Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_090443360.1 BLS63_RS09655 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_900100495.1:WP_090443360.1 Length = 375 Score = 576 bits (1484), Expect = e-169 Identities = 274/371 (73%), Positives = 329/371 (88%) Query: 1 MKKGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQI 60 M K T+++S+LFAAMA+AG ASYS+AAD IKI +AGPVTG VAQYG+MQ GA MAIEQI Sbjct: 1 MNKATKQISKLFAAMAMAGVASYSLAADAIKIGMAGPVTGAVAQYGEMQFIGAKMAIEQI 60 Query: 61 NKAGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEG 120 NKAGGVNGA LEGV+YDDACDPKQAVAVANK+VND VKFV+GH+CSSSTQPA+DIYEDEG Sbjct: 61 NKAGGVNGAMLEGVVYDDACDPKQAVAVANKIVNDEVKFVIGHLCSSSTQPASDIYEDEG 120 Query: 121 VLMITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEG 180 +LM++P++T+P+IT+RGY+LIFRTIGLD++QGP AG FIA+ K K +AVLHDKQQYGEG Sbjct: 121 ILMVSPASTSPDITARGYELIFRTIGLDSLQGPTAGNFIADHIKPKNVAVLHDKQQYGEG 180 Query: 181 IATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQA 240 IAT VK+T+E G+KVA+FEG+NAGDKDF+A+I+KLK+AGV FVY+GGYHPE+GLLLRQ+ Sbjct: 181 IATAVKQTLEGKGVKVALFEGINAGDKDFSAMIAKLKQAGVDFVYYGGYHPELGLLLRQS 240 Query: 241 KQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPS 300 + GL R+MGPEGVGN EI+AIAG ASEG+L TLP++F+QDPKN+AL++AFKAKN+DPS Sbjct: 241 AEKGLKVRYMGPEGVGNKEISAIAGPASEGLLVTLPKSFDQDPKNQALVEAFKAKNEDPS 300 Query: 301 GIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTV 360 G FV PAY+AV VIA+ IEKAG D KVA ALRAN+FETPTG L FDEKGDLK+F F V Sbjct: 301 GPFVFPAYAAVQVIAESIEKAGSTDTAKVAAALRANSFETPTGTLAFDEKGDLKDFSFVV 360 Query: 361 YEWHKDATRTE 371 YEWH+D T+TE Sbjct: 361 YEWHQDGTKTE 371 Lambda K H 0.316 0.133 0.377 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: 572 Number of extensions: 14 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: 373 Length of database: 375 Length adjustment: 30 Effective length of query: 343 Effective length of database: 345 Effective search space: 118335 Effective search space used: 118335 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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