Align Phthalate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate RR42_RS11305 RR42_RS11305 hexuronate transporter
Query= uniprot:D8IX31 (418 letters) >FitnessBrowser__Cup4G11:RR42_RS11305 Length = 432 Score = 696 bits (1797), Expect = 0.0 Identities = 336/415 (80%), Positives = 373/415 (89%), Gaps = 2/415 (0%) Query: 1 MKYVRGIRWYMVTLVTLALIVNYLARNTLSVAAPTMMKELDMSTQQYSYIVVAWQICYAV 60 MK+++G+RW+MV+LVT+ LIVNYLARNTLSVAAPTMM EL M+TQQYSY+VVAWQ+CYA+ Sbjct: 1 MKHIKGMRWWMVSLVTMGLIVNYLARNTLSVAAPTMMSELHMTTQQYSYVVVAWQVCYAM 60 Query: 61 MQPVAGYILDAVGTKIGFGIFALAWSLVCAAAAFATGWQSLAFFRALLGITEAAGIPGGV 120 MQPVAG +LDA+GTKIGFGIFALAWSL CAAAA A+GWQ LAFFR LLG+ EAAGIPGGV Sbjct: 61 MQPVAGLVLDAIGTKIGFGIFALAWSLACAAAALASGWQGLAFFRGLLGLAEAAGIPGGV 120 Query: 121 KASTEWFPAKERSVAIGWFNIGSSIGALCAPPLVVWTILHGGWKMSFVVVGALGVIWFVL 180 KA+TEWFPAKERS+AIGWFNIGSSIGALCAPPLVVWTIL+GGW+ +F++VGALGV W VL Sbjct: 121 KATTEWFPAKERSIAIGWFNIGSSIGALCAPPLVVWTILNGGWQRAFIIVGALGVAWTVL 180 Query: 181 WMLFYKSPRDQKLLSPEERAYILEGQEKSPE--KVQRESWTKIVRSRNFWSIAIPRFLSE 238 WML YK P++Q+ LS +ER YIL GQE + + + SW +I+RSRNFWSIAIPRFLSE Sbjct: 181 WMLCYKHPKNQQRLSDQEREYILAGQEAQHKDANMAKASWLEIMRSRNFWSIAIPRFLSE 240 Query: 239 PAWQTFNAWIPLYMATERHMNIKEIAMFAWLPFLAADIGCVLGGYLSPLFHKHLKVSLFT 298 PAWQTFNAWIPLYMATERHMNIKEIAMFAWLPFLAADIGCVLGGYLSP FHKHLKVSLFT Sbjct: 241 PAWQTFNAWIPLYMATERHMNIKEIAMFAWLPFLAADIGCVLGGYLSPWFHKHLKVSLFT 300 Query: 299 SRKLVMLVGSLSMIGPACVGFVDSPYVAIALLSIGGFAHQTLSGALYSITSDVFTKNQVA 358 SRKLVMLVG L+MIGPACVG VDSPY AIALL +GGFAHQTLSGALYSITSD F KN+VA Sbjct: 301 SRKLVMLVGCLAMIGPACVGLVDSPYSAIALLCVGGFAHQTLSGALYSITSDAFGKNEVA 360 Query: 359 TATGLTGMSGYLGATLFTLLFGILVTQIGYGPLFVLLAAFDLVAVAVVFAIARPR 413 TATGL GMSGYLGATLFTLLFGI VT IGY PLFVLLA FDL+A A+VF +AR R Sbjct: 361 TATGLAGMSGYLGATLFTLLFGIAVTHIGYSPLFVLLAVFDLIAAAIVFLMARER 415 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: 794 Number of extensions: 30 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: 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