Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 171 bits (434), Expect = 2e-47 Identities = 98/296 (33%), Positives = 162/296 (54%) Query: 28 LVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIAC 87 L +L + A+ F T N+ + S+ ++A G+ + +G DLSV + +A Sbjct: 21 LFALGLLCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTLVILTGGLDLSVGANVAM 80 Query: 88 AGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVRGLAY 147 + A V+ T S +GV AGL G L GL NG ++A L+I I T + ++ G+ Y Sbjct: 81 SACVAATVMKATGSTMLGVGAGLGTGALIGLANGLLVAMLRIPPFIATYGMLWVLHGVTY 140 Query: 148 IISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLAIGGNE 207 G+ + +F A+G +G+P P++L + L+ + KTT+G+ AIG N Sbjct: 141 WFMAGETIHGFPPAFRAIGSGYLWGVPIPVYLMLVFLVAGTAMSQKTTYGQEIYAIGANP 200 Query: 208 EAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISACVLGGV 267 AARL+GVPV R ++++++SG ++ IA ++ +R+ S + L I+A ++GG Sbjct: 201 VAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAEGDIGEALTLPAIAAVLIGGT 260 Query: 268 SLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQK 323 SL GG+G++S + G +IL V N MNLL +S Q +V G+I++ AV D +K Sbjct: 261 SLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSANWQPLVTGVIVVLAVFLDTLSRK 316 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: 302 Number of extensions: 19 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: 322 Length adjustment: 28 Effective length of query: 300 Effective length of database: 294 Effective search space: 88200 Effective search space used: 88200 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