GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Derxia gummosa DSM 723

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_028311754.1 H566_RS0112785 3-oxoadipyl-CoA thiolase

Query= uniprot:D8ITH5
         (401 letters)



>NCBI__GCF_000482785.1:WP_028311754.1
          Length = 401

 Score =  603 bits (1554), Expect = e-177
 Identities = 306/398 (76%), Positives = 340/398 (85%)

Query: 3   ALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGED 62
           A +CDAIRTPFGRYGG+L  VRADDL A PIR+LM RNP VDW+ ++D++YGCANQAGED
Sbjct: 4   AYLCDAIRTPFGRYGGSLSGVRADDLGAVPIRALMARNPSVDWAALDDVIYGCANQAGED 63

Query: 63  NRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRA 122
           NRNV RM+ LLAGLP  VPG+TVNRLCGSSLDA   AARAI++GEVQL+IAGGVESM+RA
Sbjct: 64  NRNVGRMSALLAGLPPEVPGTTVNRLCGSSLDATASAARAIRAGEVQLVIAGGVESMSRA 123

Query: 123 PFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDA 182
           PFVMGKA  AF+RSA + DTTIGWRFVNPLMKA +G+DSMPETAENVATDF + RADQDA
Sbjct: 124 PFVMGKATEAFSRSAKVEDTTIGWRFVNPLMKAMHGVDSMPETAENVATDFDVARADQDA 183

Query: 183 FALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVVR 242
           FALRSQQR AAAQAAG  + EI P+TI QK+GD LVV+ DEH RP+TTLA LAKLKGVVR
Sbjct: 184 FALRSQQRAAAAQAAGRLSQEITPVTIAQKRGDALVVSADEHLRPETTLAALAKLKGVVR 243

Query: 243 PDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPAV 302
           PDGTVTAGNASGVNDGA ALLLAS   A  + LKPRAR++  A AGVAPRIMGFGPAPA+
Sbjct: 244 PDGTVTAGNASGVNDGAAALLLASEAGAARHGLKPRARIVASAVAGVAPRIMGFGPAPAI 303

Query: 303 RKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGASG 362
            KVLA   L L Q+DVIELNEAFAAQ LAV R  GL DD A VNPNGGAIA+GHPLGASG
Sbjct: 304 TKVLALAKLRLDQIDVIELNEAFAAQALAVTRAHGLADDDARVNPNGGAIALGHPLGASG 363

Query: 363 ARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           ARLV  A+++LER+GGRY LCTMCIGVGQGIALVIERV
Sbjct: 364 ARLVIAALHELERTGGRYGLCTMCIGVGQGIALVIERV 401


Lambda     K      H
   0.320    0.135    0.394 

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: 562
Number of extensions: 13
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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: 50 (23.9 bits)

Align candidate WP_028311754.1 H566_RS0112785 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.1897357.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-223  726.8  15.1   3.8e-223  726.7  15.1    1.0  1  NCBI__GCF_000482785.1:WP_028311754.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000482785.1:WP_028311754.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  726.7  15.1  3.8e-223  3.8e-223       2     400 .]       3     401 .]       2     401 .] 1.00

  Alignments for each domain:
  == domain 1  score: 726.7 bits;  conditional E-value: 3.8e-223
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           ++y++dairtp+GrygGsls vraddl+avp++al+arnps+d+aa+ddvi+GcanqaGednrnv+rm+alla
  NCBI__GCF_000482785.1:WP_028311754.1   3 HAYLCDAIRTPFGRYGGSLSGVRADDLGAVPIRALMARNPSVDWAALDDVIYGCANQAGEDNRNVGRMSALLA 75 
                                           89*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glp +vpgttvnrlcgs+lda + aarai+aGe +lviaGGvesmsrapfv+Gka  afsrsak+edttiGwr
  NCBI__GCF_000482785.1:WP_028311754.1  76 GLPPEVPGTTVNRLCGSSLDATASAARAIRAGEVQLVIAGGVESMSRAPFVMGKATEAFSRSAKVEDTTIGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           fvnp +ka++Gvdsmpetaenva++f+v+r+dqdafalrsqqr+aaaqa+G +++ei+pv+i+qk+G++ vv+
  NCBI__GCF_000482785.1:WP_028311754.1 149 FVNPLMKAMHGVDSMPETAENVATDFDVARADQDAFALRSQQRAAAAQAAGRLSQEITPVTIAQKRGDALVVS 221
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                           +dehlr+ettl alaklk+vvr+dgtvtaGnasGvndGaaalllase  ++rhgl+prari+a+a aGv+pr+
  NCBI__GCF_000482785.1:WP_028311754.1 222 ADEHLRPETTLAALAKLKGVVRPDGTVTAGNASGVNDGAAALLLASEAGAARHGLKPRARIVASAVAGVAPRI 294
                                           ************************************************************************* PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG+gp+pa+ k+la a+l+l+++dvielneafaaqalav+r+ gladddarvnpnGGaialGhplGasGarlv
  NCBI__GCF_000482785.1:WP_028311754.1 295 MGFGPAPAITKVLALAKLRLDQIDVIELNEAFAAQALAVTRAHGLADDDARVNPNGGAIALGHPLGASGARLV 367
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400
                                           ++al++le++ggry+l+t+ciGvGqGialvierv
  NCBI__GCF_000482785.1:WP_028311754.1 368 IAALHELERTGGRYGLCTMCIGVGQGIALVIERV 401
                                           *********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (401 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: 28.92
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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