Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate WP_086510703.1 BZY95_RS14935 amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A160A0J6 (375 letters) >NCBI__GCF_002151265.1:WP_086510703.1 Length = 401 Score = 128 bits (321), Expect = 3e-34 Identities = 111/378 (29%), Positives = 173/378 (45%), Gaps = 35/378 (9%) Query: 9 SKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGV-N 67 S L A+ VA A +KIG G TGP+ + G+++A++QIN +GG+ Sbjct: 4 SVLAMAIAATSVAFVGAAQAEVKIGFIGGFTGPIESLTPPIYDGARLAVQQINEQGGILG 63 Query: 68 GKQLVAVEYDDAC-DPKQAVAVANKVVN-DGIKFVVGHLCSSSTQPASDIYE-DEGVVMI 124 G+ LV D C D A A+++VN + + +VG LC+ +T A++ GVVM+ Sbjct: 64 GQTLVMPSADTTCSDASAASNAADRMVNTENVTAIVGALCTGATVAAANSAAIPGGVVMV 123 Query: 125 TPAATSPDIT-ARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIAS 183 +PA+T+P +T ++FRT+ D+ QG + D + VAV + YG G+A Sbjct: 124 SPASTAPAVTELDDNDLVFRTVPSDAYQGEILAKLMLDKGFDE-VAVTYVNNDYGRGLAD 182 Query: 184 AVKKTLEDKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELG-LILRQSQE 242 A E G VA G D+ S + L + + + Y G ILRQ+ E Sbjct: 183 AFTAAFEAGGGMVAENLAHEDGRADYRSELGSLSASGAETLVVLAYADGSGQTILRQAYE 242 Query: 243 KGLKAKFMGPEG-VGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSG 301 G +F G +G VG+ I + + EG++ T P S + P A+A +A DP+ Sbjct: 243 SGAFTQFAGADGMVGSSLIEAVGADVLEGMIATRPGS-PELPGTEIFAEAAEAADLDPTA 301 Query: 302 PFVFPSYSAVTVIADAIKAAKSEDA-----------------------GKVAEAIHAG-- 336 F +Y A ++A AI+ S + K E I AG Sbjct: 302 VFAAQAYDAAFLLALAIEQNGSAEREGLSQALRSVSSAPGEVILPGEWEKAVELIAAGEE 361 Query: 337 -TFKTPTGDLSFDKNGDL 353 ++ +G FD+NGD+ Sbjct: 362 INYEGASGSHEFDENGDV 379 Lambda K H 0.314 0.132 0.372 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: 328 Number of extensions: 14 Number of successful extensions: 6 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: 401 Length adjustment: 30 Effective length of query: 345 Effective length of database: 371 Effective search space: 127995 Effective search space used: 127995 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 (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