Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate Pf6N2E2_3580 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3580 Length = 378 Score = 344 bits (883), Expect = 2e-99 Identities = 183/365 (50%), Positives = 242/365 (66%), Gaps = 5/365 (1%) Query: 7 LLVAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQKL 66 L +AVAA ++ A+AD+ AGP+TG A FGEQ KG + A IN AGGV G+K+ Sbjct: 11 LALAVAAALGVSAFAQADVKFGVAGPMTGANAAFGEQYMKGAQAAADAINKAGGVNGEKI 70 Query: 67 KLEVGDDACDPKQAVAVANQLAKAG-VKFVAGHFCSGSSIPASQVYAEEGVLQISPASTN 125 L GDDAC+PKQAVAVAN+L V V GHFCS ++IPAS+VY E G++ I+P STN Sbjct: 71 VLVAGDDACEPKQAVAVANRLVDQDKVIGVVGHFCSSNTIPASEVYDEAGIIAITPGSTN 130 Query: 126 PKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALN 185 P++TE+ L +FR+CGRDDQQG +AG Y+++ KGK VA+LHDK YG+GLAD T+ L Sbjct: 131 PQVTERGLSAMFRMCGRDDQQGIVAGDYIVDVLKGKKVAVLHDKDTYGQGLADATKAQLA 190 Query: 186 AGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGL-NAPI 244 G KE +YE T GEKD+SA+V+K++ DVVY GG H EAG L RQ+++QGL + Sbjct: 191 KRGVKEVLYEGLTRGEKDFSAVVTKIRAAGADVVYFGGLHPEAGPLVRQLREQGLKDVKF 250 Query: 245 VSGDALVTNEYWAITGPAG--ENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEGYTLYTY 302 +S D +VT+E G A + MTFG DPR +P++K VE+FRK G EPEGYTLY Y Sbjct: 251 MSDDGIVTDELVTTAGGAQYVDGVYMTFGADPRLLPDSKAVVEEFRKNGTEPEGYTLYAY 310 Query: 303 AALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWN-NGQ 361 A++Q A A S A L+ N TV+GK +D KGD+ YV Y+W+ +G+ Sbjct: 311 ASVQALAAGFNGAKSNKGEDAAKWLKANPVQTVMGKKEWDTKGDLKVSDYVVYQWDKDGK 370 Query: 362 YAQVK 366 Y Q++ Sbjct: 371 YHQLE 375 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: 445 Number of extensions: 17 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: 378 Length adjustment: 30 Effective length of query: 336 Effective length of database: 348 Effective search space: 116928 Effective search space used: 116928 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