Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate H281DRAFT_04148 H281DRAFT_04148 monosaccharide ABC transporter membrane protein, CUT2 family
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_04148 Length = 335 Score = 198 bits (503), Expect = 2e-55 Identities = 118/327 (36%), Positives = 190/327 (58%), Gaps = 9/327 (2%) Query: 2 SSVSTSGSGAPKSSFSFGRIWDQYGMLVVFAVLFIACAIFV---PNFATFINMKGLGLAI 58 S+VS+ GAP F++ + + + F L + C + V +F + N++ + + Sbjct: 13 STVSSDTPGAPVR-FTWAAL-KRSTLFYPFIGLLVVCIVMVFASDSFLSGANIENVLRQV 70 Query: 59 SMSGMVACGMLFCLASGDFDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGL 118 S++ ++A GM + +G DLSV SV+A AG A ++ + +A G+ +G+ G Sbjct: 71 SINAIIAVGMTCVILTGGIDLSVGSVMALAGTLAAGLMVAGMNALAALAVGVAVGLGFGA 130 Query: 119 VNGFVIAKLKINALITTLATMQIVRGLAYIISDGKAV-GIED-ESFFALGYANWFGLPAP 176 NGF +A + +I TLATM I RGLA I + G + G+ D SFF G G+ AP Sbjct: 131 ANGFFVAFAGMPPIIVTLATMGIARGLALIYTGGYPIDGLPDWVSFFGSGKI--LGIQAP 188 Query: 177 IWLTVACLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAG 236 + + +I +LL + FGR AIGGNE+A RL+GV V R K+I++ ++GL S+ A Sbjct: 189 VVIMAVIYVIAWVLLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSSFAA 248 Query: 237 IILASRMTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLL 296 I+L +R+ SGQP +G+EL I+A V+GG S+ GG G I + G L+LG + N +N++ Sbjct: 249 IVLTARLMSGQPNAGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMV 308 Query: 297 NISPFAQYVVRGLILLAAVIFDRYKQK 323 ++P+ Q V++G I+L A+ R ++K Sbjct: 309 GVNPYVQNVIKGGIILLAIYISRDRRK 335 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: 366 Number of extensions: 24 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: 335 Length adjustment: 28 Effective length of query: 300 Effective length of database: 307 Effective search space: 92100 Effective search space used: 92100 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