Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate RR42_RS16980 RR42_RS16980 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__Cup4G11:RR42_RS16980 Length = 401 Score = 219 bits (557), Expect = 1e-61 Identities = 130/353 (36%), Positives = 194/353 (54%), Gaps = 5/353 (1%) Query: 12 AATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAG-GVLGQKLKLEV 70 AATA A + + A P+TG A G+ + G AV ++N G + G+K+KLE+ Sbjct: 38 AATAPAAGSGDVVVKIGHAAPLTGGIAHLGKDNENGARLAVEEVNKTGLEINGKKIKLEL 97 Query: 71 --GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTNPKL 128 DDA DPK AVA +L A V V GH SG SIPAS++Y++ G++QISP+STNP Sbjct: 98 VGEDDAGDPKTGTAVAQKLVDAKVVAVVGHLNSGVSIPASKIYSDAGIVQISPSSTNPDY 157 Query: 129 TEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALNAGG 188 T+Q K FRV D QQG Y ++ K+VAI+ D +AYGKGLADE +K A G Sbjct: 158 TKQGFKTTFRVVATDAQQGPALANYATKSLHAKSVAIVDDATAYGKGLADEFEKTAKASG 217 Query: 189 QKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPIVSGD 248 EA D+ A+++K+K + DV+ GG G A+Q K+ G+++ IV GD Sbjct: 218 VNVVAREATNDKATDFKAILTKIKGKKPDVIMYGGMDATGGPFAKQAKELGISSKIVGGD 277 Query: 249 ALVTNEYWAITGPAGENTMMT-FGPDPREMPEAKEAVEKFRKAGYEP-EGYTLYTYAALQ 306 + T++ + G A N + + G +M + + ++++ P + Y +TY A+ Sbjct: 278 GVCTDKVAELAGDAVSNIICSEAGLALSKMEQGADFDKRYQARFNAPVQIYAPFTYDAVM 337 Query: 307 IWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNN 359 + +A K+ANST+ A I + K +Y +IG I FD KGD+ Y + + Sbjct: 338 VIVDAMKRANSTEPAAILAEMPKTNYKGLIGNIAFDEKGDMKEGTITLYEYKD 390 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: 426 Number of extensions: 21 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: 401 Length adjustment: 30 Effective length of query: 336 Effective length of database: 371 Effective search space: 124656 Effective search space used: 124656 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: 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