GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Xanthobacter autotrophicus Py2

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_012112924.1 XAUT_RS04530 3-oxoadipyl-CoA thiolase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_000017645.1:WP_012112924.1
          Length = 402

 Score =  560 bits (1442), Expect = e-164
 Identities = 284/402 (70%), Positives = 322/402 (80%), Gaps = 1/402 (0%)

Query: 1   MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           M  AFICD  RTPIGRY GAL  VRADDLAA P+R L  RNP +D E +DDVILGCANQA
Sbjct: 1   MAHAFICDFARTPIGRYAGALKDVRADDLAAHPIRVLKERNPGVDWEAVDDVILGCANQA 60

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
           GEDNR+VARMA LLAGLP S  GTT+NRLCGSGLDA+G  ARAI  GD DL++AGGVESM
Sbjct: 61  GEDNRDVARMAALLAGLPVSAPGTTVNRLCGSGLDAVGIGARAIMTGDADLIVAGGVESM 120

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180
           +RAPFV GKA  AFSRQAE++DTTIGWRFVNPLM  Q+G DSMPET ENVAE  ++SR D
Sbjct: 121 TRAPFVQGKAQEAFSRQAEIYDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDFQVSRAD 180

Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240
           QD FA RSQQR   AQ +G  A EI P+ +K KKG V  ++ DEH R ETTLEQL GLKA
Sbjct: 181 QDLFAYRSQQRVKAAQDAGFFAREIAPIEVKGKKGAVIRVEADEHPRAETTLEQLAGLKA 240

Query: 241 PFR-ANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299
           PFR A G +TAGNASGVNDGA ALI+ASE  A   GLTPRAR+V++  AGV PR+MG+GP
Sbjct: 241 PFRKAGGTVTAGNASGVNDGAGALILASEAAAKKYGLTPRARVVSVVQAGVPPRIMGIGP 300

Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359
            PATR++LE+ GL++ D+D+IELNEAFAAQAL VLR+LGLPDDA HVNPNGGAIALGHPL
Sbjct: 301 APATRKLLEKNGLALADIDLIELNEAFAAQALAVLRQLGLPDDAEHVNPNGGAIALGHPL 360

Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           GMSGARLA+ A   L  R G  A+ TMCIGVGQGIA ++ERV
Sbjct: 361 GMSGARLAMTAVSALEVRGGTRAVATMCIGVGQGIAALIERV 402


Lambda     K      H
   0.319    0.135    0.384 

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: 536
Number of extensions: 17
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: 401
Length of database: 402
Length adjustment: 31
Effective length of query: 370
Effective length of database: 371
Effective search space:   137270
Effective search space used:   137270
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_012112924.1 XAUT_RS04530 (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.2513442.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-210  685.2  11.8   1.7e-210  685.0  11.8    1.0  1  NCBI__GCF_000017645.1:WP_012112924.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017645.1:WP_012112924.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.0  11.8  1.7e-210  1.7e-210       2     400 .]       3     402 .]       2     402 .] 0.99

  Alignments for each domain:
  == domain 1  score: 685.0 bits;  conditional E-value: 1.7e-210
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           +++i+d  rtpiGry+G+l  vraddlaa p++ l +rnp +d++a+ddvilGcanqaGednr+varmaalla
  NCBI__GCF_000017645.1:WP_012112924.1   3 HAFICDFARTPIGRYAGALKDVRADDLAAHPIRVLKERNPGVDWEAVDDVILGCANQAGEDNRDVARMAALLA 75 
                                           79*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glpvs pgttvnrlcgsglda+g++arai +G+adl++aGGvesm+rapfv Gka+ afsr+a++ dttiGwr
  NCBI__GCF_000017645.1:WP_012112924.1  76 GLPVSAPGTTVNRLCGSGLDAVGIGARAIMTGDADLIVAGGVESMTRAPFVQGKAQEAFSRQAEIYDTTIGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           fvnp +ka+yGvdsmpet envae+f+vsr+dqd fa+rsqqr++aaq +Gffa+ei+p+e+k+kkG    v+
  NCBI__GCF_000017645.1:WP_012112924.1 149 FVNPLMKAQYGVDSMPETGENVAEDFQVSRADQDLFAYRSQQRVKAAQDAGFFAREIAPIEVKGKKGAVIRVE 221
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvre.dgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvepr 292
                                           +deh+raettle+la lka++r+ +gtvtaGnasGvndGa al+lase a+k++gltprar++++  aGv pr
  NCBI__GCF_000017645.1:WP_012112924.1 222 ADEHPRAETTLEQLAGLKAPFRKaGGTVTAGNASGVNDGAGALILASEAAAKKYGLTPRARVVSVVQAGVPPR 294
                                           *******************9986268*********************************************** PP

                             TIGR02430 293 vmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarl 365
                                           +mG+gp+pa++kll++ gl+l+d+d+ielneafaaqalavlr+lgl+dd+++vnpnGGaialGhplG+sGarl
  NCBI__GCF_000017645.1:WP_012112924.1 295 IMGIGPAPATRKLLEKNGLALADIDLIELNEAFAAQALAVLRQLGLPDDAEHVNPNGGAIALGHPLGMSGARL 367
                                           ************************************************************************* PP

                             TIGR02430 366 vltalkqleksggryalatlciGvGqGialvierv 400
                                           ++ta++ le +gg +a+at+ciGvGqGia +ierv
  NCBI__GCF_000017645.1:WP_012112924.1 368 AMTAVSALEVRGGTRAVATMCIGVGQGIAALIERV 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.98
//
[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