Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Pf6N2E2_3423 Putative glutathione transporter, permease component
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3423 Length = 315 Score = 170 bits (430), Expect = 5e-47 Identities = 100/320 (31%), Positives = 165/320 (51%), Gaps = 17/320 (5%) Query: 26 KFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKGF 85 +F+L R L + + + +IT+VL+ PG+ R + +TP+ L Sbjct: 7 RFILSRPLQLLPVLFGISMITFVLVRSIPGD-----PARALLGSRSTPE------ALIRI 55 Query: 86 EERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFAL 145 +YGL+ PLW Q +LK + G S ++ LI + T L L S+L AL Sbjct: 56 RAQYGLDQPLWMQYFYFLKNLLKGDLGQSLLYKVDALQ-LISTRIEPTLFLVLGSVLLAL 114 Query: 146 VVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSG---- 201 ++ VPL +AA K W D+ + G+ +P++ + + LIL+ S+ LG P SG Sbjct: 115 LIAVPLATVAARNKGGWQDHLIRLFTTAGLGMPAFWLGIMLILLLSVQLGLFPVSGYGRT 174 Query: 202 -WEGIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALR 260 W+ + +LP + +AL A + R R S+L L D A A+G +R + +H L Sbjct: 175 AWDKLHHMVLPCLTIALALSAVLVRNLRASMLMELQADHATAARARGLSERAIFRRHVLP 234 Query: 261 PSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTV 320 S++P V ++ + +L+ GTV +E++F IPG+GQL TRDY ++ +LAL Sbjct: 235 NSLVPAVNLLAVNIGWLISGTVVIESLFAIPGIGQLLVRGIFTRDYMVVQGVAMVLALAT 294 Query: 321 MIMNLIVDVLYAILDPRIKL 340 + +N + DVL ++DPR+ + Sbjct: 295 VTVNFLADVLTVMIDPRVNM 314 Lambda K H 0.328 0.143 0.429 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: 257 Number of extensions: 13 Number of successful extensions: 4 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: 341 Length of database: 315 Length adjustment: 28 Effective length of query: 313 Effective length of database: 287 Effective search space: 89831 Effective search space used: 89831 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