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 PP_4455 PP_4455 glutathione ABC transporter permease subunit
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Putida:PP_4455 Length = 313 Score = 191 bits (486), Expect = 2e-53 Identities = 109/323 (33%), Positives = 177/323 (54%), Gaps = 19/323 (5%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 ++F +KRL+ +++ ++ +VL+ L PG D A + D A +L Sbjct: 2 IQFAIKRLMLAIPTLLAMLTAVFVLVRLVPG---------DPAAVIL--GDQASAESLAA 50 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 E+ GLN P+ Q + +L + FG S + R + + P T L +S+L Sbjct: 51 MREQLGLNQPIAMQYIHFLGDMLSGNFGVSMTS-GRTVLQEVSLVLPWTLQLTFASVLIG 109 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSG--- 201 LV G+PLG+ AAL++N W DY +S+ G++ P++V A+ ++L+F+I+ W P G Sbjct: 110 LVFGLPLGVWAALRRNAWPDYVGRILSLTGLSFPAFVSAMLMLLVFAIHFRWFPVIGSLV 169 Query: 202 ----WEGIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKH 257 + LP + L L A V R TR S++ L +D+IRTA AKG ++++H Sbjct: 170 DGGFLSQLHALTLPALNLGLIMTAYVMRVTRSSMISVLGEDYIRTAKAKGVRPMRLVLRH 229 Query: 258 ALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILA 317 LR ++IP+VT+VG L+ +V E +F PGLG+L A TRDY LL + A Sbjct: 230 GLRNALIPIVTVVGLYFGTLIGNSVLTEIVFNRPGLGKLILGALNTRDYTLLQGLMVVFA 289 Query: 318 LTVMIMNLIVDVLYAILDPRIKL 340 L V+++N+I D++Y ++DPR+K+ Sbjct: 290 LCVIVVNIITDIVYGLVDPRVKI 312 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: 272 Number of extensions: 18 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: 313 Length adjustment: 28 Effective length of query: 313 Effective length of database: 285 Effective search space: 89205 Effective search space used: 89205 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: 48 (23.1 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