Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate Dsui_2877 Dsui_2877 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >FitnessBrowser__PS:Dsui_2877 Length = 248 Score = 137 bits (346), Expect = 2e-37 Identities = 85/224 (37%), Positives = 129/224 (57%), Gaps = 8/224 (3%) Query: 14 IIQMQGVNKWY----GQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 69 +I++ G++K Y G F VLK ++L + GE + + GPSGSGKST + L L+ G Sbjct: 13 VIEVAGLDKAYDTPMGPFPVLKGVSLAIHAGEFVAIMGPSGSGKSTFMNILGCLDRPSGG 72 Query: 70 RIVVDGVELTN-DLKQIEAIR-REVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAE 127 ++DG ++ D Q +R R +G VFQ FNL P +++ N L P+ + K + Sbjct: 73 DYILDGKHVSALDKDQTALLRNRTIGFVFQGFNLLPRMSLEDNVAL-PLVYCGVDKEERR 131 Query: 128 EIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKE 187 + A L +V + + A P ++SGGQQQRVAIARAL +P+++L DEPT LD +E Sbjct: 132 QRARELLAKVGLGQYAKSLPNRISGGQQQRVAIARALVNRPRLILADEPTGNLDSHTSEE 191 Query: 188 VLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQA 231 ++ L +G+T++ VTHE A+ +V F+D G IV A Sbjct: 192 IMALFEELNREGITIVLVTHEPDIAQHAKRQVRFLD-GRIVHDA 234 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: 161 Number of extensions: 8 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: 254 Length of database: 248 Length adjustment: 24 Effective length of query: 230 Effective length of database: 224 Effective search space: 51520 Effective search space used: 51520 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