Alignments for a candidate for fba in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for fba in Escherichia coli BW25113

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 17004 b2925 fructose-bisphosphate aldolase (NCBI)

Query= BRENDA::P0AB71
         (359 letters)



>FitnessBrowser__Keio:17004
          Length = 359

 Score =  728 bits (1879), Expect = 0.0
 Identities = 359/359 (100%), Positives = 359/359 (100%)

Query: 1   MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ 60
           MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ
Sbjct: 1   MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ 60

Query: 61  FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120
           FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI
Sbjct: 61  FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120

Query: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG 180
           DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG
Sbjct: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG 180

Query: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240
           GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT
Sbjct: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240

Query: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV 300
           ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV
Sbjct: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV 300

Query: 301 LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL 359
           LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL
Sbjct: 301 LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL 359


Lambda     K      H
   0.316    0.133    0.392 

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: 623
Number of extensions: 5
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: 359
Length of database: 359
Length adjustment: 29
Effective length of query: 330
Effective length of database: 330
Effective search space:   108900
Effective search space used:   108900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate 17004 b2925 (fructose-bisphosphate aldolase (NCBI))
to HMM TIGR01520 (fbaA: fructose-bisphosphate aldolase, class II (EC 4.1.2.13))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01520.hmm
# target sequence database:        /tmp/gapView.27688.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01520  [M=357]
Accession:   TIGR01520
Description: FruBisAldo_II_A: fructose-bisphosphate aldolase, class II
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-197  642.0   0.4   1.4e-197  641.8   0.4    1.0  1  lcl|FitnessBrowser__Keio:17004  b2925 fructose-bisphosphate aldo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17004  b2925 fructose-bisphosphate aldolase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.8   0.4  1.4e-197  1.4e-197       1     356 [.       4     358 ..       4     359 .] 0.99

  Alignments for each domain:
  == domain 1  score: 641.8 bits;  conditional E-value: 1.4e-197
                       TIGR01520   1 vldklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkdeaekaa 79 
                                     ++d++k+gvi+g+dv+k+f+vake++fa+Pa+n+v+++++na+le+a+++k+p+i+qfsngga+fiaGkGvk++++++a
  lcl|FitnessBrowser__Keio:17004   4 IFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGASFIAGKGVKSDVPQGA 82 
                                     6899*************************************************************************** PP

                       TIGR01520  80 siaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmldlseepieenieiakky 158
                                     +i Gai++a++v+++ae+ygvpv+lhtdhCakkllp++dgll+a+ek+f+++gkPlfsshm+dlsee+++eniei++ky
  lcl|FitnessBrowser__Keio:17004  83 AILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWIDGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKY 161
                                     ******************************************************************************* PP

                       TIGR01520 159 lkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispkfsiaaafGnvhGvykpGnvklrPd 237
                                     l+rm+ki ++leie+G+tGGeedGvdn+++d+++lyt+Pedv+++y+elskisp+f+iaa+fGnvhGvykpGnv+l+P+
  lcl|FitnessBrowser__Keio:17004 162 LERMSKIGMTLEIELGCTGGEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240
                                     ******************************************************************************* PP

                       TIGR01520 238 iladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqyaalegildyvlknedylqsqvGnp 316
                                     il+d+qeyv++k++l+ +++l+fvfhGGsGst++eik+++syGvvk+n+dtdtq+a++eg+l+y+++ne+ylq+q+Gnp
  lcl|FitnessBrowser__Keio:17004 241 ILRDSQEYVSKKHNLP-HNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGVLNYYKANEAYLQGQLGNP 318
                                     ****************.9************************************************************* PP

                       TIGR01520 317 kgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356
                                     kge++pnkk+ydPrvwlr++++sm+ar+eka++elnai++
  lcl|FitnessBrowser__Keio:17004 319 KGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDV 358
                                     *************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (359 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.01
//
[ok]

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources