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 PfGW456L13_84 Urea ABC transporter, ATPase protein UrtD
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_84 Length = 290 Score = 135 bits (340), Expect = 1e-36 Identities = 84/252 (33%), Positives = 143/252 (56%), Gaps = 12/252 (4%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 +L + SF G +A+ + + G + +IGPNGAGKTTL ++++ RP G+ F Sbjct: 49 ILTLEDISVSFDGFRALNNLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAWF 108 Query: 71 DGEPIQ--QLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQV 128 GE + Q+ QIAQ G+ R FQ LSV EN+ LA ++T ++ W L+ ++ Sbjct: 109 -GETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELA--QKTDKSVW-ASLRARL 164 Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188 +++ ++ + +L+++ L AG LS GQ++ LE+G LM +P+L+LLDEP A Sbjct: 165 SGEQKDRIAQ----VLDTIRLTSSVNRPAGLLSHGQKQFLEIGMLLMQDPQLLLLDEPVA 220 Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248 G+ + + L + + +++EH+M + S+ D V VL +G LA+G+ ++Q Sbjct: 221 GMTDAETEFTAE--LFKSLAGKHSLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQ 278 Query: 249 TNSQVLEAYLGK 260 N +V+E YLG+ Sbjct: 279 DNERVIEVYLGR 290 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: 172 Number of extensions: 7 Number of successful extensions: 4 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: 290 Length adjustment: 25 Effective length of query: 235 Effective length of database: 265 Effective search space: 62275 Effective search space used: 62275 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