Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate 206137 DVU0712 amino acid ABC transporter, periplasmic-binding protein
Query= uniprot:Q1MDE9 (367 letters) >MicrobesOnline__882:206137 Length = 376 Score = 209 bits (533), Expect = 7e-59 Identities = 126/357 (35%), Positives = 197/357 (55%), Gaps = 11/357 (3%) Query: 6 LTATLVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGILGEKV 65 +T+ L+A+ AFA + +GL+ PLTG A+ G ++N + +E+NK GGI G KV Sbjct: 13 VTSLLMAATAFAA---GPVRVGLMCPLTGKWASEGQDMRNIVELLAEEVNKAGGINGNKV 69 Query: 66 VLELADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPTATAP 125 L + DD G+P+ AA K+ G+ V+G S V ++ E G+ + +T Sbjct: 70 ELIVEDDGGDPRTAALAAQKLSTSGVTAVIGTYGSAVTEASQNIYDEAGIAQIATGSTNV 129 Query: 126 DLTKRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKATLNA 185 LT++GL LRTC RDD+Q VAAK V+KN K VA+++D +Y KGLAD KA L+ Sbjct: 130 RLTEKGLKLFLRTCPRDDEQGRVAAK-VIKNKGYKAVALLHDNSSYAKGLADETKALLDK 188 Query: 186 GGITEVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANATIIG 245 G V DA+TPG++D++A+ T++K+ D+++F GY+PE G+L RQ ++ N ++G Sbjct: 189 DGTKIVFYDALTPGERDYTAILTKLKAANPDIIFFTGYYPEVGMLLRQKMEMKWNVPMMG 248 Query: 246 GDGLSNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADALAA-----KNIPAEAFTLNA 300 GD +N + I AA F + + D+ A LAA +P +++ A Sbjct: 249 GDAANNLDLVKIAGKAAAKGYFFLSPPVPQDFDTAEAKAFLAAYKAKHNALPNSVWSVLA 308 Query: 301 YAAVEVLKAGIEKAGSAEDAEAVATALKDG-KEIPTAIGKVTYGETGDLTSQSFSLY 356 A +V+ ++K G A D +AT LK K P G++++ E GD + +Y Sbjct: 309 GDAFKVIVEAVQKGGKA-DGAGIATYLKTQLKNYPGLSGQISFNEKGDRVGDLYRVY 364 Lambda K H 0.312 0.131 0.362 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: 364 Number of extensions: 21 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: 367 Length of database: 376 Length adjustment: 30 Effective length of query: 337 Effective length of database: 346 Effective search space: 116602 Effective search space used: 116602 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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