Align ABC transporter for Lactose, ATPase component (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 336 bits (862), Expect = 5e-97 Identities = 182/362 (50%), Positives = 251/362 (69%), Gaps = 12/362 (3%) Query: 1 MSELQLSDVRKSYGG-LEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGD 59 M+ L+L V KS+ G +VIK + LD+ GEF+V VGPSGCGKSTLLRM+AGLE ++ GD Sbjct: 1 MAGLKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGD 60 Query: 60 LTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAH 119 + I+D R+ +++P RGIAMVFQ+YALYPHM+V ENM + L+ G+ + +I +RV EAA Sbjct: 61 IWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAAR 120 Query: 120 ILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARL 179 ILEL LL R+P++LSGGQRQRVA+GRAIVR P +FLFDEPLSNLDA+LRV MR+E+ +L Sbjct: 121 ILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQL 180 Query: 180 HKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKM 239 H++L TT +YVTHDQVEAMTLA +++VM GV EQ+G+P+++Y+ PA+LFVA FIGSP M Sbjct: 181 HRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAM 240 Query: 240 NFLKGVIEIDEDQAYARLPDYGDAKIPVT--LQAAAGTAVTIGIRPEHFDEAGPA--ALD 295 N L G ++ + + L G ++P+ + AG +T+GIRPEH + A + Sbjct: 241 NLLTG--RVNNEGTHFELD--GGIELPLNGGYRQYAGRKMTLGIRPEHIALSSQAEGGVP 296 Query: 296 LAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGE-GK 354 + +D LE LG + A+ R + +VV + G L + +FDGE G+ Sbjct: 297 MVMDTLEILGADNLAHGR--WGEQKLVVRLAHQERPTAGSTLWLHLAENQLHLFDGETGQ 354 Query: 355 RL 356 R+ Sbjct: 355 RV 356 Lambda K H 0.321 0.139 0.396 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: 369 Number of extensions: 11 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: 358 Length of database: 356 Length adjustment: 29 Effective length of query: 329 Effective length of database: 327 Effective search space: 107583 Effective search space used: 107583 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