Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 187 bits (474), Expect = 4e-52 Identities = 104/323 (32%), Positives = 180/323 (55%), Gaps = 6/323 (1%) Query: 7 SGSGAPKSSFSFGRIWDQ-----YGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMS 61 + +GAP + + GR+ Q GML V +L I ++ NFA + N+ + S++ Sbjct: 6 ASTGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASIN 65 Query: 62 GMVACGMLFCLASGDFDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNG 121 ++A GM F + +G DLSV S+++ + V +V + + + V A LL G+L G+VNG Sbjct: 66 MVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNG 125 Query: 122 FVIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTV 181 ++A +K+ I TL T+ VRGLA ++ + + D F +G G+P + + Sbjct: 126 ALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAF 185 Query: 182 ACLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILAS 241 A + + +L +T G A+GGN EAARL+G+ V + ++ +SGL++ + G++ ++ Sbjct: 186 AVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSA 245 Query: 242 RMTSGQPM-TSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISP 300 R+ + + YEL I+A +LGG S GG G I + G LI+ + N + LL +S Sbjct: 246 RLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSD 305 Query: 301 FAQYVVRGLILLAAVIFDRYKQK 323 QY+++GL+++ AV D Y++K Sbjct: 306 IWQYIIKGLVIIGAVALDSYRRK 328 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: 337 Number of extensions: 28 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: 328 Length of database: 333 Length adjustment: 28 Effective length of query: 300 Effective length of database: 305 Effective search space: 91500 Effective search space used: 91500 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: 49 (23.5 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