Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 171 bits (434), Expect = 2e-47 Identities = 101/304 (33%), Positives = 165/304 (54%), Gaps = 7/304 (2%) Query: 29 VVFAVLFIACAIFVPNFATFINMKGLGLAISMSG---MVACGMLFCLASGDFDLSVASVI 85 ++ A + + A+ F FI L + + ++A G + + + DLSVA+ + Sbjct: 12 LLIAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAANL 71 Query: 86 ACAGVTTAVVINLTESLWIGV--AAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVR 143 A G+ ++V L I V A + LG L G+ NG ++ KL+I ++ TL TM I R Sbjct: 72 ALTGMVVSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTIFR 131 Query: 144 GLAYIISDGKAVGIEDES--FFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTL 201 G+ ++ISDGK V + S F A A GLP W+ + +I+F +++ +TT GR Sbjct: 132 GIIFLISDGKWVNSHEMSPAFKAFPRAELLGLPVLSWIAILAVILFTIVMTRTTLGRAFY 191 Query: 202 AIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISA 261 A GGN AA AG+ V +T+ F +SG ++ + G + SR + G+EL V++A Sbjct: 192 AAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGFELDVVAA 251 Query: 262 CVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYK 321 CV+GGVS+ GG+G + + G L LG ++NA+ +++ISPF Q + G ++ AV + Sbjct: 252 CVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQLAISGGAIIIAVALNAQA 311 Query: 322 QKAK 325 + K Sbjct: 312 NRKK 315 Lambda K H 0.327 0.141 0.414 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: 297 Number of extensions: 22 Number of successful extensions: 2 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: 328 Length of database: 327 Length adjustment: 28 Effective length of query: 300 Effective length of database: 299 Effective search space: 89700 Effective search space used: 89700 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 (21.7 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