Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate GFF4163 PS417_21325 arabinose ABC transporter permease
Query= uniprot:A0A161GM94 (322 letters) >FitnessBrowser__WCS417:GFF4163 Length = 321 Score = 542 bits (1397), Expect = e-159 Identities = 274/305 (89%), Positives = 292/305 (95%) Query: 18 RRFLDDWVMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFD 77 R+FLDDWVMLLAA+ IFVL L IDNFLSPLNMRGLGLAIST GIAACTML+CLASGHFD Sbjct: 17 RKFLDDWVMLLAALSIFVLSALFIDNFLSPLNMRGLGLAISTVGIAACTMLFCLASGHFD 76 Query: 78 LSVGSVIACAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLAT 137 LSVGSVIACAGVVA +V+RDT+SV LG+SAAL MGL+VGLINGIVIAKLR+NALI TLAT Sbjct: 77 LSVGSVIACAGVVAGIVIRDTDSVVLGVSAALAMGLVVGLINGIVIAKLRINALIATLAT 136 Query: 138 MQIVRGLAYIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGR 197 MQIVRGLAYIF+NGKAVGV E FFVFGNGQ+ GVPVPI+IT++CF+FFGWLLNYTTYGR Sbjct: 137 MQIVRGLAYIFSNGKAVGVMDEGFFVFGNGQLLGVPVPIIITVLCFVFFGWLLNYTTYGR 196 Query: 198 NTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTV 257 NTMAIGGNQEAALLAGVNVDRTKIIIFAVHG+IGALAGVILASRMTSGQPMIGQGFELTV Sbjct: 197 NTMAIGGNQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILASRMTSGQPMIGQGFELTV 256 Query: 258 ISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVID 317 ISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAV+ID Sbjct: 257 ISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVIID 316 Query: 318 RLKQR 322 R+KQR Sbjct: 317 RMKQR 321 Lambda K H 0.330 0.144 0.420 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: 455 Number of extensions: 12 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: 322 Length of database: 321 Length adjustment: 28 Effective length of query: 294 Effective length of database: 293 Effective search space: 86142 Effective search space used: 86142 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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