Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= TCDB::O30494 (367 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 345 bits (884), Expect = 1e-99 Identities = 189/358 (52%), Positives = 247/358 (68%), Gaps = 8/358 (2%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 MA+++I+ ++K F II+G+D+++ D EF V VGPSGCGKSTLLR++AGLEE++ G I Sbjct: 1 MASVQIRAVKKQFGSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEI 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARI 120 + G + V P RD+AMVFQ YALYPHM+VR NM+F+L LA DK V+ +V +AA I Sbjct: 61 LIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADI 120 Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L L LL+R P+QLSGGQRQRVA+GRAIVR+P++FLFDEPLSNLDA LRVQMR E+ LH Sbjct: 121 LGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELH 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 + L+ T IYVTHDQ+EAMT+AD++VV+ G +EQ G PL+LY PANLFVAGF+G+P M Sbjct: 181 QRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAMN 240 Query: 241 FLKGKVTRVDGQGCEVQLDAGTLISLPLSGASL--SVGSAVTLGIRPEHLEIASPGQTTL 298 F+ + R + G EV+ GT + P GA+L + G VT G+RPEHL I + GQ Sbjct: 241 FIPATLRR-NATGAEVEFADGTRVPAPY-GAALQGNDGQKVTYGVRPEHLSIGAAGQGIA 298 Query: 299 TVTADVGERLGSDTFCHVITSNGE-PLTMRIRGDMASQYGETLHLHLDPAHCHLFDTD 355 T V E G+DT V + G+ LT R G+ +HL D + HLFD + Sbjct: 299 TKVI-VVEPTGADT--EVFSRFGDTSLTSIFRERHDFGAGDVIHLVPDHSRTHLFDAE 353 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: 387 Number of extensions: 15 Number of successful extensions: 3 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: 361 Length adjustment: 29 Effective length of query: 338 Effective length of database: 332 Effective search space: 112216 Effective search space used: 112216 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