Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF2759 HP15_2703 branched-chain amino acid ABC transporter ATP-binding protein
Query= TCDB::P73650 (240 letters) >FitnessBrowser__Marino:GFF2759 Length = 454 Score = 200 bits (509), Expect = 4e-56 Identities = 107/235 (45%), Positives = 156/235 (66%), Gaps = 3/235 (1%) Query: 3 DLLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEI 62 ++L +K + Y + +L ++ I GE+V+++G NGAGKSTL TI GL +G I Sbjct: 220 EMLSIKGLVTSY-GQIEVLHDVDIHINSGEIVSLVGANGAGKSTLLMTISGLQPTDRGAI 278 Query: 63 IFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKD--RIY 120 F+G++++ + +DQ V G+ VP+ VF L+V +NL +GA+ + + D R+Y Sbjct: 279 TFEGKDLSKITADQRVADGIVQVPEGRQVFKDLSVHDNLLLGAYTRGKTPEVMDDLERMY 338 Query: 121 TMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIK 180 T FP L Q+R+ AG LSGG++QMLAMGRALM P LLLLDEPS L+P++++++F +K Sbjct: 339 TKFPILRQKRHNLAGELSGGQQQMLAMGRALMAKPRLLLLDEPSMGLAPLIIEEIFNIVK 398 Query: 181 AINATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235 + G I LVEQNA QAL +ADRGYVLE G+ +EG+G+ LL++ V E YLG Sbjct: 399 ELKEEGITIFLVEQNASQALALADRGYVLETGKVVIEGTGRELLSNEKVREAYLG 453 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: 260 Number of extensions: 13 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: 454 Length adjustment: 28 Effective length of query: 212 Effective length of database: 426 Effective search space: 90312 Effective search space used: 90312 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