GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Escherichia coli BW25113

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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