Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BPHYT_RS31755 BPHYT_RS31755 amino acid ABC transporter ATPase
Query= TCDB::P73650 (240 letters) >FitnessBrowser__BFirm:BPHYT_RS31755 Length = 237 Score = 190 bits (483), Expect = 2e-53 Identities = 98/237 (41%), Positives = 152/237 (64%), Gaps = 3/237 (1%) Query: 1 MSDLLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQG 60 M+ +L +K + Y + ++ ++ + G+LVT+IG NGAGK+T K I GL S G Sbjct: 1 MATILKIKGLQVNY-GGIQAVKNVDMEVKTGDLVTLIGANGAGKTTTMKAIAGLKPYSVG 59 Query: 61 EIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKD--R 118 +I + G +I G+ + ++++RG+ VP+ +F +++ EN+ MGA+L +D R Sbjct: 60 DIEYMGASIKGIPTHELLKRGLAMVPEGRGIFARMSIIENMQMGAYLRDDLHGVKRDIER 119 Query: 119 IYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQ 178 ++ FP+L +R+ Q AGTLSGGE+QMLAM RA++ P LLLLDEPS LSPI+V+ +F Sbjct: 120 MFGFFPRLEERKLQFAGTLSGGEQQMLAMARAIISKPKLLLLDEPSMGLSPIMVEKIFEV 179 Query: 179 IKAINATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 ++ ++ G ++LVEQNA+ AL A RGYV+E+G + G +L+DP V YLG Sbjct: 180 VREVSREGITVLLVEQNARLALQAASRGYVMESGTVTMSGDASKMLDDPKVRAAYLG 236 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: 141 Number of extensions: 4 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: 240 Length of database: 237 Length adjustment: 23 Effective length of query: 217 Effective length of database: 214 Effective search space: 46438 Effective search space used: 46438 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: 46 (22.3 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