Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BPHYT_RS15610 BPHYT_RS15610 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__BFirm:BPHYT_RS15610 Length = 399 Score = 363 bits (932), Expect = e-105 Identities = 179/365 (49%), Positives = 245/365 (67%), Gaps = 3/365 (0%) Query: 11 AAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIK 70 A+ A A +++ VVKIGH AP++G AH GKDNENGAR+AI+E+N QG+TI G KI+ Sbjct: 33 ASAATVAAAPASEATVVKIGHAAPLTGPIAHLGKDNENGARLAIDEINTQGLTIDGHKIQ 92 Query: 71 FELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATN 130 EL A+DDAADPK GTA A+K D V VVGHLNSG +IPASK+Y+D GI ++ ++TN Sbjct: 93 LELDAQDDAADPKTGTAVAEKFVDDHVVAVVGHLNSGVSIPASKIYSDAGILEISPSSTN 152 Query: 131 PNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTAT 190 P T+ G+KTT+R++A D G LA YA L K +AI+DD + YG+G+AD F KT Sbjct: 153 PGYTQQGFKTTYRVVATDAQQGPALANYATKVLNAKRIAIVDDSSVYGKGLADEFAKTVQ 212 Query: 191 AKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKY 250 A G K+V + T D+AT+F A+L IK PD I +GGMD GGP +Q LG+ K Sbjct: 213 ASGAKIVARESTNDRATEFQAVLRKIKRVQPDVIMFGGMDATGGPFTKQAAALGI-RAKI 271 Query: 251 FGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310 GGDG+CT ++ +LA A + N++C+E G +L+KM G ++ KY ++ Q+Y+P+ Sbjct: 272 LGGDGVCTDKVGELAGTA--VQNLVCSEAGLALSKMDKGADFEKKYVDRFHTPVQIYAPF 329 Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDG 370 TYDA ++IVDAMKRANS++ + + + GV IAF+ G++K AITLY +KDG Sbjct: 330 TYDAVYVIVDAMKRANSIEAPKVLAAMPSTDYNGVIGHIAFDDKGDLKEGAITLYDFKDG 389 Query: 371 KKTPL 375 KK L Sbjct: 390 KKAVL 394 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: 445 Number of extensions: 14 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: 399 Length adjustment: 30 Effective length of query: 345 Effective length of database: 369 Effective search space: 127305 Effective search space used: 127305 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