Align Putative amino-acid binding periplasmic protein (characterized, see rationale)
to candidate WP_043529788.1 JH15_RS09820 ABC transporter substrate-binding protein
Query= uniprot:Q92PA9 (260 letters) >NCBI__GCF_000759345.1:WP_043529788.1 Length = 256 Score = 173 bits (438), Expect = 4e-48 Identities = 96/246 (39%), Positives = 140/246 (56%), Gaps = 9/246 (3%) Query: 17 VLMAGVAMAEG-------EKVVIGTEGAYPPFNNLESDGTLTGFDIDIAKALCEEMKAEC 69 V + G A+A G E+V IG + Y P +G LTGFDID+ ALC+E+ EC Sbjct: 7 VTLLGAAIAAGSAQARDYEEVRIGVDVPYEPMEYRTPEGELTGFDIDLGNALCDEIGVEC 66 Query: 70 TFVTQDWDGIIPALIAKKFDAIVASMSITEERKQQVDFTNKYYNTPPAIVVPKDSPITEA 129 ++ Q WDGIIP L+++K+DAI++SM+I +ER++QV F++ Y+ P A P D+ I Sbjct: 67 EWIVQGWDGIIPGLMSRKYDAIMSSMTINDERREQVLFSDPYFTPPSAWFAPADTDIEMP 126 Query: 130 TAAALSGKALGAQGSTTHSNYAEAHMKE-SEVKLYPTADEYKLDLANGRIDAAIDDVVVL 188 L GK +G Q T NY + + ++V Y TAD+ LD+ +GR+D D V Sbjct: 127 YPQTLEGKTIGVQRGTLQDNYVTDNFGDVADVNRYATADDMVLDMDSGRLDILFLDFPVG 186 Query: 189 SEWLKTEDGACCKLLGTLPIDP-VINGEGAGIAIRKGDDALREKLNKAIEAIRANGKYKQ 247 L + K++G + +P G+G GIA RK D+AL EK N A+ +R NG Y + Sbjct: 187 KATLLDSEEGNYKVVGEMITEPKEYFGDGFGIAFRKRDEALAEKFNDALATLRDNGTYDE 246 Query: 248 INEKYF 253 I +YF Sbjct: 247 IYNRYF 252 Lambda K H 0.315 0.132 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: 196 Number of extensions: 12 Number of successful extensions: 3 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: 260 Length of database: 256 Length adjustment: 24 Effective length of query: 236 Effective length of database: 232 Effective search space: 54752 Effective search space used: 54752 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: 47 (22.7 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