GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Escherichia coli BW25113

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 15138 b1014 fused DNA-binding transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (NCBI)

Query= BRENDA::P09546
         (1320 letters)



>FitnessBrowser__Keio:15138
          Length = 1320

 Score = 2587 bits (6706), Expect = 0.0
 Identities = 1320/1320 (100%), Positives = 1320/1320 (100%)

Query: 1    MGTTTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLENSDTLPELPALLSGA 60
            MGTTTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLENSDTLPELPALLSGA
Sbjct: 1    MGTTTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLENSDTLPELPALLSGA 60

Query: 61   ANESDEAPTPAEEPHQPFLDFAEQILPQSVSRAAITAAYRRPETEAVSMLLEQARLPQPV 120
            ANESDEAPTPAEEPHQPFLDFAEQILPQSVSRAAITAAYRRPETEAVSMLLEQARLPQPV
Sbjct: 61   ANESDEAPTPAEEPHQPFLDFAEQILPQSVSRAAITAAYRRPETEAVSMLLEQARLPQPV 120

Query: 121  AEQAHKLAYQLADKLRNQKNASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRIPDKAT 180
            AEQAHKLAYQLADKLRNQKNASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRIPDKAT
Sbjct: 121  AEQAHKLAYQLADKLRNQKNASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRIPDKAT 180

Query: 181  RDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSG 240
            RDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSG
Sbjct: 181  RDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSG 240

Query: 241  EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAY 300
            EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAY
Sbjct: 241  EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAY 300

Query: 301  MVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRVMEELYPRLKSLTLLA 360
            MVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRVMEELYPRLKSLTLLA
Sbjct: 301  MVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRVMEELYPRLKSLTLLA 360

Query: 361  RQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDL 420
            RQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDL
Sbjct: 361  RQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDL 420

Query: 421  ATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLI 480
            ATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLI
Sbjct: 421  ATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLI 480

Query: 481  YPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIY 540
            YPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIY
Sbjct: 481  YPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIY 540

Query: 541  APVGTHETLLAYLVRRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGL 600
            APVGTHETLLAYLVRRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGL
Sbjct: 541  APVGTHETLLAYLVRRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGL 600

Query: 601  PHPKIPLPRDLYGHGRDNSAGLDLANEHRLASLSSALLNSALQKWQALPMLEQPVAAGEM 660
            PHPKIPLPRDLYGHGRDNSAGLDLANEHRLASLSSALLNSALQKWQALPMLEQPVAAGEM
Sbjct: 601  PHPKIPLPRDLYGHGRDNSAGLDLANEHRLASLSSALLNSALQKWQALPMLEQPVAAGEM 660

Query: 661  SPVINPAEPKDIVGYVREATPREVEQALESAVNNAPIWFATPPAERAAILHRAAVLMESQ 720
            SPVINPAEPKDIVGYVREATPREVEQALESAVNNAPIWFATPPAERAAILHRAAVLMESQ
Sbjct: 661  SPVINPAEPKDIVGYVREATPREVEQALESAVNNAPIWFATPPAERAAILHRAAVLMESQ 720

Query: 721  MQQLIGILVREAGKTFSNAIAEVREAVDFLHYYAGQVRDDFANETHRPLGPVVCISPWNF 780
            MQQLIGILVREAGKTFSNAIAEVREAVDFLHYYAGQVRDDFANETHRPLGPVVCISPWNF
Sbjct: 721  MQQLIGILVREAGKTFSNAIAEVREAVDFLHYYAGQVRDDFANETHRPLGPVVCISPWNF 780

Query: 781  PLAIFTGQIAAALAAGNSVLAKPAEQTPLIAAQGIAILLEAGVPPGVVQLLPGRGETVGA 840
            PLAIFTGQIAAALAAGNSVLAKPAEQTPLIAAQGIAILLEAGVPPGVVQLLPGRGETVGA
Sbjct: 781  PLAIFTGQIAAALAAGNSVLAKPAEQTPLIAAQGIAILLEAGVPPGVVQLLPGRGETVGA 840

