Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate HSERO_RS16730 HSERO_RS16730 sugar ABC transporter permease
Query= reanno::psRCH2:GFF851 (296 letters) >FitnessBrowser__HerbieS:HSERO_RS16730 Length = 293 Score = 115 bits (289), Expect = 9e-31 Identities = 88/291 (30%), Positives = 137/291 (47%), Gaps = 27/291 (9%) Query: 12 RLWAT-HAALLAFVAAILFPLLMVISISFREGN---FATGSLF-PENPTLEHWSLALGIP 66 R W T + LL F+ +LFP ++ +F+ N +G+ F PTL H+ L Sbjct: 22 RKWVTIYIPLLIFLFVLLFPFYWMVITAFKPDNELLSQSGNPFWVIAPTLAHFKKLL--- 78 Query: 67 YTHADGSVTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSML 126 TQ P WL N+V ++ VS+ L S +AYA R+RF G + + Sbjct: 79 ------FDTQYP----AWLLNTVIVSVVSTFASLAASVFAAYAIERLRFQGSKQVGLGIF 128 Query: 127 IFQMFPPVLSLVAIYALFDQLGQH-VSWLGVNSHGAVIVASLGGMALHIWTIKGYFESID 185 + + PP + + + A+ +LG W + ++ ++ W + GYF SI Sbjct: 129 LAYLIPPSILFIPLAAIVFKLGLFDTRWALILTYPTFLIPFC------TWLLMGYFRSIP 182 Query: 186 ASLEEAAIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTL 245 LEE A++DGAT W+ I+LP++VP L I AF S E+ A + + T+ Sbjct: 183 YELEECALIDGATRWEILVKIILPLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVKTV 242 Query: 246 SVGAQQYLYPQN-YLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295 VG L + Y WG A A+L LP+ V+ + ++ V G+T G VK Sbjct: 243 PVGIVTELVEGDVYHWGALMAGALLGSLPVAVVYSFFVEYYVSGMT-GAVK 292 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: 260 Number of extensions: 20 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: 293 Length adjustment: 26 Effective length of query: 270 Effective length of database: 267 Effective search space: 72090 Effective search space used: 72090 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: 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