Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate H281DRAFT_02383 H281DRAFT_02383 amino acid/amide ABC transporter membrane protein 2, HAAT family /amino acid/amide ABC transporter ATP-binding protein 1, HAAT family
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__Burk376:H281DRAFT_02383 Length = 594 Score = 179 bits (454), Expect = 1e-49 Identities = 104/249 (41%), Positives = 148/249 (59%), Gaps = 2/249 (0%) Query: 17 SLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVL 76 +LL K FGGL AV+ VK G I GLIGPNGAGK+T FNL++ ++ GE+ Sbjct: 345 NLLTVNKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGEIT 404 Query: 77 FNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRV 136 F G+ I L+ +I RG RTFQ K+L +TVLEN+ + H G + R I R Sbjct: 405 FRGERIDALSSREIVKRGIGRTFQHVKLLPGMTVLENVAIG-AHLRGHAGVWRSI-VRLN 462 Query: 137 QKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAG 196 EE +A + VGL D AG+L+ GQ+++LE+ARAL +P L+LLDEPAAG Sbjct: 463 SVEEARLMAEAARQIRRVGLEQHMYDEAGSLALGQQRILEIARALCCDPTLLLLDEPAAG 522 Query: 197 VNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSD 256 + Q+ + + +G++ L++EH+MD +M L + V+ G +A+G P+++Q D Sbjct: 523 LRYQEKLQLADLLRRLKAEGMSVLLVEHDMDFVMNLTDRLVVMEFGTRIAEGLPQEVQQD 582 Query: 257 PRVLEAYLG 265 P VLEAYLG Sbjct: 583 PAVLEAYLG 591 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: 375 Number of extensions: 20 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: 594 Length adjustment: 31 Effective length of query: 236 Effective length of database: 563 Effective search space: 132868 Effective search space used: 132868 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: 50 (23.9 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