Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 6939496 Sama_3588 putative ABC-type multidrug transport system, ATPase component (RefSeq)
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__SB2B:6939496 Length = 322 Score = 118 bits (296), Expect = 1e-31 Identities = 76/253 (30%), Positives = 132/253 (52%), Gaps = 20/253 (7%) Query: 1 MSDRITPAENLGSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTL 60 MS+ + P +P + + +G+++ FG L+AVD D+ + GSI G +GPNG GK+T Sbjct: 1 MSEVLAPQTLTTAPLA--IETRGMTRQFGALKAVDGVDLAIPRGSIYGFLGPNGCGKSTS 58 Query: 61 FNLLSNFIRPDQGEVLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQH 120 +L+ ++P GE+ G+ + + A ++ R T Q + LTVLEN+ Sbjct: 59 IRMLTGLLKPTSGEIRVLGEPL-KGAEEKLRRRIGYMT-QKFSLYENLTVLENL------ 110 Query: 121 QTGEKFLPRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARA 180 +F+ R+ + + ++R + +L L + AG++SGGQ++ L +A A Sbjct: 111 ----RFVARIYGLQGNKAKDRIEQ-----LLSLYSLEGRESQMAGSMSGGQKQRLALAAA 161 Query: 181 LMSNPKLILLDEPAAGVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLA 240 + P+L+ LDEP + V+P + E + + + +G T LV H MD CH + +L Sbjct: 162 TIHEPELLFLDEPTSAVDPENRREFWERLFDLSAKGCTILVSTHYMDE-AERCHGLAILE 220 Query: 241 EGRNLADGTPEQI 253 G ADG+P+ + Sbjct: 221 RGIKRADGSPKAL 233 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: 176 Number of extensions: 8 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: 322 Length adjustment: 26 Effective length of query: 241 Effective length of database: 296 Effective search space: 71336 Effective search space used: 71336 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 Apr 09 2024. 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