Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate AO353_06035 AO353_06035 amino acid ABC transporter permease/ATP-binding protein
Query= TCDB::P73650 (240 letters) >FitnessBrowser__pseudo3_N2E3:AO353_06035 Length = 512 Score = 116 bits (290), Expect = 1e-30 Identities = 67/214 (31%), Positives = 121/214 (56%), Gaps = 8/214 (3%) Query: 20 ILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLG---SDQ 76 +L+GI+ ++ G+++++IGP+G+GK++L +TI GL + QGEI+ GE+ G + Sbjct: 275 VLKGIDLTVGSGQVISIIGPSGSGKTSLIRTINGLESIDQGEIMLFGESFIGSNDTPNSA 334 Query: 77 IVRRGMCYVPQVC---NVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPK--LAQRRN 131 VR G+ ++ V N+F + +N+ + H + R Y + K L + Sbjct: 335 KVRSGVRHIGMVFQNFNLFPHRCILDNITLAPRFHGSAKPLSEQRAYALLDKVGLLAHAH 394 Query: 132 QRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIIL 191 + LSGG++Q +A+ RAL ++P ++L DEP++AL P LV DV I+ + G +++ Sbjct: 395 KYPHQLSGGQQQRVAIARALAMEPKIMLFDEPTSALDPELVGDVLNVIRDLAKEGMTMLI 454 Query: 192 VEQNAKQALMMADRGYVLENGRDKLEGSGQSLLN 225 V A+ ++DR +ENG +L+ S ++ N Sbjct: 455 VTHEMDFAMSISDRVIFMENGNVQLDASPYAIRN 488 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: 226 Number of extensions: 11 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: 512 Length adjustment: 29 Effective length of query: 211 Effective length of database: 483 Effective search space: 101913 Effective search space used: 101913 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: 49 (23.5 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