Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (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:G8ALJ3 (366 letters) >FitnessBrowser__Marino:GFF3112 Length = 370 Score = 277 bits (708), Expect = 4e-79 Identities = 145/357 (40%), Positives = 211/357 (59%), Gaps = 2/357 (0%) Query: 4 KLSLLVAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLG 63 KL V+ + M A A A+I + AGP+TG A +G+ G A+ INA GGV+G Sbjct: 7 KLVTAVSTSVALMGAGHAAAEIQIGIAGPMTGPVAQYGDMQFSGARMAIEQINANGGVMG 66 Query: 64 QKLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPAS 123 ++L DD CDPKQAV VAN L GV+FV GH CS S+ PAS +Y +EG+L ++PAS Sbjct: 67 EELVAVEYDDVCDPKQAVTVANSLVNDGVRFVIGHLCSSSTQPASDIYEDEGILMVTPAS 126 Query: 124 TNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKA 183 T+P++TE+ + VFR G D QG +A +Y + + + VAI+HDK YG+G+A + Sbjct: 127 TSPEITERGYELVFRTIGLDSMQGPVAARY-IASQNPERVAIVHDKQQYGEGIATAVRDT 185 Query: 184 LNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAP 243 L G + ++E TAG+KD+S+LV+KLKQ VD VY GGYH E GL+ RQ L+A Sbjct: 186 LKDAGVEIAMFEGITAGDKDFSSLVTKLKQADVDYVYYGGYHPELGLILRQANSADLDAR 245 Query: 244 IVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEG-YTLYTY 302 + + + + I G A E ++T P + E + V+ F G +P G + L +Y Sbjct: 246 FMGPEGVGNKDINTIAGEAAEGLLVTLPPAFDQKAENQALVKAFEDKGEDPSGPFVLTSY 305 Query: 303 AALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNN 359 A+Q+ AE + A STD +A LR+ ++ T IG + +D GD+ S +V Y W++ Sbjct: 306 TAVQLVAEGIEAAGSTDPFDVAAALREGTFQTPIGTVEYDKAGDMKSFEFVVYEWHS 362 Lambda K H 0.312 0.129 0.366 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: 369 Number of extensions: 24 Number of successful extensions: 3 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: 366 Length of database: 370 Length adjustment: 30 Effective length of query: 336 Effective length of database: 340 Effective search space: 114240 Effective search space used: 114240 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 (21.9 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