Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_028312608.1 H566_RS0118530 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::O30494 (367 letters) >NCBI__GCF_000482785.1:WP_028312608.1 Length = 370 Score = 316 bits (810), Expect = 6e-91 Identities = 170/364 (46%), Positives = 235/364 (64%), Gaps = 13/364 (3%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 M L I+N++K + I+KGID+E+ EF++ VGPSGCGKSTLL +IAGL+ V+ G I Sbjct: 1 MGALSIRNVRKSYNNVEILKGIDIEIEKGEFLILVGPSGCGKSTLLSMIAGLDSVTSGEI 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARI 120 + R + +++P RD+AMVFQ+YALYP+MSVR+N+SF L++ V K + VN A+ Sbjct: 61 RIGDRVVNDLSPKDRDIAMVFQSYALYPNMSVRENISFGLEIRKVPKATQDEIVNRVAKT 120 Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L++ LL+RKP QLSGGQRQRVA+GRAI R+P +FLFDEPLSNLDA LRV+MR E+ LH Sbjct: 121 LQMEHLLDRKPSQLSGGQRQRVAMGRAIARDPALFLFDEPLSNLDAKLRVEMRTEIKLLH 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 + + T++YVTHDQ+EAMTL DK+ V+ +G ++Q G+P ++Y PANLFVA F+G+P M Sbjct: 181 QRMGTTIVYVTHDQIEAMTLGDKIAVMKAGELQQFGTPQQIYDNPANLFVASFMGSPSMN 240 Query: 241 FLKGKVTRVDGQGCEVQLDAG-TLISLPLSGASLSV----GSAVTLGIRPEHLEIASPG- 294 F+ KV + G G V+LD G + P A + G V GIRPE + G Sbjct: 241 FIPAKVESLGG-GYGVRLDGGKSSYVFPAVSADSRLKAWEGREVVFGIRPEQITHFQDGV 299 Query: 295 -----QTTLTVTADVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHC 349 T + + E G DT ++ NG+ +T R+ A Q GET+ L+ D + Sbjct: 300 PLPEHVRTAELPVSLIEPTGPDTLV-LVPINGKGVTCRVHPAHARQPGETMALNFDLSKA 358 Query: 350 HLFD 353 FD Sbjct: 359 VFFD 362 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: 370 Number of extensions: 14 Number of successful extensions: 2 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: 370 Length adjustment: 30 Effective length of query: 337 Effective length of database: 340 Effective search space: 114580 Effective search space used: 114580 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 24 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