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 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_015929945.1 MNOD_RS15895 3-oxoadipyl-CoA thiolase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>NCBI__GCF_000022085.1:WP_015929945.1
          Length = 402

 Score =  558 bits (1438), Expect = e-163
 Identities = 287/402 (71%), Positives = 329/402 (81%), Gaps = 2/402 (0%)

Query: 1   MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60
           M+ AYICD  RTPIGRYGGALKDVRADDL A PI+ L +RNPG+DW AVDDV+ GCANQA
Sbjct: 1   MSHAYICDFARTPIGRYGGALKDVRADDLAAYPIRVLKERNPGIDWEAVDDVVLGCANQA 60

Query: 61  GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120
           GEDNR+VARM+ALLAGLP  APG T+NRLCGSG+DAVG AARAI  G+A LM+AGGVESM
Sbjct: 61  GEDNRDVARMAALLAGLPVSAPGTTVNRLCGSGLDAVGIAARAIMTGDADLMLAGGVESM 120

Query: 121 TRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180
           TRAPFVMGKA  AF+RQAE+ DTTIGWRFVNPLMK QYG+DSMPET ENVAE+F ISR D
Sbjct: 121 TRAPFVMGKATEAFSRQAEVFDTTIGWRFVNPLMKAQYGIDSMPETGENVAEEFRISRQD 180

Query: 181 QDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPR-ETSLESLARLKG 239
           QD FAL SQQ+AA AQ +G   +EIV +E+  KKG  IRV  DEHPR +T+LE LA LK 
Sbjct: 181 QDLFALRSQQRAAAAQAEGFFDREIVALEVKGKKGAVIRVDRDEHPRPDTTLEQLAALKT 240

Query: 240 VVRPD-GTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGP 298
             R + GTVTAGNASGVNDGA AL++AS++AA +YGL  RARVV +  AGV PRIMGIGP
Sbjct: 241 SFRKEGGTVTAGNASGVNDGAGALILASEEAARKYGLTPRARVVSVVQAGVPPRIMGIGP 300

Query: 299 APATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPL 358
           APAT+KLL + G++L ++D+IELNEAFASQ LAVLR LGL DD   VNP+GGAIALGHPL
Sbjct: 301 APATRKLLAKNGLSLSEIDLIELNEAFASQALAVLRELGLPDDAEHVNPHGGAIALGHPL 360

Query: 359 GASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400
           G SGARL  TA+  LE   G+ A+ TMCIGVGQGIA +IER+
Sbjct: 361 GMSGARLAMTAVSALEVRGGKRAVATMCIGVGQGIAALIERV 402


Lambda     K      H
   0.319    0.134    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: 513
Number of extensions: 12
Number of successful extensions: 2
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: 402
Length adjustment: 31
Effective length of query: 369
Effective length of database: 371
Effective search space:   136899
Effective search space used:   136899
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_015929945.1 MNOD_RS15895 (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.1642561.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.4e-213  692.4   8.6   1.1e-212  692.3   8.6    1.0  1  NCBI__GCF_000022085.1:WP_015929945.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015929945.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.3   8.6  1.1e-212  1.1e-212       2     400 .]       3     402 .]       2     402 .] 0.99

  Alignments for each domain:
  == domain 1  score: 692.3 bits;  conditional E-value: 1.1e-212
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           ++yi+d  rtpiGrygG+l  vraddlaa p++ l +rnp +d++a+ddv+lGcanqaGednr+varmaalla
  NCBI__GCF_000022085.1:WP_015929945.1   3 HAYICDFARTPIGRYGGALKDVRADDLAAYPIRVLKERNPGIDWEAVDDVVLGCANQAGEDNRDVARMAALLA 75 
                                           79*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glpvs pgttvnrlcgsglda+g+aarai +G+adl++aGGvesm+rapfv+Gka  afsr+a+++dttiGwr
  NCBI__GCF_000022085.1:WP_015929945.1  76 GLPVSAPGTTVNRLCGSGLDAVGIAARAIMTGDADLMLAGGVESMTRAPFVMGKATEAFSRQAEVFDTTIGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           fvnp +ka+yG+dsmpet envaeef++sr+dqd falrsqqr+aaaqa+Gff++eiv +e+k+kkG    vd
  NCBI__GCF_000022085.1:WP_015929945.1 149 FVNPLMKAQYGIDSMPETGENVAEEFRISRQDQDLFALRSQQRAAAAQAEGFFDREIVALEVKGKKGAVIRVD 221
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvred.gtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvepr 292
                                           +deh+r++ttle+la lk+ +r++ gtvtaGnasGvndGa al+laseea++++gltprar++++  aGv pr
  NCBI__GCF_000022085.1:WP_015929945.1 222 RDEHPRPDTTLEQLAALKTSFRKEgGTVTAGNASGVNDGAGALILASEEAARKYGLTPRARVVSVVQAGVPPR 294
                                           *******************99875279********************************************** PP

                             TIGR02430 293 vmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarl 365
                                           +mG+gp+pa++klla+ glsl+++d+ielneafa+qalavlrelgl+dd+++vnp GGaialGhplG+sGarl
  NCBI__GCF_000022085.1:WP_015929945.1 295 IMGIGPAPATRKLLAKNGLSLSEIDLIELNEAFASQALAVLRELGLPDDAEHVNPHGGAIALGHPLGMSGARL 367
                                           ************************************************************************* PP

                             TIGR02430 366 vltalkqleksggryalatlciGvGqGialvierv 400
                                           ++ta++ le +gg++a+at+ciGvGqGia +ierv
  NCBI__GCF_000022085.1:WP_015929945.1 368 AMTAVSALEVRGGKRAVATMCIGVGQGIAALIERV 402
                                           **********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (402 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 22.89
//
[ok]

This GapMind analysis is from Apr 09 2024. 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