Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 7025598 Shewana3_2749 ABC transporter related (RefSeq)
Query= TCDB::P73650 (240 letters) >FitnessBrowser__ANA3:7025598 Length = 346 Score = 103 bits (257), Expect = 4e-27 Identities = 64/206 (31%), Positives = 117/206 (56%), Gaps = 5/206 (2%) Query: 21 LQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVRR 80 ++ ++ +I G + +GPNG GKST + + GLL+P+ G+I GE + G +++ +RR Sbjct: 44 VEDLDLAIPKGTIYGFLGPNGCGKSTSIRMLTGLLSPTSGDIRVLGETLPG--AEEKLRR 101 Query: 81 GMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFP--KLAQRRNQRAGTLS 138 + Y+ Q +++ +L+V ENL+ A ++ + K R+ + LA R Q AG++S Sbjct: 102 RIGYMTQKFSLYDNLSVRENLEFVAQIYGLNRRQTKARLAELLSLYDLAGREKQMAGSMS 161 Query: 139 GGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIILVEQNAKQ 198 GG++Q LA+ A + P+LL LDEP++A+ P ++ + ++ + A G I++ + Sbjct: 162 GGQKQRLALAAATLHHPELLFLDEPTSAVDPENRREFWERLFDLCAQGTTILVSTHYMDE 221 Query: 199 ALMMADRGYVLENGRDKLEGSGQSLL 224 A +LE G + +GS Q L+ Sbjct: 222 AERCHGLA-ILERGIKRADGSPQQLM 246 Lambda K H 0.320 0.139 0.393 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: 165 Number of extensions: 11 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: 240 Length of database: 346 Length adjustment: 26 Effective length of query: 214 Effective length of database: 320 Effective search space: 68480 Effective search space used: 68480 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 (21.8 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