Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Ac3H11_4987 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= TCDB::P73650 (240 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4987 Length = 272 Score = 184 bits (468), Expect = 1e-51 Identities = 107/240 (44%), Positives = 148/240 (61%), Gaps = 8/240 (3%) Query: 4 LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLT-----PS 58 +L V ++ Y V L+G++ ++ G++V ++G NGAGKST K I GLL Sbjct: 9 VLEVNNIEVIYNKVVQALRGLSLAVPRGQIVALLGSNGAGKSTTLKAISGLLALEDGVVE 68 Query: 59 QGEIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKD- 117 G I F G+ + Q+VR G+ +V + VF LTV ENL + G + T D Sbjct: 69 SGSIHFNGQPTAAVAPQQLVRNGLSHVMEGRRVFEDLTVEENLVAATYALTGRSGTTPDF 128 Query: 118 -RIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVF 176 +Y+ FP+L +RR AG LSGGE+QMLA+GRAL+ P L+LLDEPS LSP LV+D+F Sbjct: 129 DLVYSYFPRLHERRKGLAGYLSGGEQQMLAIGRALIAQPQLILLDEPSLGLSPKLVEDIF 188 Query: 177 AQIKAINA-TGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 I INA G +++LVEQNA AL +A RGY++ENG+ ++G+ + L NDP V E YLG Sbjct: 189 TIIARINAERGTSMLLVEQNATVALAVAHRGYIMENGKIVIDGTAERLANDPDVREFYLG 248 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: 183 Number of extensions: 8 Number of successful extensions: 4 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: 272 Length adjustment: 24 Effective length of query: 216 Effective length of database: 248 Effective search space: 53568 Effective search space used: 53568 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