Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate GFF1279 Psest_1312 ABC-type branched-chain amino acid transport systems, periplasmic component
Query= uniprot:A0A160A0J6 (375 letters) >FitnessBrowser__psRCH2:GFF1279 Length = 372 Score = 564 bits (1454), Expect = e-165 Identities = 275/370 (74%), Positives = 315/370 (85%) Query: 3 KATKQISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINA 62 K +++SK+F AM L G AS++ AADTI+IG+AGP TGPVAQYGDMQF G++MAIEQIN Sbjct: 2 KTKQRLSKIFLAMALTGAASYTLAADTIRIGLAGPVTGPVAQYGDMQFIGAEMAIEQINK 61 Query: 63 KGGVNGKQLVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVV 122 GGVNG QL V YDDACDPKQAVAVANK+VND +KFVVGHLCSSSTQPASDIYEDEG++ Sbjct: 62 AGGVNGAQLKGVRYDDACDPKQAVAVANKIVNDNVKFVVGHLCSSSTQPASDIYEDEGIL 121 Query: 123 MITPAATSPDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIA 182 MIT A+TSPDIT+RGY++IFRTIGLDS QGP AGN+IADHVKPK VAV+HDKQQYGEGIA Sbjct: 122 MITAASTSPDITSRGYELIFRTIGLDSLQGPTAGNFIADHVKPKNVAVIHDKQQYGEGIA 181 Query: 183 SAVKKTLEDKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQE 242 +AVK+TLE K +KV +FEG+NAGDKDFSS+IAKLK+ VDFVYYGGYHPELGL+LRQS+E Sbjct: 182 TAVKQTLEGKNIKVGLFEGINAGDKDFSSLIAKLKREGVDFVYYGGYHPELGLLLRQSKE 241 Query: 243 KGLKAKFMGPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGP 302 KGL +FMGPEGVGN IS IA +SEG+ VTLPKSFDQDP N L D FKAKK+DPSGP Sbjct: 242 KGLNVRFMGPEGVGNSEISAIAGPASEGMYVTLPKSFDQDPRNKELVDGFKAKKQDPSGP 301 Query: 303 FVFPSYSAVTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVYE 362 FVFP+Y+AV VIA+ I+ A S D KVAEA+ + TF TPTG LSFD+ GDLKDF FVVYE Sbjct: 302 FVFPAYAAVQVIAEGIEKAGSTDTDKVAEALRSNTFDTPTGMLSFDEKGDLKDFNFVVYE 361 Query: 363 WHFGKPKTEA 372 WH KTEA Sbjct: 362 WHQDGTKTEA 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: 571 Number of extensions: 24 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: 372 Length adjustment: 30 Effective length of query: 345 Effective length of database: 342 Effective search space: 117990 Effective search space used: 117990 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