Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_108401420.1 B9Z44_RS00730 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_003063475.1:WP_108401420.1 Length = 380 Score = 452 bits (1163), Expect = e-132 Identities = 229/374 (61%), Positives = 286/374 (76%), Gaps = 3/374 (0%) Query: 1 MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60 M L KLT VA +AA + +A AQEQVVKIGHVAPVSGA AH GKDNE GAR+AIEELNA+ Sbjct: 1 MHLSFKLTAVATLAALSSLALAQEQVVKIGHVAPVSGAIAHLGKDNEYGARLAIEELNAK 60 Query: 61 GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120 GV I GKK+K ELVAEDDAADPKQGTAAAQKL DAKV+GV+GHLNSGTTIPASK+Y+D G Sbjct: 61 GVNINGKKVKLELVAEDDAADPKQGTAAAQKLVDAKVSGVIGHLNSGTTIPASKIYSDAG 120 Query: 121 IPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQG 180 IP ++ ++TNP T+ GYKT FR++A+D LG L YAV+ LK K++A+IDDRTAYGQG Sbjct: 121 IPQISPSSTNPKYTRQGYKTAFRVVADDVHLGGTLGRYAVNELKGKSIAVIDDRTAYGQG 180 Query: 181 VADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQM 240 VA+ F+K A G +V +FTTDKATDFM ILT +K K PD IF+GGMD GGPM++QM Sbjct: 181 VAEEFEKAVKAAGGNLVGHEFTTDKATDFMPILTTLKGKKPDIIFFGGMDAVGGPMMKQM 240 Query: 241 EQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAE-GGSSLAKMPGGTAWKAKYDAK 299 + LG+ K+ GGDGICT+E+ KLA A G V+CAE GG A G + AK+ + Sbjct: 241 KSLGI-KAKFMGGDGICTNEMIKLAGDAMADGQVVCAEAGGVDGALKKGMDDFSAKFKKR 299 Query: 300 YPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSS-FKGVTSTIAFEPNGEMK 358 + + ++YSPY YDA +++VDAM+RA S +P Y PELAK++ FKGVT TI+F+ G++K Sbjct: 300 FNDDVKLYSPYVYDAVYVMVDAMQRAKSSEPAKYLPELAKTTGFKGVTGTISFDAKGDIK 359 Query: 359 NPAITLYVYKDGKK 372 N A+TLY +K GK+ Sbjct: 360 NGALTLYTFKAGKR 373 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: 521 Number of extensions: 19 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: 380 Length adjustment: 30 Effective length of query: 345 Effective length of database: 350 Effective search space: 120750 Effective search space used: 120750 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