Alignments for a candidate for carB in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Escherichia coli BW25113

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate 14178 b0033 carbamoyl-phosphate synthase large subunit (NCBI)

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Keio:14178
          Length = 1073

 Score = 2104 bits (5451), Expect = 0.0
 Identities = 1073/1073 (100%), Positives = 1073/1073 (100%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA
Sbjct: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG
Sbjct: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM
Sbjct: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM
Sbjct: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA
Sbjct: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG
Sbjct: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT
Sbjct: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN
Sbjct: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP
Sbjct: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL
Sbjct: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME
Sbjct: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI
Sbjct: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF
Sbjct: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL
Sbjct: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR
Sbjct: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
            RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK
Sbjct: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073


Lambda     K      H
   0.318    0.135    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: 3539
Number of extensions: 137
Number of successful extensions: 11
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: 1073
Length of database: 1073
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1028
Effective search space:  1056784
Effective search space used:  1056784
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: 58 (26.9 bits)

Align candidate 14178 b0033 (carbamoyl-phosphate synthase large subunit (NCBI))
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))

# 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.aa/TIGR01369.hmm
# target sequence database:        /tmp/gapView.19920.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01369  [M=1052]
Accession:   TIGR01369
Description: CPSaseII_lrg: carbamoyl-phosphate synthase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
          0 1622.9   0.0          0 1622.7   0.0    1.0  1  lcl|FitnessBrowser__Keio:14178  b0033 carbamoyl-phosphate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14178  b0033 carbamoyl-phosphate synthase large subunit (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1622.7   0.0         0         0       1    1051 [.       2    1053 ..       2    1054 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1622.7 bits;  conditional E-value: 0
                       TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveavekii 77  
                                      pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+e+ad++YieP+++e+v+kii
  lcl|FitnessBrowser__Keio:14178    2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADATYIEPIHWEVVRKII 78  
                                      689************************************************************************** PP

                       TIGR01369   78 ekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseivesveea 154 
                                      ekErpDa+l+t+GGqtaLn+a+ele++GvLe++gv+++G++ +ai+kaedR++F+ a+k+i++e+a+s i++++eea
  lcl|FitnessBrowser__Keio:14178   79 EKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEA 155 
                                      ***************************************************************************** PP

                       TIGR01369  155 leaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskdnciivc 231 
                                      l++a+++g+P+i+R++ft+gG+G+gia+n+ee++e+++++l++sp+k++l+++sl gwkE+E+EvvRD++dnciivc
  lcl|FitnessBrowser__Keio:14178  156 LAVAADVGFPCIIRPSFTMGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVC 232 
                                      ***************************************************************************** PP

                       TIGR01369  232 niEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssA 307 
                                      +iEn+D++G+HtGdsi+vaP+qtLtdkeyq++R+as++++re+gve++ +nvqfa++P++ r++viE+npRvsRssA
  lcl|FitnessBrowser__Keio:14178  233 SIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGgSNVQFAVNPKNGRLIVIEMNPRVSRSSA 309 
                                      **********************************************988**************************** PP

                       TIGR01369  308 LAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvma 383 
                                      LAskAtG+PiAkvaaklavGy+Ldel+nd+t+ +t+AsfEPs+DYvv+kiPr++++kf++++++l+tqmksvGEvma
  lcl|FitnessBrowser__Keio:14178  310 LASKATGFPIAKVAAKLAVGYTLDELMNDITGgRTPASFEPSIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMA 386 
                                      *******************************879******************************************* PP

                       TIGR01369  384 igrtfeealqkalrsleekllglklk..ekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffl 458 
                                      igrt +e+lqkalr le +++g++ k   +  e+ ++++++lk++ ++R+++ia+a+r+g+sv+ v++lt+idr+fl
  lcl|FitnessBrowser__Keio:14178  387 IGRTQQESLQKALRGLEVGATGFDPKvsLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFL 463 
                                      **********************76551055677889999************************************** PP

                       TIGR01369  459 eklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeakt 535 
                                       ++++lv+le++++e+ ++ l+++ l+++k++Gf+d+++akl++v+eae+rklr++++++pv+krvDt+aaEf ++t
  lcl|FitnessBrowser__Keio:14178  464 VQIEELVRLEEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540 
                                      ***************************************************************************** PP

                       TIGR01369  536 pYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLy 612 
                                      +Y+Ystyeee++ +++t+++k++vlG+Gp+Rigqg+EFDyc+vha+lalre gy+ti++n+nPEtvstDyd++drLy
  lcl|FitnessBrowser__Keio:14178  541 AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLY 617 
                                      ***************************************************************************** PP

                       TIGR01369  613 FeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgke 689 
                                      Fe++t+edvl+i++ ek++gvivq+gGqt+l+la++le+agv+++Gts+++idraEdRe+F++++++l++kqp++++
  lcl|FitnessBrowser__Keio:14178  618 FEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANAT 694 
                                      ***************************************************************************** PP

                       TIGR01369  690 atsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadge 766 
                                      +t++e+a+e+akeigyP++vRpsyvlgGrameiv++e++l+ry+++av+vs+++Pvl+d++l+davEvdvDa++dge
  lcl|FitnessBrowser__Keio:14178  695 VTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGE 771 
                                      ***************************************************************************** PP

                       TIGR01369  767 evliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasR 843 
                                      +vli gi+eHiE+aGvHsGDs+++lp+ +ls+e+++ ++++v+k+a el+v+Gl+n+qf+vk++evy+iEvn+Ra+R
  lcl|FitnessBrowser__Keio:14178  772 MVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAAR 848 
                                      ***************************************************************************** PP

                       TIGR01369  844 tvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrd 920 
                                      tvPfvska+gvpl+k+a++v++gk+l+e  +gv+ke  + +++vk++v++f+k+ gvd++lgpem+stGEvmg+gr+
  lcl|FitnessBrowser__Keio:14178  849 TVPFVSKATGVPLAKVAARVMAGKSLAE--QGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRT 923 
                                      ****************************..889******************************************** PP

                       TIGR01369  921 leeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaek 997 
                                      ++ea++ka+l s++++kk+g++llsv++ dke++++la+kl ++g+++ at+gta vl eagi+ ++v+kv+e +++
  lcl|FitnessBrowser__Keio:14178  924 FAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPH 1000
                                      ***************************************************************************** PP

                       TIGR01369  998 ilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
                                      i++ +k++e++++in+ts +++a e++ +irr+a++ykv++ t+l++  a+++a
  lcl|FitnessBrowser__Keio:14178 1001 IQDRIKNGEYTYIINTTS-GRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMA 1053
                                      ***************998.77799999******************998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1073 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: 0.09u 0.04s 00:00:00.13 Elapsed: 00:00:00.12
# Mc/sec: 9.26
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

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

Related tools

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis