Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_072908499.1 BUB13_RS10005 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_900142125.1:WP_072908499.1 Length = 374 Score = 135 bits (339), Expect = 2e-36 Identities = 109/373 (29%), Positives = 167/373 (44%), Gaps = 12/373 (3%) Query: 3 LKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGV 62 +K ++A +A A A +K+G AP++G+ A+ G+ +NGAR+ E+LNA+G Sbjct: 1 MKFGKIMLALVAIALIAVPAFADTLKVGVQAPITGSYANEGQGIDNGARLLAEQLNAKGG 60 Query: 63 TIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIP 122 +G E++ DD A+ L + V VVG S A K Y G+ Sbjct: 61 VLGKN---IEVITCDDQGTAMASAICAKDLVNKGVKLVVGSYTSTAAEAAQKTYYKAGVL 117 Query: 123 HVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVA 182 T T +LT+ GY T R ++A +A Y VD K K + +I D + Y G+A Sbjct: 118 Q-TSDGTADSLTEKGYWTFLRNSFPNSAEAEFVAKYLVDVKKYKRIVVISDFSTYADGLA 176 Query: 183 DVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQ 242 + + G VV + +F +LT IK+KNPDAIF+ G GG + Q Sbjct: 177 NAAEAAIKKMGGNVVSRDKIKADSQNFTPVLTNIKSKNPDAIFFAGYYTDGGLLRAQQVA 236 Query: 243 LGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPN 302 LG+ ++GGD + KL AG+ G I + P ++ A Y KY Sbjct: 237 LGI-KADFYGGDANDNPDFVKL-AGSAAEGAFIVNVPEPAALPTPIAKSFIADYQKKYGE 294 Query: 303 Q-FQVYSPYTYDATFLIVDAMKRANSVDPKV---YTPELAKSSFKGVTSTIAFEPNGEMK 358 ++ D I+ A ++ + D K Y +A+ G+T IAF +G K Sbjct: 295 MPPSIWGLMNIDGMRAILHAFEQNGNFDTKAAADYLHNMAQ-PLDGITGPIAFAKDGNRK 353 Query: 359 NPA-ITLYVYKDG 370 A + + KDG Sbjct: 354 GGAYVVKRIQKDG 366 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: 360 Number of extensions: 18 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: 374 Length adjustment: 30 Effective length of query: 345 Effective length of database: 344 Effective search space: 118680 Effective search space used: 118680 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 24 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