Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate BPHYT_RS31425 BPHYT_RS31425 arginine ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__BFirm:BPHYT_RS31425 Length = 233 Score = 257 bits (656), Expect = 2e-73 Identities = 135/241 (56%), Positives = 167/241 (69%), Gaps = 8/241 (3%) Query: 14 IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73 +I++ V+KWYG VL D ++ +GE +V+CGPSGSGKST I+ +N LE Q G+IVV Sbjct: 1 MIELNNVSKWYGGNRVLNDCTASIARGEVVVICGPSGSGKSTLIKSVNGLEAVQSGQIVV 60 Query: 74 DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133 DG+++T + +R VGMVFQHF LFPHL++ +N LA M V + KA E A Sbjct: 61 DGIDVTAKRADLSRLRARVGMVFQHFELFPHLSVQRNLMLAQMNVLGRARDKAAERARLL 120 Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193 L RV + HKYP QLSGGQQQRVAIARAL M P MLFDEPTSALDPEMV EVLD Sbjct: 121 LLRVGLSGHEHKYPAQLSGGQQQRVAIARALSMDPVAMLFDEPTSALDPEMVNEVLDV-- 178 Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQIL 253 MTMLCVTHEMGFA+ VA+RV+FMD+G IVE FF+ P+++R + FLS+IL Sbjct: 179 ------MTMLCVTHEMGFAKRVADRVLFMDRGVIVEDDTREAFFERPRSERARDFLSRIL 232 Query: 254 H 254 H Sbjct: 233 H 233 Lambda K H 0.322 0.137 0.407 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: 182 Number of extensions: 2 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: 254 Length of database: 233 Length adjustment: 23 Effective length of query: 231 Effective length of database: 210 Effective search space: 48510 Effective search space used: 48510 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 46 (22.3 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