Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate RR42_RS34785 RR42_RS34785 ABC transporter permease
Query= TCDB::P74318 (286 letters) >FitnessBrowser__Cup4G11:RR42_RS34785 Length = 287 Score = 188 bits (477), Expect = 1e-52 Identities = 104/281 (37%), Positives = 160/281 (56%), Gaps = 3/281 (1%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTS-GINLWLSM 63 Q + NG+ +G + +L A+GLTL YGIL + NFAHG F AY++++ TS G+N WL+M Sbjct: 6 QQVLNGLTLGGVYSLVALGLTLVYGILHVPNFAHGAFYMAGAYVSYYLMTSLGMNYWLAM 65 Query: 64 ALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGGNNQNYRV 123 + + + + L++ P+R A +I +IG+ LFL G +WG + Sbjct: 66 GAAAIAVAVLSMLADRLVFHPLR--NAPELHDMIAAIGIMLFLEAGAQAMWGADFHRMPT 123 Query: 124 PIVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDLAKVSGIN 183 P + MG+ RLL+IA A MV+LHL L RT G + A+A N + A + GI+ Sbjct: 124 PYGQMVEVMGLSAPAQRLLIIAAAFGLMVLLHLFLTRTVTGSTIVAMAQNREGAALVGID 183 Query: 184 VEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGGIGNPYGAIAGG 243 V + + ++ L A+ ++Y + + P+MG +I F +ILGG+G+ GAI GG Sbjct: 184 ATRVTLLVFAISGALAAIAATLYAPINLVYPSMGNLVITKAFVIIILGGMGSIPGAIVGG 243 Query: 244 IIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLFKG 284 +IIG+A+ + T YK +A L+++IL IRPQGLF G Sbjct: 244 LIIGMAESFGGFYVSTDYKDIIAFALLVLILSIRPQGLFAG 284 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: 228 Number of extensions: 14 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: 287 Length adjustment: 26 Effective length of query: 260 Effective length of database: 261 Effective search space: 67860 Effective search space used: 67860 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