GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Hafnia paralvei ATCC 29927

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_004846864.1 M988_RS16965 class II fructose-bisphosphate aldolase

Query= BRENDA::P0AB71
         (359 letters)



>NCBI__GCF_001655005.1:WP_004846864.1
          Length = 359

 Score =  677 bits (1747), Expect = 0.0
 Identities = 328/359 (91%), Positives = 344/359 (95%)

Query: 1   MSKIFDFVKPGVITGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQ 60
           MSKIFDFVKPGVITGDDVQKVFQ+AKENNFALPAVNCVGTDSINAV+E AAKV+APVIVQ
Sbjct: 1   MSKIFDFVKPGVITGDDVQKVFQIAKENNFALPAVNCVGTDSINAVMEAAAKVRAPVIVQ 60

Query: 61  FSNGGASFIAGKGVKSDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWI 120
           FSNGGA+FIAGKGVK+DVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPW+
Sbjct: 61  FSNGGAAFIAGKGVKTDVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWL 120

Query: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIGMTLEIELGCTG 180
           DGLLDAGEKHFAATGKPLFSSHMIDLSEESL+ENIEICSKYL RMSKIGMTLEIELGCTG
Sbjct: 121 DGLLDAGEKHFAATGKPLFSSHMIDLSEESLEENIEICSKYLTRMSKIGMTLEIELGCTG 180

Query: 181 GEEDGVDNSHMDASALYTQPEDVDYAYTELSKISPRFTIAASFGNVHGVYKPGNVVLTPT 240
           GEEDGVDNSHMD+SALYTQPEDVDYAYT+L+ ISPRFTIAASFGNVHGVYKPGNV LTP 
Sbjct: 181 GEEDGVDNSHMDSSALYTQPEDVDYAYTKLNAISPRFTIAASFGNVHGVYKPGNVQLTPK 240

Query: 241 ILRDSQEYVSKKHNLPHNSLNFVFHGGSGSTAQEIKDSVSYGVVKMNIDTDTQWATWEGV 300
           IL +SQEYVSKKHNLPHNSLNFVFHGGSGSTA EIK++VSYGVVKMNIDTDTQWATWEG+
Sbjct: 241 ILHNSQEYVSKKHNLPHNSLNFVFHGGSGSTAAEIKEAVSYGVVKMNIDTDTQWATWEGI 300

Query: 301 LNYYKANEAYLQGQLGNPKGEDQPNKKYYDPRVWLRAGQTSMIARLEKAFQELNAIDVL 359
           LNYYK NE YLQGQLGNP+G D+PNKKYYDPRVWLRA QTSMIARLE AF ELN  DVL
Sbjct: 301 LNYYKKNEGYLQGQLGNPEGADKPNKKYYDPRVWLRAAQTSMIARLELAFDELNCKDVL 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: 582
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: 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 WP_004846864.1 M988_RS16965 (class II fructose-bisphosphate aldolase)
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.1528989.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-193  628.7   0.4   1.5e-193  628.6   0.4    1.0  1  NCBI__GCF_001655005.1:WP_004846864.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001655005.1:WP_004846864.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  628.6   0.4  1.5e-193  1.5e-193       1     356 [.       4     358 ..       4     359 .] 0.99

  Alignments for each domain:
  == domain 1  score: 628.6 bits;  conditional E-value: 1.5e-193
                             TIGR01520   1 vldklktgvilgedvaklfevakeekfaiPainvvssetvnaaleaardakspiilqfsnggaafiaGkGvkd 73 
                                           ++d++k+gvi+g+dv+k+f++ake++fa+Pa+n+v+++++na++eaa+++++p+i+qfsnggaafiaGkGvk+
  NCBI__GCF_001655005.1:WP_004846864.1   4 IFDFVKPGVITGDDVQKVFQIAKENNFALPAVNCVGTDSINAVMEAAAKVRAPVIVQFSNGGAAFIAGKGVKT 76 
                                           6899********************************************************************* PP

                             TIGR01520  74 eaekaasiaGaiaaaeyvrsiaekygvpvvlhtdhCakkllpyvdglleadekyfkkegkPlfsshmldlsee 146
                                           +++++a+i Gai++a++v+++ae+ygvpv+lhtdhCakkllp++dgll+a+ek+f+++gkPlfsshm+dlsee
  NCBI__GCF_001655005.1:WP_004846864.1  77 DVPQGAAILGAISGAHHVHQMAEHYGVPVILHTDHCAKKLLPWLDGLLDAGEKHFAATGKPLFSSHMIDLSEE 149
                                           ************************************************************************* PP

                             TIGR01520 147 pieenieiakkylkrmakiklileieiGitGGeedGvdneeadkeelytkPedvekvyeelskispkfsiaaa 219
                                           ++eeniei++kyl rm+ki ++leie+G+tGGeedGvdn+++d+++lyt+Pedv+++y++l++isp+f+iaa+
  NCBI__GCF_001655005.1:WP_004846864.1 150 SLEENIEICSKYLTRMSKIGMTLEIELGCTGGEEDGVDNSHMDSSALYTQPEDVDYAYTKLNAISPRFTIAAS 222
                                           ************************************************************************* PP

                             TIGR01520 220 fGnvhGvykpGnvklrPdiladgqeyvaeklglkeakplsfvfhGGsGstkeeikealsyGvvkvnvdtdtqy 292
                                           fGnvhGvykpGnv+l+P+il+++qeyv++k++l+ +++l+fvfhGGsGst+ eikea+syGvvk+n+dtdtq+
  NCBI__GCF_001655005.1:WP_004846864.1 223 FGNVHGVYKPGNVQLTPKILHNSQEYVSKKHNLP-HNSLNFVFHGGSGSTAAEIKEAVSYGVVKMNIDTDTQW 294
                                           **********************************.9************************************* PP

                             TIGR01520 293 aalegildyvlknedylqsqvGnpkgeekpnkkvydPrvwlreaeksmkarvekaleelnaink 356
                                           a++egil+y++kne ylq+q+Gnp+g +kpnkk+ydPrvwlr+a++sm+ar+e a++eln+ ++
  NCBI__GCF_001655005.1:WP_004846864.1 295 ATWEGILNYYKKNEGYLQGQLGNPEGADKPNKKYYDPRVWLRAAQTSMIARLELAFDELNCKDV 358
                                           ************************************************************9875 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.68
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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