Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate 206137 DVU0712 amino acid ABC transporter, periplasmic-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >MicrobesOnline__882:206137 Length = 376 Score = 151 bits (382), Expect = 2e-41 Identities = 112/362 (30%), Positives = 170/362 (46%), Gaps = 19/362 (5%) Query: 9 VVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKK 68 ++AA A AAG V++G + P++G A G+D N + EE+N G I G K Sbjct: 17 LMAATAFAAGP-------VRVGLMCPLTGKWASEGQDMRNIVELLAEEVNKAG-GINGNK 68 Query: 69 IKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAA 128 + EL+ EDD DP+ AAQKL + V V+G S T + +Y++ GI + + Sbjct: 69 V--ELIVEDDGGDPRTAALAAQKLSTSGVTAVIGTYGSAVTEASQNIYDEAGIAQIATGS 126 Query: 129 TNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKT 188 TN LT+ G K R D+ G +A + K VA++ D ++Y +G+AD K Sbjct: 127 TNVRLTEKGLKLFLRTCPRDDEQGR-VAAKVIKNKGYKAVALLHDNSSYAKGLADETKAL 185 Query: 189 ATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNV 248 G K+V T D+ AILT +KA NPD IF+ G P+ G +LRQ ++ NV Sbjct: 186 LDKDGTKIVFYDALTPGERDYTAILTKLKAANPDIIFFTGYYPEVGMLLRQKMEM-KWNV 244 Query: 249 KYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKY---PNQFQ 305 GGD ++ K+A A G + A+ A Y AK+ PN Sbjct: 245 PMMGGDAANNLDLVKIAGKAAAKGYFFLSPPVPQDFDTAEAKAFLAAYKAKHNALPN--S 302 Query: 306 VYSPYTYDATFLIVDAMKRANSVDPKVYTPELAK--SSFKGVTSTIAFEPNGEMKNPAIT 363 V+S DA +IV+A+++ D L ++ G++ I+F G+ Sbjct: 303 VWSVLAGDAFKVIVEAVQKGGKADGAGIATYLKTQLKNYPGLSGQISFNEKGDRVGDLYR 362 Query: 364 LY 365 +Y Sbjct: 363 VY 364 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: 335 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: 376 Length adjustment: 30 Effective length of query: 345 Effective length of database: 346 Effective search space: 119370 Effective search space used: 119370 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