Alignments for a candidate for paaJ2 in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Methylobacterium nodulans ORS 2060

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_015929439.1 MNOD_RS13390 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_000022085.1:WP_015929439.1
          Length = 404

 Score =  563 bits (1451), Expect = e-165
 Identities = 286/400 (71%), Positives = 334/400 (83%), Gaps = 2/400 (0%)

Query: 2   RDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAG 61
           RDV+ICD +RTPIGR+GGALA VRADDLAA+PL AL+  NP+++ D V+EVF GCANQAG
Sbjct: 5   RDVYICDFVRTPIGRYGGALASVRADDLAAIPLAALLHRNPSLK-DGVEEVFLGCANQAG 63

Query: 62  EDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMS 121
           EDNRNVARMALLLAGLPE++PG+TLNRLCASG+DA+G A RAI SG+++LA+AGGVESM+
Sbjct: 64  EDNRNVARMALLLAGLPETVPGLTLNRLCASGLDAVGAAARAIRSGDIDLALAGGVESMT 123

Query: 122 RAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQ 181
           RAPFVMGK+E  + R  ++ DTTIGWRFINP++K QYGVDSMPETA+NVA+D+Q+SRADQ
Sbjct: 124 RAPFVMGKSEGAWQRQAEIHDTTIGWRFINPMLKHQYGVDSMPETAENVAEDFQISRADQ 183

Query: 182 DAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKLKPV 240
           DAFALRSQ++AA AQA G  A+EI  V I  ++G+   V+RDEH RPETT E L KLKP 
Sbjct: 184 DAFALRSQERAARAQADGILAQEITAVAIPTRQGDHRRVDRDEHPRPETTAEGLAKLKPF 243

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
              D TVTAGNASGVNDGAAAL+LASAEA  +HGLTP  RVLG+AS GV PRVMGIGPVP
Sbjct: 244 VRRDGTVTAGNASGVNDGAAALVLASAEAAARHGLTPLTRVLGLASAGVPPRVMGIGPVP 303

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           AV  L  RLG+  SDFDVIELNEAFASQ LA LR LG+ DDA  VNP+GGAIA GHPLGM
Sbjct: 304 AVTALCARLGLKPSDFDVIELNEAFASQSLACLRGLGLPDDAEHVNPHGGAIAFGHPLGM 363

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGAR+   A  +L + GGR GLAT+CVGVGQG+ALA+ERV
Sbjct: 364 SGARIAGAATRELVRRGGRLGLATLCVGVGQGVALAVERV 403


Lambda     K      H
   0.318    0.134    0.383 

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: 552
Number of extensions: 17
Number of successful extensions: 3
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: 400
Length of database: 404
Length adjustment: 31
Effective length of query: 369
Effective length of database: 373
Effective search space:   137637
Effective search space used:   137637
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_015929439.1 MNOD_RS13390 (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.1940440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-207  673.8   7.2   4.9e-207  673.6   7.2    1.0  1  NCBI__GCF_000022085.1:WP_015929439.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015929439.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.6   7.2  4.9e-207  4.9e-207       1     400 []       5     403 ..       5     403 .. 0.99

  Alignments for each domain:
  == domain 1  score: 673.6 bits;  conditional E-value: 4.9e-207
                             TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaall 73 
                                           ++vyi+d +rtpiGrygG+l+svraddlaa+pl+all+rnpsl+ + +++v+lGcanqaGednrnvarma+ll
  NCBI__GCF_000022085.1:WP_015929439.1   5 RDVYICDFVRTPIGRYGGALASVRADDLAAIPLAALLHRNPSLK-DGVEEVFLGCANQAGEDNRNVARMALLL 76 
                                           689****************************************7.689************************* PP

                             TIGR02430  74 aGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGw 146
                                           aGlp++vpg t+nrlc+sglda+g aarai++G+ dl +aGGvesm+rapfv+Gk+++a+ r+a+++dttiGw
  NCBI__GCF_000022085.1:WP_015929439.1  77 AGLPETVPGLTLNRLCASGLDAVGAAARAIRSGDIDLALAGGVESMTRAPFVMGKSEGAWQRQAEIHDTTIGW 149
                                           ************************************************************************* PP

                             TIGR02430 147 rfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvv 219
                                           rf+np lk++yGvdsmpetaenvae+f++sr+dqdafalrsq+r+a+aqa G++a+ei+ v+i+ ++G++  v
  NCBI__GCF_000022085.1:WP_015929439.1 150 RFINPMLKHQYGVDSMPETAENVAEDFQISRADQDAFALRSQERAARAQADGILAQEITAVAIPTRQGDHRRV 222
                                           ************************************************************************* PP

                             TIGR02430 220 dkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvepr 292
                                           d+deh+r+ett e+laklk+ vr+dgtvtaGnasGvndGaaal+las+ea++rhgltp +r+l+ asaGv pr
  NCBI__GCF_000022085.1:WP_015929439.1 223 DRDEHPRPETTAEGLAKLKPFVRRDGTVTAGNASGVNDGAAALVLASAEAAARHGLTPLTRVLGLASAGVPPR 295
                                           ************************************************************************* PP

                             TIGR02430 293 vmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarl 365
                                           vmG+gpvpav  l ar+gl+ +d+dvielneafa+q+la+lr lgl+dd+++vnp GGaia+GhplG+sGar+
  NCBI__GCF_000022085.1:WP_015929439.1 296 VMGIGPVPAVTALCARLGLKPSDFDVIELNEAFASQSLACLRGLGLPDDAEHVNPHGGAIAFGHPLGMSGARI 368
                                           ************************************************************************* PP

                             TIGR02430 366 vltalkqleksggryalatlciGvGqGialvierv 400
                                           + +a ++l ++ggr +latlc+GvGqG+al++erv
  NCBI__GCF_000022085.1:WP_015929439.1 369 AGAATRELVRRGGRLGLATLCVGVGQGVALAVERV 403
                                           **********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (404 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: 00:00:00.00
# Mc/sec: 19.70
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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 2024 update 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