Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate PP_1141 PP_1141 branched-chain amino acids ABC transporter - periplasmic leucine binding subunit
Query= uniprot:A0A160A0J6 (375 letters) >lcl|FitnessBrowser__Putida:PP_1141 PP_1141 branched-chain amino acids ABC transporter - periplasmic leucine binding subunit Length = 371 Score = 639 bits (1647), Expect = 0.0 Identities = 317/369 (85%), Positives = 338/369 (91%) Query: 7 QISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGV 66 +ISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPV QYGDMQF G+K AI+ INA GGV Sbjct: 3 KISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVTQYGDMQFIGAKQAIKDINAAGGV 62 Query: 67 NGKQLVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITP 126 +GK L A EYDDACDPKQAVAVANKVVNDG+KFVVGHLCSSSTQPASDIYEDEGV+MITP Sbjct: 63 DGKMLEAKEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIMITP 122 Query: 127 AATSPDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVK 186 AATSP+ITARGYK+IFRTIGLDSAQGPAAGNYIADHVKPK+VAVLHDKQQYGEGIA+AVK Sbjct: 123 AATSPEITARGYKLIFRTIGLDSAQGPAAGNYIADHVKPKVVAVLHDKQQYGEGIATAVK 182 Query: 187 KTLEDKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLK 246 +TLE KG KVAVFEG+NAGDKDFSS+I KLKQ NVDFVYYGGYHPELGLILRQ+QEKGLK Sbjct: 183 QTLESKGTKVAVFEGLNAGDKDFSSIIQKLKQNNVDFVYYGGYHPELGLILRQAQEKGLK 242 Query: 247 AKFMGPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFP 306 AKFMGPEGVGNDSISQIA+ +SEGLLVTLPKSFD DPAN + DA KA +DPSGPFVFP Sbjct: 243 AKFMGPEGVGNDSISQIAQNASEGLLVTLPKSFDADPANKKIVDAIKADGKDPSGPFVFP 302 Query: 307 SYSAVTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVYEWHFG 366 +YSAV +IA IK A S+D KVAEAIH GTFKTPTGDLSFD GDLKDFKFVVYEWHFG Sbjct: 303 AYSAVELIAQGIKKAGSDDTDKVAEAIHKGTFKTPTGDLSFDDKGDLKDFKFVVYEWHFG 362 Query: 367 KPKTEASPQ 375 KPKTE SPQ Sbjct: 363 KPKTEVSPQ 371 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: 662 Number of extensions: 28 Number of successful extensions: 1 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: 371 Length adjustment: 30 Effective length of query: 345 Effective length of database: 341 Effective search space: 117645 Effective search space used: 117645 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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