Align TM0028, 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 AO353_21860 AO353_21860 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21860 Length = 328 Score = 178 bits (451), Expect = 2e-49 Identities = 114/305 (37%), Positives = 160/305 (52%), Gaps = 12/305 (3%) Query: 22 VKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVEL 81 V VD LSF++ E E++G+VGESG GKT + + P V GK ++L Sbjct: 22 VTLVDRLSFDLAEGEILGLVGESGSGKTMACRALMRLLPSPSLRVQGKAVQLAGKNLLQL 81 Query: 82 SSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESH-GIDEEELLDKARRR 140 ++ G+ + +I Q + L P +R+ + + H G + E +A Sbjct: 82 DEAGMRAIR----GRRLGMIFQNPSSHLDPLMRIGEQIGEGIRLHQGASKREARAQAIEV 137 Query: 141 FEEVGLD--PLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLK 198 +VG+ P + Y E SGGMRQRA+IA+A NP +LIADEPT+ALDV Q +L+ Sbjct: 138 LRQVGIPDPPRRVDSYAHEFSGGMRQRAMIAVALACNPQVLIADEPTTALDVTVQAQILR 197 Query: 199 VLMQMKRQ-GIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQG 257 +L+ ++ Q G+ SII ITHD+ V Q D + +MYAG++ E LL +P HPYT G Sbjct: 198 LLLDLRDQRGL--SIILITHDLGVVAQTCDSIAVMYAGRLCEHGSKHELLVRPRHPYTAG 255 Query: 258 LFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEPG 317 L + P V + TI G PP L PSGC F+PRC C P L + G Sbjct: 256 LID--CQPASSVGHAMLRTIAGQPPLLDALPSGCSFNPRCLQQGSQCTMLLPDLQIMAEG 313 Query: 318 RRVAC 322 +RVAC Sbjct: 314 QRVAC 318 Lambda K H 0.321 0.138 0.405 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: 261 Number of extensions: 10 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: 330 Length of database: 328 Length adjustment: 28 Effective length of query: 302 Effective length of database: 300 Effective search space: 90600 Effective search space used: 90600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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