Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q52815 (257 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 132 bits (331), Expect = 8e-36 Identities = 83/224 (37%), Positives = 132/224 (58%), Gaps = 13/224 (5%) Query: 18 VEIVNMNKWYGD----FHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGK 73 + I N++K Y VL DINL V G+ I I GPSGSGK+T++ L+ G Sbjct: 4 LSIENVSKIYQSGSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSGS 63 Query: 74 IVVDGTELT--NDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEE 131 + ++G L ++ ++ +E+G +FQ+F L P LT LEN + P+ ++K +K A++ Sbjct: 64 VALNGHRLEGLSEDQRAAVRSQEIGFIFQNFQLLPTLTALEN-VMVPLELKK--RKDAKQ 120 Query: 132 VAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEV 191 A L++V + ++ YP QLSGG+QQRV+IAR+ PKI+ DEPT LD E E+ Sbjct: 121 KATELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTE-TGEL 179 Query: 192 LDTMVGLAEE--GMTMLCVTHEMGFARQVANRVIFMDQGQIVEQ 233 ++T++ + G T++ VTH+ A + NR+I + G+I E+ Sbjct: 180 IETLIFDLNKALGTTLILVTHDTDLAAK-TNRIIHIKGGKIQEE 222 Lambda K H 0.321 0.135 0.394 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: 134 Number of extensions: 9 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: 257 Length of database: 225 Length adjustment: 23 Effective length of query: 234 Effective length of database: 202 Effective search space: 47268 Effective search space used: 47268 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