Query: 841  QLTGDDRVRGVMFTGSTEVATLLQRNIASRLDAQGRPIPLIAETGGMNAMIVDSSALTEQ 900
            QLTGDDRVRGVMFTGSTEVATLLQRNIASRLDAQGRPIPLIAETGGMNAMIVDSSALTEQ
Sbjct: 841  QLTGDDRVRGVMFTGSTEVATLLQRNIASRLDAQGRPIPLIAETGGMNAMIVDSSALTEQ 900

Query: 901  VVVDVLASAFDSAGQRCSALRVLCLQDEIADHTLKMLRGAMAECRMGNPGRLTTDIGPVI 960
            VVVDVLASAFDSAGQRCSALRVLCLQDEIADHTLKMLRGAMAECRMGNPGRLTTDIGPVI
Sbjct: 901  VVVDVLASAFDSAGQRCSALRVLCLQDEIADHTLKMLRGAMAECRMGNPGRLTTDIGPVI 960

Query: 961  DSEAKANIERHIQTMRSKGRPVFQAVRENSEDAREWQSGTFVAPTLIELDDFAELQKEVF 1020
            DSEAKANIERHIQTMRSKGRPVFQAVRENSEDAREWQSGTFVAPTLIELDDFAELQKEVF
Sbjct: 961  DSEAKANIERHIQTMRSKGRPVFQAVRENSEDAREWQSGTFVAPTLIELDDFAELQKEVF 1020

Query: 1021 GPVLHVVRYNRNQLPELIEQINASGYGLTLGVHTRIDETIAQVTGSAHVGNLYVNRNMVG 1080
            GPVLHVVRYNRNQLPELIEQINASGYGLTLGVHTRIDETIAQVTGSAHVGNLYVNRNMVG
Sbjct: 1021 GPVLHVVRYNRNQLPELIEQINASGYGLTLGVHTRIDETIAQVTGSAHVGNLYVNRNMVG 1080

Query: 1081 AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLANRPESALAVTLARQDAKYPVDAQLKAALT 1140
            AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLANRPESALAVTLARQDAKYPVDAQLKAALT
Sbjct: 1081 AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLANRPESALAVTLARQDAKYPVDAQLKAALT 1140

Query: 1141 QPLNALREWAANRPELQALCTQYGELAQAGTQRLLPGPTGERNTWTLLPRERVLCIADDE 1200
            QPLNALREWAANRPELQALCTQYGELAQAGTQRLLPGPTGERNTWTLLPRERVLCIADDE
Sbjct: 1141 QPLNALREWAANRPELQALCTQYGELAQAGTQRLLPGPTGERNTWTLLPRERVLCIADDE 1200

Query: 1201 QDALTQLAAVLAVGSQVLWPDDALHRQLVKALPSAVSERIQLAKAENITAQPFDAVIFHG 1260
            QDALTQLAAVLAVGSQVLWPDDALHRQLVKALPSAVSERIQLAKAENITAQPFDAVIFHG
Sbjct: 1201 QDALTQLAAVLAVGSQVLWPDDALHRQLVKALPSAVSERIQLAKAENITAQPFDAVIFHG 1260

Query: 1261 DSDQLRALCEAVAARDGTIVSVQGFARGESNILLERLYIERSLSVNTAAAGGNASLMTIG 1320
            DSDQLRALCEAVAARDGTIVSVQGFARGESNILLERLYIERSLSVNTAAAGGNASLMTIG
Sbjct: 1261 DSDQLRALCEAVAARDGTIVSVQGFARGESNILLERLYIERSLSVNTAAAGGNASLMTIG 1320


Lambda     K      H
   0.318    0.133    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: 4807
Number of extensions: 180
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: 1320
Length of database: 1320
Length adjustment: 48
Effective length of query: 1272
Effective length of database: 1272
Effective search space:  1617984
Effective search space used:  1617984
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: 59 (27.3 bits)

