Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate SM_b20854 SM_b20854 sugar uptake ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Smeli:SM_b20854 Length = 331 Score = 187 bits (476), Expect = 2e-52 Identities = 119/323 (36%), Positives = 173/323 (53%), Gaps = 14/323 (4%) Query: 13 KSSFSFGRIWDQYGMLVVFAVLFIACAIFVPNFATFINMKG-LGLAISMSGMVACGMLFC 71 K + I ++G L +F VL + +F T N+ L S +G++A GMLF Sbjct: 14 KGFVDYHSIVQRFGTLAIFLVLVAVATWWSDSFLTRGNLLNVLRQVASTAGIMAVGMLFV 73 Query: 72 LASGDFDLSVASVIACAGVTTAVVINLTESLWIGVAAG------LLLGVLCGLVNGFVIA 125 + + DLSV SV+A V T + +G G LL G CGLV G IA Sbjct: 74 ILTRGIDLSVGSVMALGSVLTGYFCAM-----LGYGTGATIFLVLLCGAACGLVTGGFIA 128 Query: 126 KLKINALITTLATMQIVRGLAYIISDGKAVGIEDE--SFFALGYANWFGLPAPIWLTVAC 183 L++ + + +LA M + RGL+ IIS+G+ + + D +F + G G+P P+ L A Sbjct: 129 YLRLPSFVMSLAMMAVARGLSLIISEGRPIPLSDAGAAFSSFGSGFVLGIPQPVILMFAI 188 Query: 184 LIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRM 243 I G++LN T FGR AIG NEEA RL+G+ V R + ++V+SGL++ +AGII ASR Sbjct: 189 YIAGGVVLNFTRFGRVITAIGSNEEAVRLSGIAVPRYIVAVYVISGLLAGLAGIIAASRT 248 Query: 244 TSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQ 303 G IG EL VI+A V+GG SL GG G + + G L++G + N MNL + + Q Sbjct: 249 GVGSAQVGIGAELNVIAAVVIGGASLMGGKGGVINTLLGALVMGIITNIMNLAGVPGYHQ 308 Query: 304 YVVRGLILLAAVIFDRYKQKAKR 326 V G I++ A++ KR Sbjct: 309 QVYMGAIIVVAMLLQYSTGSLKR 331 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: 351 Number of extensions: 24 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: 331 Length adjustment: 28 Effective length of query: 300 Effective length of database: 303 Effective search space: 90900 Effective search space used: 90900 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