Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD
Query= TCDB::P73650 (240 letters) >FitnessBrowser__Pedo557:CA265_RS04345 Length = 216 Score = 87.8 bits (216), Expect = 2e-22 Identities = 52/156 (33%), Positives = 86/156 (55%), Gaps = 5/156 (3%) Query: 17 DVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQ 76 ++ IL+G+NF + GE+V++IGP+GAGKSTL + L P G + KG I L D Sbjct: 13 NLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQLKGTVINKLNGDL 72 Query: 77 IV---RRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFP--KLAQRRN 131 + + + +V Q ++ + EN+ + AF+ + + + R + + L R Sbjct: 73 LSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAFELLDLFGLKDRAQ 132 Query: 132 QRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAAL 167 + LSGGE+Q +A+ RAL+ +P ++L DEPS L Sbjct: 133 HKPNQLSGGEQQRVAIARALINNPSIILADEPSGNL 168 Lambda K H 0.320 0.139 0.393 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: 129 Number of extensions: 8 Number of successful extensions: 2 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: 240 Length of database: 216 Length adjustment: 23 Effective length of query: 217 Effective length of database: 193 Effective search space: 41881 Effective search space used: 41881 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 (21.8 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