Alignments for a candidate for putA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Klebsiella michiganensis M5al

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate BWI76_RS10795 BWI76_RS10795 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= reanno::Koxy:BWI76_RS10795
         (1320 letters)



>FitnessBrowser__Koxy:BWI76_RS10795
          Length = 1320

 Score = 2599 bits (6737), Expect = 0.0
 Identities = 1320/1320 (100%), Positives = 1320/1320 (100%)

Query: 1    MGTTTMGVKLDDATRERIKSAASRIDRTPHWLIKQAIFNYLEKLENDETLPELPALLSGA 60
            MGTTTMGVKLDDATRERIKSAASRIDRTPHWLIKQAIFNYLEKLENDETLPELPALLSGA
Sbjct: 1    MGTTTMGVKLDDATRERIKSAASRIDRTPHWLIKQAIFNYLEKLENDETLPELPALLSGA 60

Query: 61   ANESDEAGNPADEPYQPFLDFAEQILPQSVSRASITAAWRWAETDAVPMLLEQARLPQTL 120
            ANESDEAGNPADEPYQPFLDFAEQILPQSVSRASITAAWRWAETDAVPMLLEQARLPQTL
Sbjct: 61   ANESDEAGNPADEPYQPFLDFAEQILPQSVSRASITAAWRWAETDAVPMLLEQARLPQTL 120

Query: 121  GEQAHKLAYQLAEKLRNQKTASGRAGMVQSLLQEFSLSSQEGVALMCLAEALLRIPDKAT 180
            GEQAHKLAYQLAEKLRNQKTASGRAGMVQSLLQEFSLSSQEGVALMCLAEALLRIPDKAT
Sbjct: 121  GEQAHKLAYQLAEKLRNQKTASGRAGMVQSLLQEFSLSSQEGVALMCLAEALLRIPDKAT 180

Query: 181  RDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSPHNETSLSRSLNRIIGKSG 240
            RDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSPHNETSLSRSLNRIIGKSG
Sbjct: 181  RDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSPHNETSLSRSLNRIIGKSG 240

Query: 241  EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEDKGFRYSYDMLGEAALTADDAQAY 300
            EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEDKGFRYSYDMLGEAALTADDAQAY
Sbjct: 241  EPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEDKGFRYSYDMLGEAALTADDAQAY 300

Query: 301  MVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRAMEELYPRLKSLTLLA 360
            MVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRAMEELYPRLKSLTLLA
Sbjct: 301  MVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRAMEELYPRLKSLTLLA 360

Query: 361  RQYDIGINIDAEEADRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPFVIDYLIDL 420
            RQYDIGINIDAEEADRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPFVIDYLIDL
Sbjct: 361  RQYDIGINIDAEEADRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPFVIDYLIDL 420

Query: 421  ATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLI 480
            ATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLI
Sbjct: 421  ATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLI 480

Query: 481  YPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKIADGKLNRPCRIY 540
            YPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKIADGKLNRPCRIY
Sbjct: 481  YPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKIADGKLNRPCRIY 540

Query: 541  APVGTHETLLAYLVRRLLENGANTSFVNRIADSTLPLDELVADPVAAVEKLAQQEGQVGL 600
            APVGTHETLLAYLVRRLLENGANTSFVNRIADSTLPLDELVADPVAAVEKLAQQEGQVGL
Sbjct: 541  APVGTHETLLAYLVRRLLENGANTSFVNRIADSTLPLDELVADPVAAVEKLAQQEGQVGL 600

Query: 601  PHPKIPLPRDLYGKGRSNSAGLDLANEHRLASLSSSLLNSALHKWQALPMLEQPVAEGEM 660
            PHPKIPLPRDLYGKGRSNSAGLDLANEHRLASLSSSLLNSALHKWQALPMLEQPVAEGEM
Sbjct: 601  PHPKIPLPRDLYGKGRSNSAGLDLANEHRLASLSSSLLNSALHKWQALPMLEQPVAEGEM 660

Query: 661  QPVINPAEPKDIVGYVREASDDEVQQALTSAVNNAPIWFATPPQERAAILERAAVLMEGQ 720
            QPVINPAEPKDIVGYVREASDDEVQQALTSAVNNAPIWFATPPQERAAILERAAVLMEGQ
Sbjct: 661  QPVINPAEPKDIVGYVREASDDEVQQALTSAVNNAPIWFATPPQERAAILERAAVLMEGQ 720

