Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate Pf6N2E2_672 ABC-type polar amino acid transport system, ATPase component
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_672 Length = 240 Score = 242 bits (618), Expect = 4e-69 Identities = 122/226 (53%), Positives = 163/226 (72%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIV 60 MI I+NV+K +GD +V+ S V KGEV+ + G SGSGKSTL+ C+N LEP QKG++ V Sbjct: 1 MIEIENVHKSFGDLEVVKGVSLTVDKGEVVSIIGGSGSGKSTLLMCINGLEPIQKGNIRV 60 Query: 61 DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQL 120 DG + D T+L +LR ++G+VFQ + FPHL++++N+ +A KVLG+SK++A A+Q Sbjct: 61 DGIEVHDRATDLNRLRQKIGIVFQQWNAFPHLTVLENVMLAPRKVLGKSKQDAEALAVQQ 120 Query: 121 LERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180 LE VGL K PG+LSGGQQQR+AIARALAM P MLFDE TSALDP++V EVLD M Sbjct: 121 LEHVGLGDKLKAFPGKLSGGQQQRMAIARALAMSPDYMLFDEATSALDPQLVGEVLDTMR 180 Query: 181 QLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGD 226 LA +GMTM+ VTHE+ FAR V+DRV F G++ E ++ G+ Sbjct: 181 MLAEDGMTMVLVTHEIRFARDVSDRVAFFCNGRVHEIGPPDQVIGN 226 Lambda K H 0.321 0.135 0.390 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: 179 Number of extensions: 3 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: 244 Length of database: 240 Length adjustment: 23 Effective length of query: 221 Effective length of database: 217 Effective search space: 47957 Effective search space used: 47957 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