYLWNSLLVTGAATLLALVIGVPAGYGIARLKAEKSAMII---MIARMTPGLSFLIPLFL 124 Query: 143 LFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEAAIVDGATTWQA 202 LF Q ++ LG +I+ + + + +W + GYFE+ LEEAA +DGAT WQ Sbjct: 125 LF----QWLNLLGTLMP-QIIIHLVVTVPIVVWIMIGYFETTPMELEEAASIDGATPWQV 179 Query: 203 FFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQYLYPQNYLWGD 262 F + LP++ P + V FIL+ I S + + ++L + TL V L + WG Sbjct: 180 FRLVALPIARPGIVVAFILSVIFSWNNF-VFGIVLASRETRTLPVAVYNMLSFEQVSWGP 238 Query: 263 FAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295 AAAA++ LP+ + ++ Q+ IV GLTAG VK Sbjct: 239 LAAAALIVTLPVLILTVFAQRQIVAGLTAGAVK 271 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: 243 Number of extensions: 15 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: 271 Length adjustment: 26 Effective length of query: 270 Effective length of database: 245 Effective search space: 66150 Effective search space used: 66150 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 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