Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_024329178.1 B1A74_RS10700 ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >NCBI__GCF_001995255.1:WP_024329178.1 Length = 286 Score = 97.1 bits (240), Expect = 3e-25 Identities = 62/202 (30%), Positives = 108/202 (53%), Gaps = 10/202 (4%) Query: 19 PILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIV 78 P LQ I +++PGE + +IG +G GKSTL + GLL PS+G + G + Sbjct: 20 PTLQDIELTVSPGETIALIGQSGCGKSTLLHMLAGLLIPSEGAVRINGHQVI----KPSP 75 Query: 79 RRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPK--LAQRRNQRAGT 136 R M + Q +++ +TV N +G + QG + + R+ + LA++ + Sbjct: 76 RWNMMF--QKPSLYPWMTVRRNASLG-LIFQGRQEGMNKRVDALLETVGLAEKAEVNVQS 132 Query: 137 LSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINA-TGKAIILVEQN 195 LSGG++Q +A+ R+L DP+LLLLDEP +AL ++ ++ ++ G ++ V + Sbjct: 133 LSGGQQQRVALARSLATDPELLLLDEPFSALDAFTKTELQDEVVRLSRDRGITVVFVTHD 192 Query: 196 AKQALMMADRGYVLENGRDKLE 217 ++A+ MADR V+ + L+ Sbjct: 193 IEEAVAMADRVVVMGSNPGTLQ 214 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: 127 Number of extensions: 3 Number of successful extensions: 1 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: 286 Length adjustment: 25 Effective length of query: 215 Effective length of database: 261 Effective search space: 56115 Effective search space used: 56115 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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