Query: 721  MPTLMGILVREAGKTFSNAIAEVREAVDFLHYYAGQVRNDFDNETHRPLGPVVCISPWNF 780
            MPTLMGILVREAGKTFSNAIAEVREAVDFLHYYAGQVRNDFDNETHRPLGPVVCISPWNF
Sbjct: 721  MPTLMGILVREAGKTFSNAIAEVREAVDFLHYYAGQVRNDFDNETHRPLGPVVCISPWNF 780

Query: 781  PLAIFSGQIAAALAAGNTVLAKPAEQTPLIAAQGVAILLEAGVPPGVIQLLPGRGETVGA 840
            PLAIFSGQIAAALAAGNTVLAKPAEQTPLIAAQGVAILLEAGVPPGVIQLLPGRGETVGA
Sbjct: 781  PLAIFSGQIAAALAAGNTVLAKPAEQTPLIAAQGVAILLEAGVPPGVIQLLPGRGETVGA 840

Query: 841  ALTSDERVRGVMFTGSTEVATLLQRNIASRLDAQGRPTPLIAETGGMNAMIVDSSALTEQ 900
            ALTSDERVRGVMFTGSTEVATLLQRNIASRLDAQGRPTPLIAETGGMNAMIVDSSALTEQ
Sbjct: 841  ALTSDERVRGVMFTGSTEVATLLQRNIASRLDAQGRPTPLIAETGGMNAMIVDSSALTEQ 900

Query: 901  VVIDVLASAFDSAGQRCSALRVLCLQDDIADHTLTMLRGAMAECRMGNPGRLTTDIGPVI 960
            VVIDVLASAFDSAGQRCSALRVLCLQDDIADHTLTMLRGAMAECRMGNPGRLTTDIGPVI
Sbjct: 901  VVIDVLASAFDSAGQRCSALRVLCLQDDIADHTLTMLRGAMAECRMGNPGRLTTDIGPVI 960

Query: 961  DAEAKENIERHIQTLRAKGRKVFQAVRENGEDSREWASGTFVPPTLIELDSFDELKKEVF 1020
            DAEAKENIERHIQTLRAKGRKVFQAVRENGEDSREWASGTFVPPTLIELDSFDELKKEVF
Sbjct: 961  DAEAKENIERHIQTLRAKGRKVFQAVRENGEDSREWASGTFVPPTLIELDSFDELKKEVF 1020

Query: 1021 GPVLHVVRYNRNELEGLVEQINASGYGLTLGVHTRIDETIAQVTGSANVGNLYVNRNMVG 1080
            GPVLHVVRYNRNELEGLVEQINASGYGLTLGVHTRIDETIAQVTGSANVGNLYVNRNMVG
Sbjct: 1021 GPVLHVVRYNRNELEGLVEQINASGYGLTLGVHTRIDETIAQVTGSANVGNLYVNRNMVG 1080

Query: 1081 AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSSRPQNAVGITLARQDPEYPLDAQLKTLLE 1140
            AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSSRPQNAVGITLARQDPEYPLDAQLKTLLE
Sbjct: 1081 AVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSSRPQNAVGITLARQDPEYPLDAQLKTLLE 1140

Query: 1141 KPLVALQQWAADRPELQALCQQFSKQAQAGTQRLLPGPTGERNTLTFMPRDRVLCVADNE 1200
            KPLVALQQWAADRPELQALCQQFSKQAQAGTQRLLPGPTGERNTLTFMPRDRVLCVADNE
Sbjct: 1141 KPLVALQQWAADRPELQALCQQFSKQAQAGTQRLLPGPTGERNTLTFMPRDRVLCVADNE 1200

Query: 1201 QDALTQLAGVTAVGCEVLWPDAPLQRELAKKLPREVSERIHFAKAETLTTEPFDAVIYHG 1260
            QDALTQLAGVTAVGCEVLWPDAPLQRELAKKLPREVSERIHFAKAETLTTEPFDAVIYHG
Sbjct: 1201 QDALTQLAGVTAVGCEVLWPDAPLQRELAKKLPREVSERIHFAKAETLTTEPFDAVIYHG 1260

Query: 1261 DSDQLRELCEQVAARDGAIVSVQGFARGESNLLLERLYIERSLSVNTAAAGGNASLMTIG 1320
            DSDQLRELCEQVAARDGAIVSVQGFARGESNLLLERLYIERSLSVNTAAAGGNASLMTIG
Sbjct: 1261 DSDQLRELCEQVAARDGAIVSVQGFARGESNLLLERLYIERSLSVNTAAAGGNASLMTIG 1320


