GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Neptunomonas antarctica S3-22

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_054341003.1 Nant_RS07360 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_001305295.1:WP_054341003.1
          Length = 402

 Score =  569 bits (1467), Expect = e-167
 Identities = 286/402 (71%), Positives = 332/402 (82%), Gaps = 1/402 (0%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M +A I DAVRTP GRY G L+SVR DDLGAIPLKAL+ R+P ++W++V+DVIYG ANQA
Sbjct: 1   MKDAFICDAVRTPFGRYGGGLSSVRPDDLGAIPLKALMERNPDVNWASVEDVIYGNANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ALLAG PVSVPGTT+NRLCGSG+DA+G AARA++ GE  LM+AGG ESM
Sbjct: 61  GEDNRNVARMSALLAGFPVSVPGTTVNRLCGSGMDAIGMAARAIKSGETELMIAGGCESM 120

Query: 121 SRAPFVMGKSEQAFGRSAE-IFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179
           SRAPFVMGK+E AF R+   ++DTTIGWRF+NK M++ +G+DSMPETAENVA +FNISRA
Sbjct: 121 SRAPFVMGKAESAFSRTPNGLYDTTIGWRFINKKMKEQYGVDSMPETAENVAEEFNISRA 180

Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239
           DQD FA RSQ K A A+  G   +EIV V I QRKG   +V+ DEHPR  TTLE LAKL 
Sbjct: 181 DQDLFAFRSQQKTAIAMQKGLFNEEIVPVVIPQRKGDPIVVDTDEHPRASTTLEDLAKLK 240

Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299
            PFR GGSVTAGNASGVNDGACALL+AS+EAA+ +GL  +AR+V MA AG+EPRIMG GP
Sbjct: 241 APFRAGGSVTAGNASGVNDGACALLIASAEAAKANGLVPKARIVAMAAAGLEPRIMGFGP 300

Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPL 359
            PATR VL+  GL L  MDVIELNEAFA+QGLAVLR+LGL DD   VNPNGGAI+LGHPL
Sbjct: 301 APATRNVLKKAGLTLDQMDVIELNEAFASQGLAVLRDLGLPDDAAHVNPNGGAISLGHPL 360

Query: 360 GMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           G SGARLV TA+++L    GRYALCTMCIGVGQGIA+IIER+
Sbjct: 361 GASGARLVMTAMYQLHRTGGRYALCTMCIGVGQGIAMIIERV 402


Lambda     K      H
   0.319    0.134    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: 553
Number of extensions: 16
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_054341003.1 Nant_RS07360 (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.2394570.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-225  734.6   4.7   1.7e-225  734.4   4.7    1.0  1  NCBI__GCF_001305295.1:WP_054341003.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001305295.1:WP_054341003.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  734.4   4.7  1.7e-225  1.7e-225       1     400 []       2     402 .]       2     402 .] 1.00

  Alignments for each domain:
  == domain 1  score: 734.4 bits;  conditional E-value: 1.7e-225
                             TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaall 73 
                                           k+++i+da+rtp+GrygG+lssvr ddl+a+plkal++rnp++++a+++dvi+G anqaGednrnvarm+all
  NCBI__GCF_001305295.1:WP_054341003.1   2 KDAFICDAVRTPFGRYGGGLSSVRPDDLGAIPLKALMERNPDVNWASVEDVIYGNANQAGEDNRNVARMSALL 74 
                                           689********************************************************************** PP

                             TIGR02430  74 aGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsak.ledttiG 145
                                           aG+pvsvpgttvnrlcgsg+da+g+aaraik+Ge++l+iaGG esmsrapfv+Gka+safsr+ + l dttiG
  NCBI__GCF_001305295.1:WP_054341003.1  75 AGFPVSVPGTTVNRLCGSGMDAIGMAARAIKSGETELMIAGGCESMSRAPFVMGKAESAFSRTPNgLYDTTIG 147
                                           ***************************************************************888******* PP

                             TIGR02430 146 wrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetv 218
                                           wrf+n k+k++yGvdsmpetaenvaeef++sr+dqd fa+rsqq+ta a +kG+f+eeivpv+i+q+kG++ v
  NCBI__GCF_001305295.1:WP_054341003.1 148 WRFINKKMKEQYGVDSMPETAENVAEEFNISRADQDLFAFRSQQKTAIAMQKGLFNEEIVPVVIPQRKGDPIV 220
                                           ************************************************************************* PP

                             TIGR02430 219 vdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvep 291
                                           vd+deh+ra+ttle laklka++r++g+vtaGnasGvndGa+all+as+ea+k++gl+p+ari+a+a+aG+ep
  NCBI__GCF_001305295.1:WP_054341003.1 221 VDTDEHPRASTTLEDLAKLKAPFRAGGSVTAGNASGVNDGACALLIASAEAAKANGLVPKARIVAMAAAGLEP 293
                                           ************************************************************************* PP

                             TIGR02430 292 rvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGar 364
                                           r+mG+gp+pa++++l++agl+l+++dvielneafa+q+lavlr+lgl+dd+a+vnpnGGai+lGhplGasGar
  NCBI__GCF_001305295.1:WP_054341003.1 294 RIMGFGPAPATRNVLKKAGLTLDQMDVIELNEAFASQGLAVLRDLGLPDDAAHVNPNGGAISLGHPLGASGAR 366
                                           ************************************************************************* PP

                             TIGR02430 365 lvltalkqleksggryalatlciGvGqGialvierv 400
                                           lv+ta++ql+++ggryal+t+ciGvGqGia++ierv
  NCBI__GCF_001305295.1:WP_054341003.1 367 LVMTAMYQLHRTGGRYALCTMCIGVGQGIAMIIERV 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.99
//
[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:

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