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 Ac3H11_1435 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1435 Length = 256 Score = 177 bits (449), Expect = 2e-49 Identities = 99/251 (39%), Positives = 147/251 (58%), Gaps = 11/251 (4%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 +L L K F G AV + + V +GSI LIGPNGAGKTT FNLL+ F+ P G + F Sbjct: 5 ILETKSLTKEFKGFTAVSDVNLAVRRGSIHALIGPNGAGKTTCFNLLTKFLEPTSGVIRF 64 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGE--NFWQVQLQPQV 128 +G I + QP QIA++G++R+FQ++ L+++EN+ L Q++ G +FW+ + Sbjct: 65 NGHDITREQPAQIARRGVIRSFQISAVFPHLTLMENVRLGLQRKLGTSFHFWRSE----- 119 Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188 + QL ++AM LL VGL A E L G+++ LE+ L P+L+LLDEP Sbjct: 120 --RTLSQLDDRAMQLLTEVGLEDLADEVTVNLPYGRKRALEIATTLSMEPELMLLDEPTQ 177 Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248 G+ +D + I + G T L++EHNM V+ ++ DR+ VL G LA+G E+ Sbjct: 178 GMGHEDVDRVTQLIKKVSA--GRTILMVEHNMKVVSTIADRITVLQRGAVLAEGPYEEVS 235 Query: 249 TNSQVLEAYLG 259 N QV+EAY+G Sbjct: 236 NNPQVMEAYMG 246 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: 146 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: 260 Length of database: 256 Length adjustment: 24 Effective length of query: 236 Effective length of database: 232 Effective search space: 54752 Effective search space used: 54752 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 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