Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate WP_108360184.1 B9Z44_RS12855 amino acid ABC transporter substrate-binding protein
Query= uniprot:Q1MDE9 (367 letters) >NCBI__GCF_003063475.1:WP_108360184.1 Length = 381 Score = 130 bits (326), Expect = 8e-35 Identities = 117/372 (31%), Positives = 159/372 (42%), Gaps = 12/372 (3%) Query: 2 TLKTLTATLVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGIL 61 TLK + A + +LA A I I I L+GP G KNG + AV EIN GGIL Sbjct: 6 TLKAVAAAAIFALAGVAHAQQTIKIANIVELSGPGTTAGTVFKNGVELAVKEINDNGGIL 65 Query: 62 GEKVVLELADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPT 121 G+K+ D P K V DG+ + GPV SG +I VS ++ G + Sbjct: 66 GKKIENYTVDTQTNPGVAKGLTQKAVDDGVFAIFGPVYSG-SIMVSMAESKRGEVPNFTG 124 Query: 122 ATAPDLTKRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKA 181 A +T +G V RT AK++ N K K +A++ +GKG D A Sbjct: 125 GEAASITAQGNPYVFRTAFGQSTSFPKLAKFI--NTKAKTLAVIYVNNDFGKGGRDTL-A 181 Query: 182 TLNAGGITEVVNDAIT-PGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAAN 240 L G T+VV D T G DFSA + K D ++ E L R+L Sbjct: 182 KLLDGSPTKVVADISTDAGQVDFSAAVLKAKQSNADAIFAYTNEEESARLLRELKKQGWT 241 Query: 241 ATIIGGDGLSNTEFWAIGTDAAGGTI--FTNASDATKSPDSKAAADALAAKNIPAEAFTL 298 +IG L+ + + DAA G + DA K A A ++ + Sbjct: 242 KPVIGETTLTGQKVIELAGDAANGAMAHVGLTVDAPNPEMLKFKAKYYQAYGSISDHNGI 301 Query: 299 NAYAAVEVLKAGIEKAGSAEDAEAVATALK----DGKEIPTAIGKVTYGETGDLTSQSFS 354 Y V VLKA IEK G D +AVA AL K+ P I V++ GDL +SF Sbjct: 302 KGYTGVYVLKAAIEKVGKL-DRKAVAQALHGINISAKKNPGVIMDVSFDANGDLDRESFL 360 Query: 355 LYKWEAGKIVAA 366 + ++V A Sbjct: 361 IEVKNGRQVVTA 372 Lambda K H 0.312 0.131 0.362 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: 347 Number of extensions: 23 Number of successful extensions: 4 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: 367 Length of database: 381 Length adjustment: 30 Effective length of query: 337 Effective length of database: 351 Effective search space: 118287 Effective search space used: 118287 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 (21.9 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