Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_110804047.1 C8J30_RS02045 branched-chain amino acid ABC transporter permease
Query= TCDB::P74318 (286 letters) >NCBI__GCF_003217355.1:WP_110804047.1 Length = 335 Score = 164 bits (415), Expect = 2e-45 Identities = 114/324 (35%), Positives = 173/324 (53%), Gaps = 44/324 (13%) Query: 3 LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMT----LAAYLTWWANTSGIN 58 L+ +I A G+ +ALGA+G+TL YGILR SNFAHGD M L +TW ++G++ Sbjct: 11 LNYIIVPATAYGAQLALGALGVTLIYGILRFSNFAHGDTMAFGTGLTILVTWAMQSAGLS 70 Query: 59 LW------LSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILL 112 L++ +G T + + +++ R RA + ++S+G+ +F+ NG+ Sbjct: 71 FGPLPTALLALPIGIALTAALVLATDKVVYSYYRKVRAAPIYITMVSVGV-MFVMNGLTR 129 Query: 113 IWGGNNQNYRVP----IVPAQDFMGIKFEYYRLLV-----IAMAIAAMVV--LHLILQRT 161 + G ++ ++ A DF + L + I + AA+VV L L RT Sbjct: 130 VLIGVDEIKFADGARFLISAPDFKAMTGLTEPLAIRATTAITVITAALVVWALFWFLART 189 Query: 162 KVGKAMRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLI 221 + GK+MRA ADN DLA +SGI+ VV TWV+ A L + G++YGL + K + L+ Sbjct: 190 RTGKSMRAYADNEDLALLSGIDPNRVVAVTWVIAAALATIAGTLYGLDKSFKAFNYFQLL 249 Query: 222 LPMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPW---------------------FGTS 260 LP+FA+ I+GG+GNP GAIAGG +I + EVSV + T Sbjct: 250 LPIFAAAIVGGLGNPLGAIAGGFVIAFS-EVSVTYAWKKVAMYLIPGYEPEGLLQLLSTE 308 Query: 261 YKMGVALLLMIIILFIRPQGLFKG 284 YK V+ ++II+L +P GLFKG Sbjct: 309 YKFAVSFAILIIVLLFKPTGLFKG 332 Lambda K H 0.329 0.143 0.450 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: 258 Number of extensions: 10 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: 286 Length of database: 335 Length adjustment: 27 Effective length of query: 259 Effective length of database: 308 Effective search space: 79772 Effective search space used: 79772 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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