Align TM0030, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate Pf1N1B4_5102 Putative glutathione transporter, permease component
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5102 Length = 315 Score = 168 bits (426), Expect = 1e-46 Identities = 101/331 (30%), Positives = 176/331 (53%), Gaps = 21/331 (6%) Query: 5 SMFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERT 64 S ++++L R + LL + I F+L R+IPG+P +L +++ PE + Sbjct: 4 SRYRFILSRPLQLLPVLFGISLITFVLVRSIPGDPARALLG-----SRSTPEGLLRVRA- 57 Query: 65 LMEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVA 124 +FGL +P ++QYF F+ GDLG S+ Y + LI I TL L+L + ++A Sbjct: 58 ---QFGLDQPLWMQYFYFLKNLFNGDLGQSL-LYKVDALKLISTRIEPTLFLVLGSVLLA 113 Query: 125 WILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYS 184 ++ L +AA + W D + + +P +WLG++ I LF V+LGW PV G Y Sbjct: 114 MLIAVPLATVAARNKGGWGDNLIRLFTTAGLGMPAFWLGIMLILLFSVQLGWFPVSG-YG 172 Query: 185 QGTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMK 244 + SW D L H ++P +I ++ +R ++ EL +D+ + G+ Sbjct: 173 R------SWP---DKLHHMVLPCLTIALALSAVLIRNLRASMLMELQADHVTAARARGLP 223 Query: 245 DKRIFK-YVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLI 303 + +F+ +V NSL+P + LA+++G ++ G ++ E +F PG G LL R + T DY ++ Sbjct: 224 ENVVFRRHVLPNSLVPAVNLLAVNIGWLISGTVVIESLFAIPGIGQLLVRGIFTRDYMVV 283 Query: 304 QGIFVILIASIYLANFIVDFLYALIDPRIRL 334 QG+ ++L + NF+ D + IDPR+++ Sbjct: 284 QGVAMVLACATVAVNFLADVVTVAIDPRVKI 314 Lambda K H 0.329 0.146 0.449 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: 299 Number of extensions: 20 Number of successful extensions: 5 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: 338 Length of database: 315 Length adjustment: 28 Effective length of query: 310 Effective length of database: 287 Effective search space: 88970 Effective search space used: 88970 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 (21.8 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