Align Branched chain amino acid ABC transporter substrate-binding protein (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:A0A165KTD4 (375 letters) >FitnessBrowser__Marino:GFF3112 Length = 370 Score = 172 bits (435), Expect = 2e-47 Identities = 118/381 (30%), Positives = 193/381 (50%), Gaps = 24/381 (6%) Query: 3 LKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGV 62 +K +T V+ A G A ++ +IG P++G A YG +GARMAIE++NA G Sbjct: 5 VKKLVTAVSTSVALMGAGHAAAEI-QIGIAGPMTGPVAQYGDMQFSGARMAIEQINANGG 63 Query: 63 TIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIP 122 +G + + E DD DPKQ A L + V V+GHL S +T PAS +Y D GI Sbjct: 64 VMGEELVAVEY---DDVCDPKQAVTVANSLVNDGVRFVIGHLCSSSTQPASDIYEDEGIL 120 Query: 123 HVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVA 182 VT A+T+P +T+ GY+ FR I D+ G A Y + + + VAI+ D+ YG+G+A Sbjct: 121 MVTPASTSPEITERGYELVFRTIGLDSMQGPVAARY-IASQNPERVAIVHDKQQYGEGIA 179 Query: 183 DVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQ 242 + T G+++ + T DF +++T +K + D ++YGG P+ G +LRQ Sbjct: 180 TAVRDTLKDAGVEIAMFEGITAGDKDFSSLVTKLKQADVDYVYYGGYHPELGLILRQANS 239 Query: 243 LGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAK------- 295 + + ++ G +G+ +I +A A AEG L +P KA+ Sbjct: 240 ADL-DARFMGPEGVGNKDINTIAGEA--------AEG--LLVTLPPAFDQKAENQALVKA 288 Query: 296 YDAKYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNG 355 ++ K + + +Y A L+ + ++ A S DP L + +F+ T+ ++ G Sbjct: 289 FEDKGEDPSGPFVLTSYTAVQLVAEGIEAAGSTDPFDVAAALREGTFQTPIGTVEYDKAG 348 Query: 356 EMKNPAITLYV-YKDGKKTPL 375 +MK+ +Y + DG KTP+ Sbjct: 349 DMKSFEFVVYEWHSDGSKTPV 369 Lambda K H 0.315 0.131 0.375 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: 379 Number of extensions: 17 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: 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 ( 7.3 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