Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate AZOBR_RS19790 AZOBR_RS19790 amino acid ABC transporter ATPase
Query= TCDB::P73650 (240 letters) >FitnessBrowser__azobra:AZOBR_RS19790 Length = 234 Score = 201 bits (511), Expect = 1e-56 Identities = 108/235 (45%), Positives = 154/235 (65%), Gaps = 5/235 (2%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63 +L V D+ Y D L G++ ++A G ++G NGAGK++L +TI G+L P++G I Sbjct: 1 MLTVSDLDLFY-GDAQALDGVSIAVAEGTTTAIVGANGAGKTSLIRTISGILKPARGTIR 59 Query: 64 FKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFL---HQGPTQTLKDRIY 120 F+G++I GL S + G+ V + +F +L++ ENL+MGA + G T +R+ Sbjct: 60 FRGKDIAGLPSHVVCDLGIGQVAEGRQIFPTLSIRENLEMGAVIPRARDGAKDTF-ERVL 118 Query: 121 TMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIK 180 T+FP+L +R Q AGTLSGGE+QMLA+GR LM PDL++ DEPS LSP +V+++F I+ Sbjct: 119 TLFPRLKERLEQAAGTLSGGEQQMLAIGRCLMGKPDLIMFDEPSLGLSPTMVQELFRTIR 178 Query: 181 AINATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 A+ A G IILVEQN +L +A R YVLENGR L G+G+ LL DP V + YLG Sbjct: 179 ALAAEGMTIILVEQNVAASLKLAQRAYVLENGRVVLAGTGEELLADPAVKQAYLG 233 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: 160 Number of extensions: 7 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: 234 Length adjustment: 23 Effective length of query: 217 Effective length of database: 211 Effective search space: 45787 Effective search space used: 45787 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