Align Phthalate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate AO356_20660 AO356_20660 glucarate transporter
Query= uniprot:D8IX31 (418 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20660 Length = 443 Score = 218 bits (555), Expect = 3e-61 Identities = 125/385 (32%), Positives = 204/385 (52%), Gaps = 7/385 (1%) Query: 8 RWYMVTLVTLALIVNYLARNTLSVAAPTMMKELDMSTQQYSYIVVAWQICYAVMQPVAGY 67 RW+M++L+ +A I+NY+ R +S+AAP + K+L + + I A+ YA+ AG+ Sbjct: 26 RWFMLSLLLIATIINYIDRVNISIAAPFLAKDLGLDKIEMGLIFSAFAWTYAIALVPAGF 85 Query: 68 ILDAVGTKIGFGIFALAWSLVCAAAAFATGWQSLAFFRALLGITEAAGIPGGVKASTEWF 127 I D G++ +G+ ++WS V FATG+ SL R +G EA P +A T WF Sbjct: 86 IADRFGSRFTYGVSLISWSTVTVCQGFATGFASLFGLRLAVGAMEAPAFPANSRAVTVWF 145 Query: 128 PAKERSVAIGWFNIGSSIGALCAPPLVVWTILHGGWKMSFVVVGALGVIWFVLWMLFYKS 187 PA+ER +A + G +G ++W W+ F GALG+++ V W+ Y+ Sbjct: 146 PARERGLASSIYVCGQYLGTALFTGALLWLATTYDWRHVFYSTGALGIVFGVAWLFLYRD 205 Query: 188 PRDQKLLSPEERAYILE--GQEKSPEKVQRESWTKIVR---SRNFWSIAIPRFLSEPAWQ 242 P + K +S EE YI G KS ++ R +W +I R W+I I +F S A Sbjct: 206 PMNCKKVSKEELKYIEAGGGLVKSSQERTRFNWRQIAELFSYRQVWAICIGKFASTSALY 265 Query: 243 TFNAWIPLYMATERHMNIKEIAMFAWLPFLAADIGCVLGGYLSPLFHKHLKVSLFTSRKL 302 F W P Y+ ER + + + +FA LPF+ A +G +L G +S L + SL +RKL Sbjct: 266 FFLTWFPTYLIEERQLTMIKAGIFAVLPFVGATVGILLAGIVSDLLIRR-GYSLSFARKL 324 Query: 303 VMLVGSLSMIGPACVGFVDSPYVAIALLSIGGFAHQTLSGALYSITSDVFTKNQVATATG 362 ++VGS+ + V F DS + IA+L+I FA Q ++ + ++ S+V K + G Sbjct: 325 PLVVGSMLGMSIVLVNFTDSNVICIAVLTIAFFA-QGIASSSWAAVSEVAPKELIGLTGG 383 Query: 363 LTGMSGYLGATLFTLLFGILVTQIG 387 +T ++ +G + ++ G +V + G Sbjct: 384 ITSLAANIGGIVTPIVIGAIVHKTG 408 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: 527 Number of extensions: 27 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: 418 Length of database: 443 Length adjustment: 32 Effective length of query: 386 Effective length of database: 411 Effective search space: 158646 Effective search space used: 158646 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