Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate H281DRAFT_02330 H281DRAFT_02330 L-arabinose ABC transporter membrane protein
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_02330 Length = 334 Score = 317 bits (811), Expect = 3e-91 Identities = 162/324 (50%), Positives = 230/324 (70%), Gaps = 3/324 (0%) Query: 5 STSGSGAPKSSFSFGRIWD---QYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMS 61 ST + S R WD + G+++VF +LF + VP+F + N++GL L++++ Sbjct: 9 STPAVASAGLSARAARTWDLINKSGIVMVFIILFAVLSFTVPDFLSSRNIQGLLLSVTLI 68 Query: 62 GMVACGMLFCLASGDFDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNG 121 G ++ M+F LA G+ DLSVAS++A AGV + +I +T S+ +GVAAG+L G GLVNG Sbjct: 69 GSISVTMMFVLALGEVDLSVASIVAFAGVVASTLITVTHSVLLGVAAGVLAGGAVGLVNG 128 Query: 122 FVIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTV 181 ++A+ KIN+LI TLA M++VRGLA+I S G AV I +E FF LG ++ G+ PIW + Sbjct: 129 VLVARYKINSLIVTLAMMEVVRGLAFITSSGDAVMISEERFFDLGGGSFLGISYPIWSNI 188 Query: 182 ACLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILAS 241 ++FG LL KT FG+N LA+GGN EAA LAG+PV R KI +FVL GLV+ AG++LAS Sbjct: 189 IGFVVFGFLLKKTVFGKNVLAVGGNSEAALLAGLPVTRIKITVFVLQGLVTGFAGVMLAS 248 Query: 242 RMTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPF 301 RM+ G P TS+G EL VISACVLGGVSL GG+ IS V+ G+LI+G+V++AM+L+N+ F Sbjct: 249 RMSLGDPKTSVGLELGVISACVLGGVSLTGGVATISGVLVGVLIMGSVQDAMSLMNVPTF 308 Query: 302 AQYVVRGLILLAAVIFDRYKQKAK 325 QY++RG ILL AV+FD++++ + Sbjct: 309 YQYLIRGGILLLAVLFDQFRRSKR 332 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: 389 Number of extensions: 22 Number of successful extensions: 1 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: 334 Length adjustment: 28 Effective length of query: 300 Effective length of database: 306 Effective search space: 91800 Effective search space used: 91800 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