Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate RR42_RS16980 RR42_RS16980 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__Cup4G11:RR42_RS16980 Length = 401 Score = 405 bits (1042), Expect = e-118 Identities = 203/365 (55%), Positives = 260/365 (71%), Gaps = 3/365 (0%) Query: 11 AAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIK 70 A AA A A + + VVKIGH AP++G AH GKDNENGAR+A+EE+N G+ I GKKIK Sbjct: 35 APAAATAPAAGSGDVVVKIGHAAPLTGGIAHLGKDNENGARLAVEEVNKTGLEINGKKIK 94 Query: 71 FELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATN 130 ELV EDDA DPK GTA AQKL DAKV VVGHLNSG +IPASK+Y+D GI ++ ++TN Sbjct: 95 LELVGEDDAGDPKTGTAVAQKLVDAKVVAVVGHLNSGVSIPASKIYSDAGIVQISPSSTN 154 Query: 131 PNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTAT 190 P+ TK G+KTTFR++A D G LA YA +L K+VAI+DD TAYG+G+AD F+KTA Sbjct: 155 PDYTKQGFKTTFRVVATDAQQGPALANYATKSLHAKSVAIVDDATAYGKGLADEFEKTAK 214 Query: 191 AKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKY 250 A G+ VV + T DKATDF AILT IK K PD I YGGMD GGP +Q ++LG+ + K Sbjct: 215 ASGVNVVAREATNDKATDFKAILTKIKGKKPDVIMYGGMDATGGPFAKQAKELGISS-KI 273 Query: 251 FGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310 GGDG+CT ++A+LA A + N+IC+E G +L+KM G + +Y A++ Q+Y+P+ Sbjct: 274 VGGDGVCTDKVAELAGDA--VSNIICSEAGLALSKMEQGADFDKRYQARFNAPVQIYAPF 331 Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDG 370 TYDA +IVDAMKRANS +P E+ K+++KG+ IAF+ G+MK ITLY YKD Sbjct: 332 TYDAVMVIVDAMKRANSTEPAAILAEMPKTNYKGLIGNIAFDEKGDMKEGTITLYEYKDK 391 Query: 371 KKTPL 375 KKT L Sbjct: 392 KKTVL 396 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: 447 Number of extensions: 12 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: 375 Length of database: 401 Length adjustment: 30 Effective length of query: 345 Effective length of database: 371 Effective search space: 127995 Effective search space used: 127995 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