Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_011767452.1 AZO_RS18715 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000061505.1:WP_011767452.1 Length = 371 Score = 394 bits (1013), Expect = e-114 Identities = 202/373 (54%), Positives = 257/373 (68%), Gaps = 2/373 (0%) Query: 3 LKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGV 62 +K + +A +A G A AQEQVVKIG VAP++G AH GKD ENG R+A+EE NA+GV Sbjct: 1 MKKSVVALAVMALGIGSAQAQEQVVKIGGVAPLTGTIAHLGKDLENGTRLAVEEANAKGV 60 Query: 63 TIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIP 122 TIGGKK+K E V EDD ADP+ GT AQ+L DA V VVGHLNSGT+IPAS++Y+ GI Sbjct: 61 TIGGKKVKLEFVGEDDQADPRTGTTVAQRLVDAGVKAVVGHLNSGTSIPASRIYDQAGIA 120 Query: 123 HVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVA 182 VT A+TNP LT+ GYK FR IAND G+ L +A L K +AIIDDRTAYGQG+A Sbjct: 121 QVTPASTNPKLTQQGYKGVFRTIANDVQQGSVLGKFAATNLGAKKIAIIDDRTAYGQGLA 180 Query: 183 DVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQ 242 D +K A A G ++V +FTTDKATDF AILT I+A NPD IF+GGMD Q GPMLRQM+Q Sbjct: 181 DETEKGAKASGAQIVAREFTTDKATDFNAILTKIRATNPDVIFFGGMDAQAGPMLRQMKQ 240 Query: 243 LGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPN 302 LG+ + K+ GDG C+ E+ KLA A + N C+ G + KMPGG ++ +Y +Y Sbjct: 241 LGI-SAKFLTGDGGCSPEMIKLAGDAIS-ANAYCSMAGLPIEKMPGGADFRERYKKRYNA 298 Query: 303 QFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAI 362 Q+YSPY YDA I+ AM++A S +P Y PEL K +F GV I+F+ G++K +I Sbjct: 299 DVQIYSPYAYDAATAIITAMQKAGSAEPAKYIPELKKVNFPGVIGNISFDDKGDLKEGSI 358 Query: 363 TLYVYKDGKKTPL 375 T+Y +K+G PL Sbjct: 359 TVYQFKNGDWAPL 371 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: 453 Number of extensions: 12 Number of successful extensions: 4 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: 371 Length adjustment: 30 Effective length of query: 345 Effective length of database: 341 Effective search space: 117645 Effective search space used: 117645 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