Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_013092422.1 BC1002_RS23155 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000092885.1:WP_013092422.1 Length = 381 Score = 392 bits (1006), Expect = e-113 Identities = 194/366 (53%), Positives = 259/366 (70%), Gaps = 4/366 (1%) Query: 10 VAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKI 69 V A A AG A+A +QVVKIGHV P++G AH GKDNENGAR+AIEE+NA+G+TI G+K+ Sbjct: 15 VVAFAGIAGTANA-DQVVKIGHVGPLTGGSAHLGKDNENGARLAIEEINAKGLTIDGQKV 73 Query: 70 KFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAAT 129 L A+DDA DP+Q T AQKL D KV VVGHLNSG +IPASK+Y+D GI ++ ++T Sbjct: 74 TLVLDAQDDAGDPRQATQVAQKLVDDKVVAVVGHLNSGASIPASKIYSDAGIVQISPSST 133 Query: 130 NPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTA 189 NP T+ G+KTT+R++A D G LA YA TL +KTVA++DD TAYGQG+A+ F+KTA Sbjct: 134 NPAYTQQGFKTTYRVVATDAQQGPALAAYAAKTLNVKTVAVVDDSTAYGQGLANEFEKTA 193 Query: 190 TAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVK 249 + G+KVV T DKA DF AILT IK +NPDAI YGGMD GGP +Q QLG+ K Sbjct: 194 KSLGLKVVSHDATNDKAVDFRAILTKIKGENPDAIMYGGMDATGGPFAKQARQLGL-RAK 252 Query: 250 YFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSP 309 GDG+CT +A LA A GNV+C++ G ++ +M GG + AKY ++ + + +P Sbjct: 253 MLSGDGVCTESLADLAGPA--AGNVVCSQAGMAVERMNGGAQFAAKYTKRFGHPIEFDAP 310 Query: 310 YTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKD 369 +TYDA +++VDAMKRANS DP +++ +++KGVT F+ G++++ I+LY YKD Sbjct: 311 FTYDAVYIVVDAMKRANSTDPAKVLAKVSGTNYKGVTGETTFDAKGDLQHGVISLYDYKD 370 Query: 370 GKKTPL 375 GKKT L Sbjct: 371 GKKTLL 376 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: 487 Number of extensions: 16 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: 381 Length adjustment: 30 Effective length of query: 345 Effective length of database: 351 Effective search space: 121095 Effective search space used: 121095 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