Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 5210167 Shew_2611 ABC transporter-related protein (RefSeq)
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__PV4:5210167 Length = 265 Score = 166 bits (421), Expect = 4e-46 Identities = 92/253 (36%), Positives = 148/253 (58%), Gaps = 2/253 (0%) Query: 15 ESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGE 74 + ++L +S +FGG++A+ V+ G++ +IGPNGAGKT++ N +S RP +G Sbjct: 2 KDTILTVDQISLAFGGVKALTDVSFEVERGAVFSIIGPNGAGKTSMLNSISGRYRPQKGT 61 Query: 75 VLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFR 134 + F+ + L P+ A G RTFQ + ++VL+N+++ H +L + + Sbjct: 62 IHFDNQDVTHLRPNARADLGIGRTFQNLALFGHMSVLDNIMVGRHHLMKNNWLTGPLYWA 121 Query: 135 R-VQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEP 193 QKEE A+R + +++ + + + AG LS G RK +E+ARA+ NPKLILLDEP Sbjct: 122 SPAQKEELAHRRQVEEIIDFLDISHVRKSIAGTLSYGLRKRVELARAMALNPKLILLDEP 181 Query: 194 AAGVNPTLIGQICEHIVNWNRQ-GITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQ 252 AG+N + +I++ N + GIT ++IEH+M V+M + H V VL G+ L G PE Sbjct: 182 MAGMNLEEKEDMARYILDLNEEFGITVVMIEHDMGVVMDISHEVMVLDFGKKLISGLPEA 241 Query: 253 IQSDPRVLEAYLG 265 + +D V +AYLG Sbjct: 242 VMADEHVRQAYLG 254 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: 175 Number of extensions: 7 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: 267 Length of database: 265 Length adjustment: 25 Effective length of query: 242 Effective length of database: 240 Effective search space: 58080 Effective search space used: 58080 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