Align AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::O30506 (254 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 128 bits (321), Expect = 1e-34 Identities = 85/232 (36%), Positives = 139/232 (59%), Gaps = 20/232 (8%) Query: 4 LEVQDLHKRYGSHE----VLKGVSLAAKAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 L ++++ K Y S VL+ ++L+ KAGD I+I+G SGSGK+T L L+ +G Sbjct: 4 LSIENVSKIYQSGSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSGS 63 Query: 60 ILLNGEELKLVPGRDGALKAADSRQLQRMRSRLSMVFQHFNLWSHMSALENVIEAPVHVL 119 + LNG L+ + + D R R + + +FQ+F L ++ALENV+ P+ + Sbjct: 64 VALNGHRLEGL--------SEDQRAAVRSQE-IGFIFQNFQLLPTLTALENVM-VPLELK 113 Query: 120 GVSKKEAIEKAEHYLAKVGVAHRKDAYPAHMSGGEQQRVAIARALAVEPEVMLFDEPTSA 179 +K+A +KA L +VG+ R YP +SGGEQQRV+IARA A EP+++ DEPT Sbjct: 114 --KRKDAKQKATELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTGN 171 Query: 180 LDPELVGEVLK-VMQDLAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGLVEE 229 LD E GE+++ ++ DL + G T+++VTH+ A + +N+++ + G ++E Sbjct: 172 LDTE-TGELIETLIFDLNKALGTTLILVTHDTDLAAK-TNRIIHIKGGKIQE 221 Lambda K H 0.317 0.133 0.373 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: 119 Number of extensions: 5 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: 225 Length adjustment: 23 Effective length of query: 231 Effective length of database: 202 Effective search space: 46662 Effective search space used: 46662 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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