Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate PfGW456L13_84 Urea ABC transporter, ATPase protein UrtD
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_84 Length = 290 Score = 134 bits (337), Expect = 2e-36 Identities = 84/261 (32%), Positives = 146/261 (55%), Gaps = 15/261 (5%) Query: 9 ENLGSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFI 68 + L + ++L + +S SF G RA+++ ++ + G + +IGPNGAGKTTL ++++ Sbjct: 40 KGLNTRHGTILTLEDISVSFDGFRALNNLNLYIGVGELRCIIGPNGAGKTTLMDVITGKT 99 Query: 69 RPDQGEVLFNGD-SIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFL 127 RP G+ F + Q++ QIA G R FQ V L+V EN+ LA Q +K + Sbjct: 100 RPSHGKAWFGETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELA---QKTDKSV 156 Query: 128 PRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKL 187 + R ++ +++ +L+++ L + AG LS GQ++ LE+ LM +P+L Sbjct: 157 WASLRARLSGEQ----KDRIAQVLDTIRLTSSVNRPAGLLSHGQKQFLEIGMLLMQDPQL 212 Query: 188 ILLDEPAAGVNPT---LIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRN 244 +LLDEP AG+ ++ + + + + +V+EH+M + ++ HV VL +G Sbjct: 213 LLLDEPVAGMTDAETEFTAELFKSLAGKH----SLMVVEHDMGFVGSIADHVTVLHQGSV 268 Query: 245 LADGTPEQIQSDPRVLEAYLG 265 LA+G+ EQ+Q + RV+E YLG Sbjct: 269 LAEGSLEQVQDNERVIEVYLG 289 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: 195 Number of extensions: 9 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: 267 Length of database: 290 Length adjustment: 25 Effective length of query: 242 Effective length of database: 265 Effective search space: 64130 Effective search space used: 64130 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