Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Pf1N1B4_1079 Lipopolysaccharide ABC transporter, ATP-binding protein LptB
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1079 Length = 241 Score = 135 bits (341), Expect = 6e-37 Identities = 86/249 (34%), Positives = 138/249 (55%), Gaps = 17/249 (6%) Query: 12 LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71 L A L KS+ + V++ + + G I GL+GPNGAGKTT F ++ ++ D+GRV+ D Sbjct: 4 LKAQHLAKSYKSRQVVRDVSLSIDSGQIVGLLGPNGAGKTTCFYMIVGLVQADQGRVLID 63 Query: 72 GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVK 131 + H A+ G+ Q A +LSV +N++ A +T + Q + ++ Sbjct: 64 DLDVSHQPMHGRAKAGIGYLPQEASIFRKLSVADNIM--AILETRKELDQAGRRQEL--- 118 Query: 132 EEKQLQE-QAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 E LQE + +++G++ LSGG+R+ +E+ RAL TNPK ILLDEP AGV Sbjct: 119 -ESLLQEFHIHHIRDNLGMS---------LSGGERRRVEIARALATNPKFILLDEPFAGV 168 Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250 +P + DI +I+ + G+ LI +HN+ + +C+ +++ +GQ +A+G A I N Sbjct: 169 DPISVGDI-KQIIHHLKAKGIGVLITDHNVRETLDICETAYIVNDGQLIAEGDSATILAN 227 Query: 251 SQVLEAYLG 259 V E YLG Sbjct: 228 ELVKEVYLG 236 Lambda K H 0.319 0.136 0.391 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: 139 Number of extensions: 8 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: 260 Length of database: 241 Length adjustment: 24 Effective length of query: 236 Effective length of database: 217 Effective search space: 51212 Effective search space used: 51212 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: 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