Align candidate 15138 b1014 (fused DNA-binding transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (NCBI))
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01238.hmm
# target sequence database:        /tmp/gapView.507794.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   7.3e-267  871.6   0.2   1.1e-266  871.0   0.2    1.3  1  lcl|FitnessBrowser__Keio:15138  b1014 fused DNA-binding transcri


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15138  b1014 fused DNA-binding transcriptional regulator/proline dehydrogenase/pyrroline-5-c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  871.0   0.2  1.1e-266  1.1e-266       1     498 [.     610    1112 ..     610    1114 .. 0.99

  Alignments for each domain:
  == domain 1  score: 871.0 bits;  conditional E-value: 1.1e-266
                       TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaaevq 77  
                                      dlyg+gr ns+G+dlane++l+sl++ ll++a++k+qa+p++ e+++a ge+ pv npa++kdivG+v+ea   ev+
  lcl|FitnessBrowser__Keio:15138  610 DLYGHGRDNSAGLDLANEHRLASLSSALLNSALQKWQALPML-EQPVAAGEMSPVINPAEPKDIVGYVREATPREVE 685 
                                      89****************************************.9********************************* PP

                       TIGR01238   78 eavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqvedvld 154 
                                      +a++sav+++++w+at+++eraail+r+a+l+es+m +l+++lvreaGkt+snaiaevreavdfl+yya+qv+d++ 
  lcl|FitnessBrowser__Keio:15138  686 QALESAVNNAPIWFATPPAERAAILHRAAVLMESQMQQLIGILVREAGKTFSNAIAEVREAVDFLHYYAGQVRDDFA 762 
                                      ***************************************************************************** PP

                       TIGR01238  155 eesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvG 231 
                                      +e++++lG+vvcispwnfplaiftGqiaaalaaGn+v+akpaeqt+liaa+++++l+eaGvp+gv+qllpGrGe+vG
  lcl|FitnessBrowser__Keio:15138  763 NETHRPLGPVVCISPWNFPLAIFTGQIAAALAAGNSVLAKPAEQTPLIAAQGIAILLEAGVPPGVVQLLPGRGETVG 839 
                                      ***************************************************************************** PP

                       TIGR01238  232 aaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamivdstalaeqvvadvlasafdsaGqr 305 
                                      a lt d+r++Gv+ftGsteva+l+++++a+r da+   +pliaetGG+namivds+al+eqvv+dvlasafdsaGqr
  lcl|FitnessBrowser__Keio:15138  840 AQLTGDDRVRGVMFTGSTEVATLLQRNIASRLDAQgrpIPLIAETGGMNAMIVDSSALTEQVVVDVLASAFDSAGQR 916 
                                      *********************************99988*************************************** PP

                       TIGR01238  306 csalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkledd... 379 
                                      csalrvlc+q+++ad++l++++Gam e+++g+p+rlttd+Gpvid+eak n+++hi+ m++k++ v+q+++e++   
  lcl|FitnessBrowser__Keio:15138  917 CSALRVLCLQDEIADHTLKMLRGAMAECRMGNPGRLTTDIGPVIDSEAKANIERHIQTMRSKGRPVFQAVRENSeda 993 
                                      ***********************************************************************998888 PP

                       TIGR01238  380 vesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvG 456 
                                      +e++ gtfvaptl+eldd++el+kevfGpvlhvvry++++l +++++ina+GygltlGvh+ri+et++q++++a+vG
  lcl|FitnessBrowser__Keio:15138  994 REWQSGTFVAPTLIELDDFAELQKEVFGPVLHVVRYNRNQLPELIEQINASGYGLTLGVHTRIDETIAQVTGSAHVG 1070
                                      9**************************************************************************** PP

                       TIGR01238  457 nvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrv 498 
                                      n+yvnrn+vGavvGvqpfGGeGlsGtGpkaGGplylyrl+  
  lcl|FitnessBrowser__Keio:15138 1071 NLYVNRNMVGAVVGVQPFGGEGLSGTGPKAGGPLYLYRLLAN 1112
                                      ***************************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1320 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: 00:00:00.01
# Mc/sec: 42.29
//
[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