GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Shewanella halifaxensis HAW-EB4

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate WP_012277177.1 SHAL_RS10910 4-hydroxy-2-oxovalerate aldolase

Query= BRENDA::P51017
         (346 letters)



>NCBI__GCF_000019185.1:WP_012277177.1
          Length = 340

 Score =  555 bits (1429), Expect = e-163
 Identities = 275/337 (81%), Positives = 306/337 (90%)

Query: 1   MNLHGKSVILHDMSLRDGMHAKRHQISLEQMVAVATGLDQAGMPLIEITHGDGLGGRSIN 60
           MNL GK VILHDMSLRDGMHA++HQI+L++MV VATGLD AG+PLIE+THGDGLGG S+N
Sbjct: 1   MNLTGKKVILHDMSLRDGMHARQHQITLKEMVDVATGLDAAGVPLIEVTHGDGLGGASLN 60

Query: 61  YGFPAHSDEEYLRAVIPQLKQAKVSALLLPGIGTVDHLKMALDCGVSTIRVATHCTEADV 120
           YGFPAH+DEEYL AVIP++KQAKVSALLLPGIGTVDHL+MA   GV+TIRVATHCTEADV
Sbjct: 61  YGFPAHTDEEYLSAVIPKMKQAKVSALLLPGIGTVDHLRMAHQLGVNTIRVATHCTEADV 120

Query: 121 SEQHIGMARKLGVDTVGFLMMAHMISAEKVLEQAKLMESYGANCIYCTDSAGYMLPDEVS 180
           S QHI ++R LG+DTVGFLMMAHM+S EK+LEQAKLMESYGANCIYCTDSAGYMLP +V+
Sbjct: 121 SGQHIALSRDLGLDTVGFLMMAHMVSPEKLLEQAKLMESYGANCIYCTDSAGYMLPGDVT 180

Query: 181 EKIGLLRAELNPATEVGFHGHHNMGMAIANSLAAIEAGAARIDGSVAGLGAGAGNTPLEV 240
             I  LR EL   T++GFHGHHNMGM+IANSLAAIEAGA RIDGSVAGLGAGAGNTPLEV
Sbjct: 181 SHIERLRGELKSDTQIGFHGHHNMGMSIANSLAAIEAGAERIDGSVAGLGAGAGNTPLEV 240

Query: 241 FVAVCKRMGVETGIDLYKIMDVAEDLVVPMMDQPIRVDRDALTLGYAGVYSSFLLFAQRA 300
           FVAV +RM V  G++LY IMDVAEDLV PMMDQPIR+DRDALTLGYAGVYSSFLLFAQRA
Sbjct: 241 FVAVLERMQVHHGVNLYDIMDVAEDLVTPMMDQPIRIDRDALTLGYAGVYSSFLLFAQRA 300

Query: 301 EKKYGVSARDILVELGRRGTVGGQEDMIEDLALDMAR 337
           EKKYGV ARDIL+ELGRRGTVGGQEDMI+D A++MAR
Sbjct: 301 EKKYGVPARDILLELGRRGTVGGQEDMIDDTAMNMAR 337


Lambda     K      H
   0.320    0.135    0.386 

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: 512
Number of extensions: 15
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: 346
Length of database: 340
Length adjustment: 29
Effective length of query: 317
Effective length of database: 311
Effective search space:    98587
Effective search space used:    98587
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)

Align candidate WP_012277177.1 SHAL_RS10910 (4-hydroxy-2-oxovalerate aldolase)
to HMM TIGR03217 (dmpG: 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39))

# 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/TIGR03217.hmm
# target sequence database:        /tmp/gapView.2726525.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03217  [M=334]
Accession:   TIGR03217
Description: 4OH_2_O_val_ald: 4-hydroxy-2-oxovalerate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-168  546.6   6.9   1.2e-168  546.5   6.9    1.0  1  NCBI__GCF_000019185.1:WP_012277177.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019185.1:WP_012277177.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  546.5   6.9  1.2e-168  1.2e-168       1     333 [.       6     338 ..       6     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 546.5 bits;  conditional E-value: 1.2e-168
                             TIGR03217   1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdlelieaaaea 73 
                                           kk++++d++LrdG+ha +hq+t +e++++a++Ld+agv+ iev+hGdGLgg+slnyGf+a++d+e+++a++ +
  NCBI__GCF_000019185.1:WP_012277177.1   6 KKVILHDMSLRDGMHARQHQITLKEMVDVATGLDAAGVPLIEVTHGDGLGGASLNYGFPAHTDEEYLSAVIPK 78 
                                           6899********************************************************************* PP

                             TIGR03217  74 vkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmshmaspekla 146
                                           +k+akv++lllPGigtv++l++a+++Gv+++rvathcteadvs qhi+l+r+lgl+tvgfLmm+hm+spekl 
  NCBI__GCF_000019185.1:WP_012277177.1  79 MKQAKVSALLLPGIGTVDHLRMAHQLGVNTIRVATHCTEADVSGQHIALSRDLGLDTVGFLMMAHMVSPEKLL 151
                                           ************************************************************************* PP

                             TIGR03217 147 eqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatrida 219
                                           eqakl+esyGa+++y++dsaG++lp dv+++++ l+ +lk++t++G+h+h+n+++++ans++a+e+Ga+rid+
  NCBI__GCF_000019185.1:WP_012277177.1 152 EQAKLMESYGANCIYCTDSAGYMLPGDVTSHIERLRGELKSDTQIGFHGHHNMGMSIANSLAAIEAGAERIDG 224
                                           ************************************************************************* PP

                             TIGR03217 220 slaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrealtlGyaGvyssflrha 292
                                           s+aglGagaGn+plev+vavl+r+ +++gv+l+ ++d+aed+v+P++d+p+r+dr+altlGyaGvyssfl++a
  NCBI__GCF_000019185.1:WP_012277177.1 225 SVAGLGAGAGNTPLEVFVAVLERMQVHHGVNLYDIMDVAEDLVTPMMDQPIRIDRDALTLGYAGVYSSFLLFA 297
                                           ************************************************************************* PP

                             TIGR03217 293 eraaekygvdardilvelGrrklvgGqedmivdvaldlake 333
                                           +ra++kygv+ardil+elGrr +vgGqedmi d+a+++a+e
  NCBI__GCF_000019185.1:WP_012277177.1 298 QRAEKKYGVPARDILLELGRRGTVGGQEDMIDDTAMNMARE 338
                                           **************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (340 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 22.05
//
[ok]

This GapMind analysis is from Sep 24 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