Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= TCDB::O30494 (367 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 353 bits (905), Expect = e-102 Identities = 188/355 (52%), Positives = 251/355 (70%), Gaps = 8/355 (2%) Query: 1 MANLKIKNLQKGFEGFS-IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGT 59 MA LK++ + K ++G + +IK + L+V D EF+V VGPSGCGKSTLLR++AGLE V+EG Sbjct: 1 MAGLKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGD 60 Query: 60 IELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAAR 119 I ++ + +TE+ P R +AMVFQ YALYPHMSV +NM++ L + G+ KQ + +V EAAR Sbjct: 61 IWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAAR 120 Query: 120 ILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179 ILEL LL+R+P++LSGGQRQRVA+GRAIVR+P +FLFDEPLSNLDA LRVQMRLEL +L Sbjct: 121 ILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQL 180 Query: 180 HKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239 H+ L+ T +YVTHDQVEAMTLA +V+V+N G EQ+G+P+E+Y +PA+LFVA F+G+P M Sbjct: 181 HRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAM 240 Query: 240 GFLKGKVTRVDGQGCEVQLDAGTLISLPLSGASLS-VGSAVTLGIRPEHLEIASPGQTTL 298 L G RV+ +G +LD G I LPL+G G +TLGIRPEH+ ++S + + Sbjct: 241 NLLTG---RVNNEGTHFELDGG--IELPLNGGYRQYAGRKMTLGIRPEHIALSSQAEGGV 295 Query: 299 TVTADVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFD 353 + D E LG+D H + L +R+ G TL LHL HLFD Sbjct: 296 PMVMDTLEILGADNLAHGRWGE-QKLVVRLAHQERPTAGSTLWLHLAENQLHLFD 349 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: 391 Number of extensions: 14 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: 356 Length adjustment: 29 Effective length of query: 338 Effective length of database: 327 Effective search space: 110526 Effective search space used: 110526 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