Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate GFF3112 HP15_3055 high-affinity leucine-specific leucine-specific-binding periplasmic protein of high-affinity branched-chain amino acid ABC transporter transport system periplasmic binding protein
Query= uniprot:A0A160A0J6 (375 letters) >FitnessBrowser__Marino:GFF3112 Length = 370 Score = 487 bits (1253), Expect = e-142 Identities = 241/369 (65%), Positives = 295/369 (79%), Gaps = 4/369 (1%) Query: 2 TKATKQISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQIN 61 T K ++ + ++ L G A H AA I+IGIAGP TGPVAQYGDMQFSG++MAIEQIN Sbjct: 3 TSVKKLVTAVSTSVALMG-AGH--AAAEIQIGIAGPMTGPVAQYGDMQFSGARMAIEQIN 59 Query: 62 AKGGVNGKQLVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGV 121 A GGV G++LVAVEYDD CDPKQAV VAN +VNDG++FV+GHLCSSSTQPASDIYEDEG+ Sbjct: 60 ANGGVMGEELVAVEYDDVCDPKQAVTVANSLVNDGVRFVIGHLCSSSTQPASDIYEDEGI 119 Query: 122 VMITPAATSPDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGI 181 +M+TPA+TSP+IT RGY+++FRTIGLDS QGP A YIA P+ VA++HDKQQYGEGI Sbjct: 120 LMVTPASTSPEITERGYELVFRTIGLDSMQGPVAARYIASQ-NPERVAIVHDKQQYGEGI 178 Query: 182 ASAVKKTLEDKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQ 241 A+AV+ TL+D GV++A+FEG+ AGDKDFSS++ KLKQA+VD+VYYGGYHPELGLILRQ+ Sbjct: 179 ATAVRDTLKDAGVEIAMFEGITAGDKDFSSLVTKLKQADVDYVYYGGYHPELGLILRQAN 238 Query: 242 EKGLKAKFMGPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSG 301 L A+FMGPEGVGN I+ IA E++EGLLVTLP +FDQ N AL AF+ K EDPSG Sbjct: 239 SADLDARFMGPEGVGNKDINTIAGEAAEGLLVTLPPAFDQKAENQALVKAFEDKGEDPSG 298 Query: 302 PFVFPSYSAVTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVY 361 PFV SY+AV ++A+ I+AA S D VA A+ GTF+TP G + +DK GD+K F+FVVY Sbjct: 299 PFVLTSYTAVQLVAEGIEAAGSTDPFDVAAALREGTFQTPIGTVEYDKAGDMKSFEFVVY 358 Query: 362 EWHFGKPKT 370 EWH KT Sbjct: 359 EWHSDGSKT 367 Lambda K H 0.314 0.132 0.372 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: 532 Number of extensions: 28 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: 375 Length of database: 370 Length adjustment: 30 Effective length of query: 345 Effective length of database: 340 Effective search space: 117300 Effective search space used: 117300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 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