Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BPHYT_RS32510 BPHYT_RS32510 ABC transporter permease
Query= TCDB::P74318 (286 letters) >FitnessBrowser__BFirm:BPHYT_RS32510 Length = 286 Score = 137 bits (346), Expect = 2e-37 Identities = 90/280 (32%), Positives = 147/280 (52%), Gaps = 11/280 (3%) Query: 7 IFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGINLWLSMALG 66 I NGI VG + L AVGL++ +G+LR NFAHG F L AY + A ++ W ++ + Sbjct: 8 IVNGIGVGMLYFLLAVGLSIVFGLLRFVNFAHGAFYLLGAYFCYQAMQWSMSFWTALVVV 67 Query: 67 CVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGGNNQNYRVPIV 126 V ++ E L+ + + A++ I++++GLAL ++ +LIWG N VP V Sbjct: 68 PVVVGALAWVVEKLILRHVYAQQHEFH--ILVTVGLALVVQECAILIWGPLGDNVAVPDV 125 Query: 127 PAQDFMGIKFEY--YRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDLAKVSGINV 184 + F Y YRL VI +L +L+ T++G A+RA +++ ++ + GINV Sbjct: 126 LNGVVIWGSFVYPKYRLFVIGFTAVLAALLWWVLEGTRLGSAVRAGSESTEMVSLLGINV 185 Query: 185 EWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGGIGNPYGAIAGGI 244 V + + A AL G + + + P MG + F V++GG+GN GA+ GG+ Sbjct: 186 LRVFSLVFALGAATAALAGVLAAPIRGVDPFMGIEALSVAFVVVVVGGMGNFLGALVGGL 245 Query: 245 IIGVAQEVSVPWFGTSYKMGVALLL---MIIILFIRPQGL 281 ++G+ Q V T + G L++ M +L +RP GL Sbjct: 246 LVGIVQSV----MSTLWPEGARLMIYVAMAAVLLLRPNGL 281 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: 218 Number of extensions: 14 Number of successful extensions: 2 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: 286 Length adjustment: 26 Effective length of query: 260 Effective length of database: 260 Effective search space: 67600 Effective search space used: 67600 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