Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate HSERO_RS19240 HSERO_RS19240 arginine ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__HerbieS:HSERO_RS19240 Length = 242 Score = 275 bits (703), Expect = 6e-79 Identities = 134/240 (55%), Positives = 178/240 (74%) Query: 14 IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73 +I++ V+KWYG F VL D + +VK+G+ +V+CGPSGSGKST I+ +N LE Q+G I V Sbjct: 1 MIELNNVSKWYGSFQVLTDCSTSVKKGDVVVVCGPSGSGKSTLIKTVNGLEPFQKGTITV 60 Query: 74 DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133 DGV + + + +R +GMVFQ+F LFPHL+I +N T+ + V K +A E + Y Sbjct: 61 DGVSVGDPKTNLSKLRARIGMVFQNFELFPHLSIRENLTIGQIKVLGRSKEEATEKGLKY 120 Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193 L+RV + K+PGQLSGGQQQRVAIARAL M P MLFDEPTSALDPEM+ EVLD M+ Sbjct: 121 LDRVGLLAHKDKFPGQLSGGQQQRVAIARALSMDPIAMLFDEPTSALDPEMINEVLDVMV 180 Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQIL 253 GLA++GMTM+ VTHEMGFAR VANRV+FMDKG +VE A ++FF P+++R + FL++I+ Sbjct: 181 GLAQEGMTMMVVTHEMGFARKVANRVVFMDKGVVVEDCAKDEFFAQPRSERARDFLAKII 240 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: 185 Number of extensions: 4 Number of successful extensions: 1 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: 242 Length adjustment: 24 Effective length of query: 230 Effective length of database: 218 Effective search space: 50140 Effective search space used: 50140 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