Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate BPHYT_RS22760 BPHYT_RS22760 sugar ABC transporter ATP-binding protein
Query= TCDB::O30494 (367 letters) >FitnessBrowser__BFirm:BPHYT_RS22760 Length = 384 Score = 375 bits (964), Expect = e-109 Identities = 196/375 (52%), Positives = 264/375 (70%), Gaps = 15/375 (4%) Query: 1 MANLKIKNLQKGF-EGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGT 59 MA++ ++ +QK + EG +I+ +DLE+ + EF VF+GPSGCGKSTLLR+IAGLE++++G Sbjct: 1 MASISLRGVQKAYGEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 IELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAAR 119 + + G+ + +V A+R +AMVFQ+YAL+PHMSV +NM+F L LA K V+ KV EAAR Sbjct: 61 LSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAAR 120 Query: 120 ILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179 IL+L LLERKPK LSGGQRQRVAIGRAIVR P +FLFDEPLSNLDA LR Q R+E+ARL Sbjct: 121 ILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 HKEL-QATMIYVTHDQVEAMTLADKVVVLNSGR-------IEQVGSPLELYHQPANLFVA 231 HK+ +A+++YVTHDQ+EAMTLADK+V+L++G+ I Q+G+PLELYH+P + FVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFVA 240 Query: 232 GFLGTPKMGFLKGKVTRVDGQGCEVQLD-AGTLISLPLSGASLSVGSAVTLGIRPEHLEI 290 GF+G+P+M FL G+V +D QG + LD + +P++GA L AVTLG+RPEHLE Sbjct: 241 GFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAGLQTSQAVTLGVRPEHLEF 300 Query: 291 -----ASPGQTTLTVTADVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLD 345 +P LT T + E+LG ++ H+ G L + G+ GE L + Sbjct: 301 VDPSSVAPDDAVLTRTVSLVEQLGEHSYVHLDQPGGAALVAKAPGNTRLAPGERASLRVP 360 Query: 346 PAHCHLFDTDGVAVA 360 A CHLF DG A A Sbjct: 361 RAACHLFTEDGFAAA 375 Lambda K H 0.319 0.137 0.387 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: 423 Number of extensions: 14 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: 367 Length of database: 384 Length adjustment: 30 Effective length of query: 337 Effective length of database: 354 Effective search space: 119298 Effective search space used: 119298 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: 50 (23.9 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