Alignments for a candidate for paaJ2 in Luteimonas huabeiensis HB2

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Luteimonas huabeiensis HB2

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_024889962.1 Z164_RS0106825 3-oxoadipyl-CoA thiolase

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



>NCBI__GCF_000559025.1:WP_024889962.1
          Length = 401

 Score =  554 bits (1428), Expect = e-162
 Identities = 276/402 (68%), Positives = 337/402 (83%), Gaps = 3/402 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M + F+CDA+RTPIGR+GG+L+GVRADDL AVP++AL+  NP +  + VD+VFFGCANQA
Sbjct: 1   MSEAFVCDAVRTPIGRYGGSLSGVRADDLGAVPIRALLARNPGLDPEAVDDVFFGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARM+LLLAGLP S+PGVTLNRLCASG++A+G A RAI SGE+ELAIAGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPASVPGVTLNRLCASGLEAVGQAARAIRSGEIELAIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           +RAPFV+GKA+S + R  +LEDTT+GWRF+NP ++++YG ++MP+T +N+A ++ VSR D
Sbjct: 121 TRAPFVVGKADSAFGRGQRLEDTTMGWRFVNPRLQARYGAETMPQTGENLAREHGVSRED 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRI-AHKKGE-TIVERDEHLRPETTLEALTKLK 238
           QDAFALRSQQ+AAAA+AAGF AEEIV V +   K+G+  + E DEH R +TTLEAL  LK
Sbjct: 181 QDAFALRSQQRAAAARAAGFLAEEIVAVEVPGRKRGDRALAEVDEHPRADTTLEALAGLK 240

Query: 239 PVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298
           P+  P  +VTAGNASG+NDGAAAL++A   AV + GL PRAR+LG+A+ GV PRVMGIGP
Sbjct: 241 PL-FPGGSVTAGNASGINDGAAALVVAGERAVARFGLRPRARILGLAAAGVEPRVMGIGP 299

Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358
           VPA RKL  RLG+ + DFD IELNEAFASQ LAVLR LG+ DDA  VN NGGAIALGHPL
Sbjct: 300 VPATRKLLARLGLGIGDFDAIELNEAFASQSLAVLRALGLPDDAAHVNANGGAIALGHPL 359

Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GMSGARL LT +HQL+K+GGR GLAT+C+GVG GLALA+ERV
Sbjct: 360 GMSGARLALTLVHQLQKTGGRYGLATLCIGVGMGLALAVERV 401


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: 598
Number of extensions: 32
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: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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_024889962.1 Z164_RS0106825 (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.645922.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-210  685.5  10.8   1.3e-210  685.4  10.8    1.0  1  NCBI__GCF_000559025.1:WP_024889962.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000559025.1:WP_024889962.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.4  10.8  1.3e-210  1.3e-210       2     400 .]       3     401 .]       2     401 .] 0.99

  Alignments for each domain:
  == domain 1  score: 685.4 bits;  conditional E-value: 1.3e-210
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           e++++da+rtpiGrygGsls vraddl+avp++allarnp ld +a+ddv++GcanqaGednrnvarm++lla
  NCBI__GCF_000559025.1:WP_024889962.1   3 EAFVCDAVRTPIGRYGGSLSGVRADDLGAVPIRALLARNPGLDPEAVDDVFFGCANQAGEDNRNVARMSLLLA 75 
                                           79*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glp+svpg+t+nrlc+sgl+a+g aarai++Ge +l iaGGvesm+rapfv+Gkadsaf+r ++ledtt+Gwr
  NCBI__GCF_000559025.1:WP_024889962.1  76 GLPASVPGVTLNRLCASGLEAVGQAARAIRSGEIELAIAGGVESMTRAPFVVGKADSAFGRGQRLEDTTMGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqk.kGeetvv 219
                                           fvnp+l+a yG ++mp+t en+a+e+gvsredqdafalrsqqr+aaa+a+Gf+aeeiv ve++++ +G+ +  
  NCBI__GCF_000559025.1:WP_024889962.1 149 FVNPRLQARYGAETMPQTGENLAREHGVSREDQDAFALRSQQRAAAARAAGFLAEEIVAVEVPGRkRGDRALA 221
                                           **************************************************************975169***** PP

                             TIGR02430 220 dkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvepr 292
                                           + deh+ra+ttleala lk+++ ++g+vtaGnasG+ndGaaal++a+e av+r+gl+praril+ a+aGvepr
  NCBI__GCF_000559025.1:WP_024889962.1 222 EVDEHPRADTTLEALAGLKPLF-PGGSVTAGNASGINDGAAALVVAGERAVARFGLRPRARILGLAAAGVEPR 293
                                           *******************998.89************************************************ PP

                             TIGR02430 293 vmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarl 365
                                           vmG+gpvpa++kllar+gl + d+d+ielneafa+q+lavlr+lgl+dd+a+vn+nGGaialGhplG+sGarl
  NCBI__GCF_000559025.1:WP_024889962.1 294 VMGIGPVPATRKLLARLGLGIGDFDAIELNEAFASQSLAVLRALGLPDDAAHVNANGGAIALGHPLGMSGARL 366
                                           ************************************************************************* PP

                             TIGR02430 366 vltalkqleksggryalatlciGvGqGialvierv 400
                                           +lt+++ql+k+ggry+latlciGvG G+al++erv
  NCBI__GCF_000559025.1:WP_024889962.1 367 ALTLVHQLQKTGGRYGLATLCIGVGMGLALAVERV 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.45
//
[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:

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