Align Phthalate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate AZOBR_RS23835 AZOBR_RS23835 hexuronate transporter ExuT
Query= uniprot:D8IX31 (418 letters) >FitnessBrowser__azobra:AZOBR_RS23835 Length = 428 Score = 462 bits (1189), Expect = e-135 Identities = 216/409 (52%), Positives = 288/409 (70%), Gaps = 2/409 (0%) Query: 1 MKYVRGIRWYMVTLVTLALIVNYLARNTLSVAAPTMMKELDMSTQQYSYIVVAWQICYAV 60 MK VRG+RW ++ L+ L I+NY+ RNTL + AP + +EL +T+QYSYIV +Q+CY++ Sbjct: 1 MKIVRGLRWKVLALIMLGTIINYIDRNTLGILAPMLKEELHFTTEQYSYIVSVFQLCYSL 60 Query: 61 MQPVAGYILDAVGTKIGFGIFALAWSLVCAAAAFATGWQSLAFFRALLGITEAAGIPGGV 120 MQP+AGY+ D +G K G+ +FA W A AF+ GWQS+AFFR LLGI+EAA +P G Sbjct: 61 MQPIAGYVTDLIGLKFGYAMFAFVWGSAAALHAFSGGWQSMAFFRGLLGISEAAAMPSGA 120 Query: 121 KASTEWFPAKERSVAIGWFNIGSSIGALCAPPLVVWTILHGGWKMSFVVVGALGVIWFVL 180 K + WFPAKERS+A GWFN GSS+GA+ APPLV+W + W+++FVV G LGV +L Sbjct: 121 KTAALWFPAKERSIATGWFNTGSSVGAMIAPPLVIWLSVTWSWQVAFVVTGMLGVGLSML 180 Query: 181 WMLFYKSPRDQKLLSPEERAYILEGQEKSPEKVQRESWTKIVRSRNFWSIAIPRFLSEPA 240 W+ Y++P + L+ EE AYIL+GQE+ ++ + S ++V R FW IA RFL+EPA Sbjct: 181 WLALYRNPENHPRLTKEEHAYILDGQEQ--VQLPKPSMKRVVTMRKFWGIAAARFLTEPA 238 Query: 241 WQTFNAWIPLYMATERHMNIKEIAMFAWLPFLAADIGCVLGGYLSPLFHKHLKVSLFTSR 300 WQTF+ WIPLYM + R M+IK+ A+FAWLPFL ADIGCVL GYLSP F K ++SL SR Sbjct: 239 WQTFSFWIPLYMVSTRGMDIKQFALFAWLPFLFADIGCVLSGYLSPFFAKRFRMSLVNSR 298 Query: 301 KLVMLVGSLSMIGPACVGFVDSPYVAIALLSIGGFAHQTLSGALYSITSDVFTKNQVATA 360 + +G++ MIGPA +G SP AI L S+G FAHQ LS LY++ +D F K VATA Sbjct: 299 IAGIGIGAVCMIGPALIGLTSSPITAIFLFSVGAFAHQMLSSLLYALVTDTFEKQDVATA 358 Query: 361 TGLTGMSGYLGATLFTLLFGILVTQIGYGPLFVLLAAFDLVAVAVVFAI 409 TG GM+GY+G +F+L+ G L + IGY PLFV L+ FD+ A VV + Sbjct: 359 TGFGGMAGYMGGMIFSLIIGQLASTIGYEPLFVCLSVFDITAFIVVLVV 407 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: 597 Number of extensions: 22 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: 418 Length of database: 428 Length adjustment: 32 Effective length of query: 386 Effective length of database: 396 Effective search space: 152856 Effective search space used: 152856 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: 50 (23.9 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