Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate Dsui_2877 Dsui_2877 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::pseudo1_N1B4:Pf1N1B4_774 (244 letters) >FitnessBrowser__PS:Dsui_2877 Length = 248 Score = 151 bits (381), Expect = 1e-41 Identities = 92/223 (41%), Positives = 131/223 (58%), Gaps = 8/223 (3%) Query: 1 MISIKNVNKWY----GDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKG 56 +I + ++K Y G F VL S + GE + + GPSGSGKST + + L+ G Sbjct: 13 VIEVAGLDKAYDTPMGPFPVLKGVSLAIHAGEFVAIMGPSGSGKSTFMNILGCLDRPSGG 72 Query: 57 DVIVDGTSI-ADPKTNLPKLRSR-VGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEAS 114 D I+DG + A K LR+R +G VFQ F L P +S+ DN+ + V G KEE Sbjct: 73 DYILDGKHVSALDKDQTALLRNRTIGFVFQGFNLLPRMSLEDNVALPLV-YCGVDKEERR 131 Query: 115 KKALQLLERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNE 174 ++A +LL +VGL +AK P ++SGGQQQRVAIARAL P ++L DEPT LD E Sbjct: 132 QRARELLAKVGLGQYAKSLPNRISGGQQQRVAIARALVNRPRLILADEPTGNLDSHTSEE 191 Query: 175 VLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIED 217 ++ + +L EG+T++ VTHE A+ +V F+D G+I+ D Sbjct: 192 IMALFEELNREGITIVLVTHEPDIAQHAKRQVRFLD-GRIVHD 233 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: 152 Number of extensions: 6 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: 244 Length of database: 248 Length adjustment: 24 Effective length of query: 220 Effective length of database: 224 Effective search space: 49280 Effective search space used: 49280 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