Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate H281DRAFT_04063 H281DRAFT_04063 amino acid/amide ABC transporter substrate-binding protein, HAAT family
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__Burk376:H281DRAFT_04063 Length = 400 Score = 374 bits (960), Expect = e-108 Identities = 189/365 (51%), Positives = 253/365 (69%), Gaps = 4/365 (1%) Query: 11 AAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIK 70 AA+AA+A AS + VVKIGH AP++G AH GKDNENGAR+A+EE+NAQG+TI G KI Sbjct: 35 AAVAASAAPAS-EAIVVKIGHAAPLTGGIAHLGKDNENGARLAVEEINAQGLTIDGHKID 93 Query: 71 FELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATN 130 +L A+DDAADPK GTA AQKL D V VVGHLNSG +IPASK+Y+D I ++ ++TN Sbjct: 94 LQLDAQDDAADPKAGTAVAQKLVDDHVVAVVGHLNSGVSIPASKIYSDASIVQISPSSTN 153 Query: 131 PNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTAT 190 P T+ G+KTT+R++A D G LA YA L K +A++DD TAYG+G+AD F KT Sbjct: 154 PAYTQQGFKTTYRVVATDAQQGPALANYATKALGAKRIAVVDDATAYGKGLADEFAKTVE 213 Query: 191 AKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKY 250 A G K+V + T D+ATDF AILT IK+ +PDAI +GGMD GGP +Q LG+ K Sbjct: 214 ASGAKIVAREATNDRATDFRAILTKIKSVHPDAIMFGGMDATGGPFAKQAAALGI-RAKI 272 Query: 251 FGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310 GGDG+CT ++ +LA A + N++C+E G +L+KM G ++ KY ++ Q+Y+P+ Sbjct: 273 LGGDGVCTDKVGELAGTA--VQNLVCSEAGLALSKMDRGADFEKKYVDRFHTPVQIYAPF 330 Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDG 370 TYDA ++IVDAMKRANS++ + + + GV IAF+ G++K AITLY +KDG Sbjct: 331 TYDAVYVIVDAMKRANSIEAPKVLAAMPSTDYNGVIGRIAFDDKGDLKEGAITLYDFKDG 390 Query: 371 KKTPL 375 KK L Sbjct: 391 KKAVL 395 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: 400 Length adjustment: 30 Effective length of query: 345 Effective length of database: 370 Effective search space: 127650 Effective search space used: 127650 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