GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lacK in Escherichia coli BW25113

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)

Query= reanno::Smeli:SM_b20002
         (358 letters)



>lcl|FitnessBrowser__Keio:14400 b0262 putative ATP-binding component
           of a transport system (VIMSS)
          Length = 348

 Score =  236 bits (603), Expect = 5e-67
 Identities = 134/325 (41%), Positives = 191/325 (58%), Gaps = 17/325 (5%)

Query: 4   LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63
           ++L +V K +G   VI  ++L I  G+ V  +GPSGCGK+T+LR++AGLE+ S G + ID
Sbjct: 7   VELRNVTKRFGSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFID 66

Query: 64  DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123
              +      +R I MVFQSYAL+PHM++ EN+G+ L+  GVPRAE++ RV EA  +++L
Sbjct: 67  GEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMVDL 126

Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183
               DR   Q+SGGQ+QRVA+ RA++  PK+ LFDEPLSNLDA LR  MR +I  L KQ 
Sbjct: 127 EGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQKQF 186

Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKM---N 240
             T +YVTHDQ EA  ++D ++VM  G + Q+GSP DLY  PA+ F+A F+G   +    
Sbjct: 187 DITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGDANLFPAT 246

Query: 241 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPE--HFDEAGPAALDLAI 298
           F  G ++I           YG   +P  L         +G+RPE     + G  +    I
Sbjct: 247 FSDGYVDI-----------YG-YHLPRPLHFGTQGEGMVGVRPEAITLSDRGEESQRCVI 294

Query: 299 DMLEHLGGETFAYARHHGNGELIVV 323
             + ++G +       HG   L+ V
Sbjct: 295 RHVAYMGPQYEVTVEWHGQEILLQV 319


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: 302
Number of extensions: 8
Number of successful extensions: 1
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: 348
Length adjustment: 29
Effective length of query: 329
Effective length of database: 319
Effective search space:   104951
Effective search space used:   104951
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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