Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate AZOBR_RS32275 AZOBR_RS32275 branched-chain amino acid ABC transporter permease
Query= TCDB::P74318 (286 letters) >FitnessBrowser__azobra:AZOBR_RS32275 Length = 290 Score = 150 bits (380), Expect = 2e-41 Identities = 99/290 (34%), Positives = 156/290 (53%), Gaps = 15/290 (5%) Query: 1 MDL-SQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWA-NTSGIN 58 MDL Q + NG+ +G AL A+GLTL +G++R+ NFAHG+F L W+ N G++ Sbjct: 1 MDLFPQFLANGLVMGVFYALSALGLTLIFGLMRVVNFAHGEFYMLGGVSGWFVTNYLGLD 60 Query: 59 LWLSMA-----LGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLI 113 + + + VG ++ F+ E R R I+++IGL++FL NG LL+ Sbjct: 61 FFSGLIVVAAFMAAVGWLVDRFLIE-------RVRGQGEEPGILLTIGLSIFLVNGTLLL 113 Query: 114 WGGNNQNYRVPIVPAQDFMG-IKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVAD 172 G + F G I RLL +A+ IA +V HL+++RT++G AMRA Sbjct: 114 VGPAPMKVAGAVAEGPLFFGPIAVTKLRLLAVAVGIALIVGAHLLIRRTRLGAAMRATFQ 173 Query: 173 NVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGG 232 + A ++GI V T+ + L AL G + + + + ++G + L F VILGG Sbjct: 174 DPMAASLAGIRTGHVYAATFALGCTLAALSGMLLASIYSAQASVGGLISLKSFVVVILGG 233 Query: 233 IGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLF 282 +G+ GAIAGG+++GVA+ + + + +L+I+IL RPQGLF Sbjct: 234 MGSFAGAIAGGLLLGVAEAMWGGYVSMGMVDVIGFVLVILILLFRPQGLF 283 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: 230 Number of extensions: 7 Number of successful extensions: 4 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: 290 Length adjustment: 26 Effective length of query: 260 Effective length of database: 264 Effective search space: 68640 Effective search space used: 68640 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: 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