Alignments for a candidate for putA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Cupriavidus basilensis 4G11

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate RR42_RS20125 RR42_RS20125 transcriptional regulator

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>FitnessBrowser__Cup4G11:RR42_RS20125
          Length = 1333

 Score = 2595 bits (6726), Expect = 0.0
 Identities = 1333/1333 (100%), Positives = 1333/1333 (100%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60
            MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS
Sbjct: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60

Query: 61   EGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARL 120
            EGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARL
Sbjct: 61   EGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARL 120

Query: 121  PHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIP 180
            PHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIP
Sbjct: 121  PHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIP 180

Query: 181  DKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRII 240
            DKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRII
Sbjct: 181  DKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRII 240

Query: 241  GKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEAD 300
            GKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEAD
Sbjct: 241  GKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEAD 300

Query: 301  AQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSL 360
            AQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSL
Sbjct: 301  AQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSL 360

Query: 361  TLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDY 420
            TLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDY
Sbjct: 361  TLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDY 420

Query: 421  LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSV 480
            LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSV
Sbjct: 421  LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSV 480

Query: 481  PDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRP 540
            PDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRP
Sbjct: 481  PDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRP 540

Query: 541  CRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEG 600
            CRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEG
Sbjct: 541  CRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEG 600

Query: 601  ALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAA 660
            ALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAA
Sbjct: 601  ALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAA 660

Query: 661  AGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALER 720
            AGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALER
Sbjct: 661  AGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALER 720

Query: 721  AAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGPV 780
            AAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGPV
Sbjct: 721  AAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGPV 780

Query: 781  VCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLP 840
            VCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLP
Sbjct: 781  VCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLP 840

Query: 841  GRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIV 900
            GRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIV
Sbjct: 841  GRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIV 900

Query: 901  DSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDRL 960
            DSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDRL
Sbjct: 901  DSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDRL 960

Query: 961  STDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIELDSIE 1020
            STDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIELDSIE
Sbjct: 961  STDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIELDSIE 1020

Query: 1021 ELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNLY 1080
            ELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNLY
Sbjct: 1021 ELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNLY 1080

Query: 1081 VNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDTVGGADE 1140
            VNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDTVGGADE
Sbjct: 1081 VNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDTVGGADE 1140

Query: 1141 TGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLPGPTGERNTYTL 1200
            TGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLPGPTGERNTYTL
Sbjct: 1141 TGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLPGPTGERNTYTL 1200

Query: 1201 LPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVRLVADWS 1260
            LPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVRLVADWS
Sbjct: 1201 LPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVRLVADWS 1260

Query: 1261 AGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLAHGEPNIAIERLLIERSLSVNT 1320
            AGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLAHGEPNIAIERLLIERSLSVNT
Sbjct: 1261 AGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLAHGEPNIAIERLLIERSLSVNT 1320

Query: 1321 AAAGGNASLMTIG 1333
            AAAGGNASLMTIG
Sbjct: 1321 AAAGGNASLMTIG 1333


Lambda     K      H
   0.318    0.133    0.383 

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: 4610
Number of extensions: 157
Number of successful extensions: 3
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: 1333
Length of database: 1333
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1284
Effective search space:  1648656
Effective search space used:  1648656
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 RR42_RS20125 RR42_RS20125 (transcriptional regulator)
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.26850.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-249  814.3   4.6   2.6e-249  813.7   4.6    1.2  1  lcl|FitnessBrowser__Cup4G11:RR42_RS20125  RR42_RS20125 transcriptional reg


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS20125  RR42_RS20125 transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  813.7   4.6  2.6e-249  2.6e-249       2     498 ..     615    1119 ..     614    1121 .. 0.98

  Alignments for each domain:
  == domain 1  score: 813.7 bits;  conditional E-value: 2.6e-249
                                 TIGR01238    2 lygegrknslGvdlaneselksleeqllkaaakkfqaapivgeka...kaegeaqpvknpadrkdiv 65  
                                                lyge+r ns+G+dl+ne++l+sl++ ll+   +   a+p++g +a   +++++  pv+np d++d+v
  lcl|FitnessBrowser__Cup4G11:RR42_RS20125  615 LYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAaagEDVNQPAPVRNPSDQRDVV 681 
                                                8*****************************************76645566777889*********** PP

                                 TIGR01238   66 GqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnai 132 
                                                G+v+ea+ aev++a+++av+a+++w+at+a+ raa ler+a+l+e +m +l++++vreaGkt+snai
  lcl|FitnessBrowser__Cup4G11:RR42_RS20125  682 GHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALERAAELMEAQMQSLMGIIVREAGKTFSNAI 748 
                                                ******************************************************************* PP

                                 TIGR01238  133 aevreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqt 199 
                                                aevreavdflryya qv+++++ +++++lG+vvcispwnfplaiftGq+aaalaaGntv+akpaeqt
  lcl|FitnessBrowser__Cup4G11:RR42_RS20125  749 AEVREAVDFLRYYAAQVRETFSSDTHRPLGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQT 815 
                                                ******************************************************************* PP

                                 TIGR01238  200 sliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap 266 
                                                +liaa+av ll+eaGvpag++qllpGrGe+vGaal  d+r++Gv+ftGstevarl+++++a r da 
  lcl|FitnessBrowser__Cup4G11:RR42_RS20125  816 PLIAAQAVRLLREAGVPAGAVQLLPGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAA 882 
                                                *****************************************************************97 PP

                                 TIGR01238  267 ...vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGam 330 
                                                   vpliaetGGqnamivds+alaeqvv dv++safdsaGqrcsalrvlc+qe+vadrvl+++kGam
  lcl|FitnessBrowser__Cup4G11:RR42_RS20125  883 grpVPLIAETGGQNAMIVDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAM 949 
                                                777**************************************************************** PP

                                 TIGR01238  331 delkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkledd..vesekgtfvaptlfel 395 
                                                del +g+p rl tdvGpvid+ea+ n+++hi++m+ak+++v+q+  +     ++++gtfv+ptl+el
  lcl|FitnessBrowser__Cup4G11:RR42_RS20125  950 DELTMGNPDRLSTDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGAlsAACRNGTFVSPTLIEL 1016
                                                ********************************************987655599************** PP

                                 TIGR01238  396 ddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnr 462 
                                                d+++el++evfGpvlhvvry +  ld ++ +in +Gyglt+G+h+ri+et+ +i +ra+vGn+yvnr
  lcl|FitnessBrowser__Cup4G11:RR42_RS20125 1017 DSIEELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNLYVNR 1083
                                                ******************************************************************* PP

                                 TIGR01238  463 nlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrv 498 
                                                n+vGavvGvqpfGGeGlsGtGpkaGGplyl+rl++v
  lcl|FitnessBrowser__Cup4G11:RR42_RS20125 1084 NIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSV 1119
                                                *********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1333 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 25.26
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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