Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate HSERO_RS08270 HSERO_RS08270 amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A160A0J6 (375 letters) >FitnessBrowser__HerbieS:HSERO_RS08270 Length = 373 Score = 450 bits (1158), Expect = e-131 Identities = 228/362 (62%), Positives = 275/362 (75%), Gaps = 7/362 (1%) Query: 12 FAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGVNGKQL 71 FAA AGVA A+T+KI IAGP TG VAQYGDM +G+ AIEQINA GG NG + Sbjct: 17 FAAF--AGVAH----AETVKIAIAGPMTGAVAQYGDMVKAGALTAIEQINAAGGANGNKF 70 Query: 72 VAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAATSP 131 AV DDAC+PKQAVAVANK+V+ GIK+V+GH+CS ST PASDIYE+EGVVMITP+AT+P Sbjct: 71 EAVMMDDACEPKQAVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEGVVMITPSATAP 130 Query: 132 DIT-ARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKTLE 190 +T A+ +K IFRTIG D QGPAA Y+ + +KPK VAVLHDKQ YG+G+AS+VK L+ Sbjct: 131 QLTEAKPHKFIFRTIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQGVASSVKAALD 190 Query: 191 DKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAKFM 250 V V VFEG+NAGD D+S+++ KLK VDFVY+GGYHPE+GLI+RQ++E+G+KA FM Sbjct: 191 AAKVPVVVFEGINAGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQAREQGIKAVFM 250 Query: 251 GPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSYSA 310 GPEGVGN I+ IA +SEG+LVTLP F DPAN AL AF A K DP+GPF P+YS Sbjct: 251 GPEGVGNKDITAIAGPASEGMLVTLPADFAADPANAALVKAFAAAKRDPNGPFQMPAYSG 310 Query: 311 VTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVYEWHFGKPKT 370 V +IADAI AKS D KVA IHA +FKTP G++ +DK GDLK FKFVV+ WH KT Sbjct: 311 VKIIADAIAGAKSTDPEKVAAYIHANSFKTPIGNVEYDKKGDLKSFKFVVFTWHKDASKT 370 Query: 371 EA 372 EA Sbjct: 371 EA 372 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: 559 Number of extensions: 28 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 375 Length of database: 373 Length adjustment: 30 Effective length of query: 345 Effective length of database: 343 Effective search space: 118335 Effective search space used: 118335 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 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