Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_011321041.1 AVA_RS22160 urea ABC transporter ATP-binding protein UrtD
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_000204075.1:WP_011321041.1 Length = 246 Score = 141 bits (356), Expect = 1e-38 Identities = 89/250 (35%), Positives = 136/250 (54%), Gaps = 8/250 (3%) Query: 16 SSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEV 75 + +L + ++ SF G +A++ + + G + +IGPNGAGKTT ++++ ++P G V Sbjct: 3 AKILETENVTVSFDGFKALNQLNFSMDVGELRVVIGPNGAGKTTFLDVITGKVQPTIGRV 62 Query: 76 LFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRR 135 LF G ++ L HQIA RG R FQ +V LT EN+ + + L F R Sbjct: 63 LFKGKNLRSLREHQIARRGIGRKFQTPRVYLNLTPRENLEITSNR--NKNVFSTL--FGR 118 Query: 136 VQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAA 195 Q E +LE++GL KA A LS G+++ LE+ + +P L+L+DEP A Sbjct: 119 SQPTE---ENSIKGLLETIGLTPKADIPAALLSHGEKQRLEIGMLVGQSPDLLLVDEPVA 175 Query: 196 GVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQS 255 G+ I E ++ Q + LVIEH+M+ + + V VL EG L +G E++QS Sbjct: 176 GLTDEETYNIGELLLTL-AQSHSILVIEHDMEFVRQIAKKVTVLHEGSVLCEGNFEEVQS 234 Query: 256 DPRVLEAYLG 265 DPRV+E YLG Sbjct: 235 DPRVVEVYLG 244 Lambda K H 0.319 0.136 0.389 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: 196 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: 267 Length of database: 246 Length adjustment: 24 Effective length of query: 243 Effective length of database: 222 Effective search space: 53946 Effective search space used: 53946 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 (21.7 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