Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= TCDB::O30494 (367 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 219 bits (558), Expect = 1e-61 Identities = 123/309 (39%), Positives = 177/309 (57%), Gaps = 3/309 (0%) Query: 2 ANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIE 61 A+L + L K FE F+ + + EV F +GPSGCGK+TLLR+IAG E G I Sbjct: 27 ADLSVTRLVKRFEKFTAVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVIA 86 Query: 62 LDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARIL 121 + GRD+ + P +R + ++FQ AL+P MSV +N++F L G+ + +V + + Sbjct: 87 IRGRDMAGIAPNRRPVNLIFQHLALFPMMSVAENVAFGLKRRGMAGGEISRRVQDVLERV 146 Query: 122 ELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHK 181 L + P QLSGGQ+QRVAI R +V P + L DEPL LD LR QM++EL L Sbjct: 147 GLPGYGVKMPAQLSGGQKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQA 206 Query: 182 ELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMGF 241 E+ T +Y+THDQ EA+ ++D V V+N+GR EQV +P LY +PA+ FVAGF+G + Sbjct: 207 EVGTTFVYITHDQSEALVMSDHVAVMNAGRFEQVDTPRNLYRRPASAFVAGFVG--ETNV 264 Query: 242 LKGKVTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIASPGQTTLTVT 301 G + G V+ D G + ++ A L+ G+ V + IRPE + I G + T Sbjct: 265 WSGTLEEATGDAGLVRTDEGAVFRARVA-AGLAKGTRVDMFIRPEAVLIDPDGASCATDG 323 Query: 302 ADVGERLGS 310 A G G+ Sbjct: 324 ATDGATDGA 332 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: 380 Number of extensions: 16 Number of successful extensions: 1 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: 418 Length adjustment: 31 Effective length of query: 336 Effective length of database: 387 Effective search space: 130032 Effective search space used: 130032 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