GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Sinorhizobium meliloti 1021

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate SM_b20589 SM_b20589 beta-ketoadipyl CoA thiolase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>FitnessBrowser__Smeli:SM_b20589
          Length = 400

 Score =  566 bits (1459), Expect = e-166
 Identities = 286/400 (71%), Positives = 330/400 (82%)

Query: 1   MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60
           M +AYICD IRTPIGR+GG+L  VRADDLGA+P+KAL+ RN  VDW AVDDVI+GCANQA
Sbjct: 1   MREAYICDYIRTPIGRFGGSLASVRADDLGAIPLKALMDRNRSVDWEAVDDVIFGCANQA 60

Query: 61  GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120
           GEDNRN+ARMS LLAGLP   PG TINRLCGSGMDAV  AARAIK GEA+LMIAGGVESM
Sbjct: 61  GEDNRNIARMSLLLAGLPVAVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVESM 120

Query: 121 TRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180
           +RAPFV+ KA SAF+R AEI+DTTIGWRFVNPLMK QYGVDSMPET ENVAE + +SR D
Sbjct: 121 SRAPFVLPKAESAFSRNAEIYDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDYKVSRED 180

Query: 181 QDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGV 240
           QDAFAL SQ KAA AQ +G LA EIV V I Q+KG  + +  DEHPR T++E+LA LK  
Sbjct: 181 QDAFALRSQAKAAAAQANGRLASEIVAVTIPQRKGGPVVIDRDEHPRATTIEALAGLKTP 240

Query: 241 VRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAP 300
            R  GTVTAGNASGVNDGA AL+IAS++AA ++GLR  AR++G A+AGV PRIMG+GP P
Sbjct: 241 FREGGTVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASAGVPPRIMGMGPVP 300

Query: 301 ATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGA 360
           A+Q+L+ +LG T D+ DVIELNEAFASQGLAVLR LG+ DDDPRVN NGGAIALGHPLG 
Sbjct: 301 ASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADDDPRVNRNGGAIALGHPLGM 360

Query: 361 SGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400
           SGAR+  TA  +L  + GR +L TMCIGVGQGIA+ +ER+
Sbjct: 361 SGARITGTAALELAETGGRTSLSTMCIGVGQGIAVALERV 400


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: 528
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 SM_b20589 SM_b20589 (beta-ketoadipyl 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.12140.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
     1e-213  695.6  10.3   1.1e-213  695.5  10.3    1.0  1  lcl|FitnessBrowser__Smeli:SM_b20589  SM_b20589 beta-ketoadipyl CoA th


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b20589  SM_b20589 beta-ketoadipyl CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.5  10.3  1.1e-213  1.1e-213       1     400 []       2     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 695.5 bits;  conditional E-value: 1.1e-213
                            TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                          +e+yi+d irtpiGr+gGsl+svraddl+a+plkal++rn s+d++a+ddvi+GcanqaGednrn+arm++lla
  lcl|FitnessBrowser__Smeli:SM_b20589   2 REAYICDYIRTPIGRFGGSLASVRADDLGAIPLKALMDRNRSVDWEAVDDVIFGCANQAGEDNRNIARMSLLLA 75 
                                          69************************************************************************ PP

                            TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrf 148
                                          Glpv+vpgtt+nrlcgsg+da+  aaraik+Gea+l+iaGGvesmsrapfvl ka+safsr+a++ dttiGwrf
  lcl|FitnessBrowser__Smeli:SM_b20589  76 GLPVAVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVESMSRAPFVLPKAESAFSRNAEIYDTTIGWRF 149
                                          ************************************************************************** PP

                            TIGR02430 149 vnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkd 222
                                          vnp +ka+yGvdsmpet envae+++vsredqdafalrsq+++aaaqa+G +a+eiv v+i+q+kG ++v+d+d
  lcl|FitnessBrowser__Smeli:SM_b20589 150 VNPLMKAQYGVDSMPETGENVAEDYKVSREDQDAFALRSQAKAAAAQANGRLASEIVAVTIPQRKGGPVVIDRD 223
                                          ************************************************************************** PP

                            TIGR02430 223 ehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGl 296
                                          eh+r  tt+eala lk+++re+gtvtaGnasGvndGaaal++aseea+++hgl+p aril+ asaGv pr+mG+
  lcl|FitnessBrowser__Smeli:SM_b20589 224 EHPR-ATTIEALAGLKTPFREGGTVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASAGVPPRIMGM 296
                                          ****.89******************************************************************* PP

                            TIGR02430 297 gpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltal 370
                                          gpvpa ++l++r+g + + +dvielneafa+q+lavlr+lg+addd rvn nGGaialGhplG+sGar+  ta 
  lcl|FitnessBrowser__Smeli:SM_b20589 297 GPVPASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADDDPRVNRNGGAIALGHPLGMSGARITGTAA 370
                                          ************************************************************************** PP

                            TIGR02430 371 kqleksggryalatlciGvGqGialvierv 400
                                           +l+++ggr +l+t+ciGvGqGia+++erv
  lcl|FitnessBrowser__Smeli:SM_b20589 371 LELAETGGRTSLSTMCIGVGQGIAVALERV 400
                                          *****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (400 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: 00:00:00.02
# Mc/sec: 7.55
//
[ok]

This GapMind analysis is from Sep 17 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:

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