Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Pf1N1B4_1346 Urea ABC transporter, ATPase protein UrtD
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1346 Length = 289 Score = 135 bits (339), Expect = 1e-36 Identities = 87/269 (32%), Positives = 148/269 (55%), Gaps = 17/269 (6%) Query: 1 MSDRITPAENLGSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTL 60 + R+ P L + ++L + +S SF G +A++ ++ + G + +IGPNGAGKTTL Sbjct: 33 LGQRVGPG--LNTRHGTILTLEDISVSFDGFKALNDLNLYIGVGELRCIIGPNGAGKTTL 90 Query: 61 FNLLSNFIRPDQGEVLFNGD-SIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQ 119 ++++ RP G+ F + Q++ QIA G R FQ V L+V EN+ LA Sbjct: 91 MDVITGKTRPSHGKAWFGETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELA-- 148 Query: 120 HQTGEKFLPRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMAR 179 Q +K + + R ++ +++ +LE++ L A AG LS GQ++ LE+ Sbjct: 149 -QKTDKSVWASLRARLSGEQ----KDRISEVLETIRLTASVNRPAGMLSHGQKQFLEIGM 203 Query: 180 ALMSNPKLILLDEPAAGVNPT---LIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHV 236 LM +P+L+LLDEP AG+ ++ + + + + +V+EH+M + ++ HV Sbjct: 204 LLMQDPQLLLLDEPVAGMTDAETEFTAELFKSLAGKH----SLMVVEHDMGFVGSIADHV 259 Query: 237 WVLAEGRNLADGTPEQIQSDPRVLEAYLG 265 VL +G LA+G+ EQ+Q + RV+E YLG Sbjct: 260 TVLHQGSVLAEGSLEQVQDNERVIEVYLG 288 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: 190 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: 289 Length adjustment: 25 Effective length of query: 242 Effective length of database: 264 Effective search space: 63888 Effective search space used: 63888 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