Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 106 bits (264), Expect = 8e-28 Identities = 80/248 (32%), Positives = 122/248 (49%), Gaps = 28/248 (11%) Query: 17 SLLLAQGLSKSFGGLR--AVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGE 74 SLL G+SK F + AV + ++EGS+ ++G NG+GKTTL L++ PD+GE Sbjct: 2 SLLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGE 61 Query: 75 VLFNGDSIGQLAPHQIALRGSVR----TFQVAKVLSRLTVLENMLLADQHQTGEKFLPRL 130 ++F+G +I + AL + R FQ + ++T+LEN+ A Sbjct: 62 IVFSGQTI---VNGKSALPANQREVGVIFQEYALFPQMTLLENVREA------------- 105 Query: 131 INFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILL 190 + +E R R+ AM L GL Y LS GQR+ +ARAL S PKL+LL Sbjct: 106 -----LHQESRNARQIAMDSLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLL 160 Query: 191 DEPAAGVNPTLIGQICEHIVN-WNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGT 249 D+P ++ +I E I + GIT +V H+ ++L + +L +G GT Sbjct: 161 DDPFRSLDTRFKNEISEDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGT 220 Query: 250 PEQIQSDP 257 P +I P Sbjct: 221 PVEIYKKP 228 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: 13 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: 345 Length adjustment: 27 Effective length of query: 240 Effective length of database: 318 Effective search space: 76320 Effective search space used: 76320 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: 48 (23.1 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