Align Phthalate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate H281DRAFT_05311 H281DRAFT_05311 MFS transporter, ACS family, hexuronate transporter
Query= uniprot:D8IX31 (418 letters) >FitnessBrowser__Burk376:H281DRAFT_05311 Length = 432 Score = 635 bits (1639), Expect = 0.0 Identities = 298/410 (72%), Positives = 356/410 (86%), Gaps = 2/410 (0%) Query: 4 VRGIRWYMVTLVTLALIVNYLARNTLSVAAPTMMKELDMSTQQYSYIVVAWQICYAVMQP 63 ++GIRW+MV+LV LI+NYLARNTLSVAAPT+MK+L ++T+QY+++VVAWQ+CYA MQP Sbjct: 3 IKGIRWWMVSLVAAGLIINYLARNTLSVAAPTLMKDLHITTEQYAHVVVAWQLCYAFMQP 62 Query: 64 VAGYILDAVGTKIGFGIFALAWSLVCAAAAFATGWQSLAFFRALLGITEAAGIPGGVKAS 123 VAG++LD VGTKIGF FALAWSL CAAAA++TGW+SLAFFR LLGI EAAGIP GVKA+ Sbjct: 63 VAGFLLDTVGTKIGFAAFALAWSLACAAAAWSTGWRSLAFFRGLLGIAEAAGIPAGVKAT 122 Query: 124 TEWFPAKERSVAIGWFNIGSSIGALCAPPLVVWTILHGGWKMSFVVVGALGVIWFVLWML 183 +EWFPAKERSVAIGWFNIGSSIGAL APPLVVW +LHG W+++FV+VG G+IW V+WM+ Sbjct: 123 SEWFPAKERSVAIGWFNIGSSIGALLAPPLVVWALLHGQWQLAFVIVGVAGIIWSVVWMV 182 Query: 184 FYKSPRDQKLLSPEERAYILEGQE--KSPEKVQRESWTKIVRSRNFWSIAIPRFLSEPAW 241 YK PR+QKLL ER YIL GQE S + SW+ ++RSR+FW+I IPR LSEPAW Sbjct: 183 LYKHPRNQKLLGDGERDYILSGQEAKHSDAGAPKRSWSAMLRSRDFWAIGIPRILSEPAW 242 Query: 242 QTFNAWIPLYMATERHMNIKEIAMFAWLPFLAADIGCVLGGYLSPLFHKHLKVSLFTSRK 301 QTFNAWIPLYM TERHMN+KEIA++AW+PFLAADIGCVLGGYLSPLFHK+ KVSLFTSRK Sbjct: 243 QTFNAWIPLYMMTERHMNLKEIALYAWMPFLAADIGCVLGGYLSPLFHKYAKVSLFTSRK 302 Query: 302 LVMLVGSLSMIGPACVGFVDSPYVAIALLSIGGFAHQTLSGALYSITSDVFTKNQVATAT 361 +V +VG+L MIGPACVG V SPYVA+ALL +GGFAHQTLSGALY+ITSD+F KN+VATAT Sbjct: 303 MVFVVGALCMIGPACVGLVASPYVAVALLCVGGFAHQTLSGALYAITSDMFGKNEVATAT 362 Query: 362 GLTGMSGYLGATLFTLLFGILVTQIGYGPLFVLLAAFDLVAVAVVFAIAR 411 G+ GM+GYLGA FT LFG+LVTQ+GY PLFV+LA FD++A AVV +A+ Sbjct: 363 GMGGMAGYLGAAAFTALFGVLVTQVGYSPLFVVLAVFDIIAAAVVCLLAK 412 Lambda K H 0.327 0.138 0.440 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: 792 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 418 Length of database: 432 Length adjustment: 32 Effective length of query: 386 Effective length of database: 400 Effective search space: 154400 Effective search space used: 154400 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: 51 (24.3 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