Lambda     K      H
   0.317    0.134    0.387 

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: 4749
Number of extensions: 157
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 BWI76_RS10795 BWI76_RS10795 (trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase)
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.21628.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.9e-277  905.9   0.0   4.4e-277  905.3   0.0    1.3  1  lcl|FitnessBrowser__Koxy:BWI76_RS10795  BWI76_RS10795 trifunctional tran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS10795  BWI76_RS10795 trifunctional transcriptional regulator/proline dehydrogenase/L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  905.3   0.0  4.4e-277  4.4e-277       1     499 [.     610    1113 ..     610    1114 .. 0.99

  Alignments for each domain:
  == domain 1  score: 905.3 bits;  conditional E-value: 4.4e-277
                               TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvs 69  
                                              dlyg+gr+ns+G+dlane++l+sl+++ll++a++k+qa+p++ e+++aege+qpv npa++kdivG+v+
  lcl|FitnessBrowser__Koxy:BWI76_RS10795  610 DLYGKGRSNSAGLDLANEHRLASLSSSLLNSALHKWQALPML-EQPVAEGEMQPVINPAEPKDIVGYVR 677 
                                              89****************************************.9************************* PP

                               TIGR01238   70 eadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevrea 138 
                                              ea+++evq+a++sav+++++w+at+++eraailer+a+l+e +mp+l+++lvreaGkt+snaiaevrea
  lcl|FitnessBrowser__Koxy:BWI76_RS10795  678 EASDDEVQQALTSAVNNAPIWFATPPQERAAILERAAVLMEGQMPTLMGILVREAGKTFSNAIAEVREA 746 
                                              ********************************************************************* PP

                               TIGR01238  139 vdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaarav 207 
                                              vdfl+yya+qv++++d+e++++lG+vvcispwnfplaif GqiaaalaaGntv+akpaeqt+liaa++v
  lcl|FitnessBrowser__Koxy:BWI76_RS10795  747 VDFLHYYAGQVRNDFDNETHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNTVLAKPAEQTPLIAAQGV 815 
                                              ********************************************************************* PP

                               TIGR01238  208 ellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaet 273 
                                              ++l+eaGvp+gviqllpGrGe+vGaaltsder++Gv+ftGsteva+l+++++a+r da+   +pliaet
  lcl|FitnessBrowser__Koxy:BWI76_RS10795  816 AILLEAGVPPGVIQLLPGRGETVGAALTSDERVRGVMFTGSTEVATLLQRNIASRLDAQgrpTPLIAET 884 
                                              *********************************************************99999******* PP

                               TIGR01238  274 GGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlt 342 
                                              GG+namivds+al+eqvv+dvlasafdsaGqrcsalrvlc+q+d+ad++lt+++Gam e+++g+p+rlt
  lcl|FitnessBrowser__Koxy:BWI76_RS10795  885 GGMNAMIVDSSALTEQVVIDVLASAFDSAGQRCSALRVLCLQDDIADHTLTMLRGAMAECRMGNPGRLT 953 
                                              ********************************************************************* PP

                               TIGR01238  343 tdvGpvidaeakqnllahiekmkakakkvaqvkledd...vesekgtfvaptlfelddldelkkevfGp 408 
                                              td+Gpvidaeak+n+++hi+ ++ak++kv+q+++e+    +e+  gtfv+ptl+eld++delkkevfGp
  lcl|FitnessBrowser__Koxy:BWI76_RS10795  954 TDIGPVIDAEAKENIERHIQTLRAKGRKVFQAVRENGedsREWASGTFVPPTLIELDSFDELKKEVFGP 1022
                                              *********************************987555599*************************** PP

                               TIGR01238  409 vlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGe 477 
                                              vlhvvry+++el+ +v++ina+GygltlGvh+ri+et++q++++a+vGn+yvnrn+vGavvGvqpfGGe
  lcl|FitnessBrowser__Koxy:BWI76_RS10795 1023 VLHVVRYNRNELEGLVEQINASGYGLTLGVHTRIDETIAQVTGSANVGNLYVNRNMVGAVVGVQPFGGE 1091
                                              ********************************************************************* PP

                               TIGR01238  478 GlsGtGpkaGGplylyrltrvr 499 
                                              GlsGtGpkaGGplylyrl+++r
  lcl|FitnessBrowser__Koxy:BWI76_RS10795 1092 GLSGTGPKAGGPLYLYRLLSSR 1113
                                              ******************9987 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 24.59
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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 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