Alignments for a candidate for carB in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Pseudomonas putida KT2440

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate PP_4723 PP_4723 Carbamoyl-phosphate synthase large chain

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Putida:PP_4723
          Length = 1076

 Score = 1590 bits (4118), Expect = 0.0
 Identities = 799/1073 (74%), Positives = 914/1073 (85%), Gaps = 1/1073 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEG+RVILVNSNPATIMTDP M
Sbjct: 4    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGFRVILVNSNPATIMTDPAM 63

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI W+ V KIIEKERPDAVLPTMGGQTALNCAL+LER GVLE+FGV MIGA A
Sbjct: 64   ADATYIEPIKWQSVAKIIEKERPDAVLPTMGGQTALNCALDLERHGVLEKFGVEMIGANA 123

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            D IDKAEDR RFD AMK IGLE  RSGIAH+MEEA AV   +GFPCIIRPSFTMGG+GGG
Sbjct: 124  DTIDKAEDRSRFDKAMKDIGLECPRSGIAHSMEEANAVLEKLGFPCIIRPSFTMGGTGGG 183

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNREEFEEIC RGLDLSPTKELLIDESLIGWKEYEMEVVRDK DNCIIVCSIENFD M
Sbjct: 184  IAYNREEFEEICTRGLDLSPTKELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPM 243

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQIMRNAS+AVLREIGVETGGSNVQF + P  GR++VIEM
Sbjct: 244  GVHTGDSITVAPAQTLTDKEYQIMRNASLAVLREIGVETGGSNVQFGICPNTGRMVVIEM 303

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAK+AAKLA+GYTLDEL NDITGGRTPASFEPSIDYVVTK+P
Sbjct: 304  NPRVSRSSALASKATGFPIAKIAAKLAIGYTLDELQNDITGGRTPASFEPSIDYVVTKLP 363

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RF FEKF  A+ RLTTQMKSVGEVMAIGRT QESLQKALRGLEVGA G DPKV L  PEA
Sbjct: 364  RFAFEKFPKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGACGLDPKVDLASPEA 423

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
             + ++REL   GA+RIWY+ADA R+G++ + +FNLT ID WFLVQ+E+L++ EEKV  + 
Sbjct: 424  ASILKRELTVPGAERIWYVADAMRSGMTCEEIFNLTGIDMWFLVQMEDLIKEEEKVKTLA 483

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            ++ ++ D++ +LKRKGF+D RLA L G+ +  +R+ R + ++ PVYKRVDTCAAEFATDT
Sbjct: 484  LSAIDKDYMLRLKRKGFSDQRLAVLLGITDKNLRRHRHKLEVFPVYKRVDTCAAEFATDT 543

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AY+YSTYEEECEANPST R+KIM+LGGGPNRIGQGIEFDYCCVHA+LALREDGYETIMVN
Sbjct: 544  AYLYSTYEEECEANPST-RDKIMILGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVN 602

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEP+TLEDVLE+ R+EKPKGVIV YGGQTPLKLARALE AGVP
Sbjct: 603  CNPETVSTDYDTSDRLYFEPLTLEDVLEVCRVEKPKGVIVHYGGQTPLKLARALEEAGVP 662

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            +IGTSPDAIDRAEDRERFQ  V+RL L QP NATV + E A+  A  IGYPLVVRPSYVL
Sbjct: 663  IIGTSPDAIDRAEDRERFQQMVQRLSLLQPPNATVRSEEEAIRAAGSIGYPLVVRPSYVL 722

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVY+  +L+RY + AV VSND+PVLLDHFL+ A+E+DVDA+CDG  V+IG IM+
Sbjct: 723  GGRAMEIVYELDELKRYLREAVQVSNDSPVLLDHFLNCAIEMDVDAVCDGTDVVIGAIMQ 782

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDSACSLP Y+LS+E+QD +R QV+K+A EL V GLMNVQ A++ +++Y+I
Sbjct: 783  HIEQAGVHSGDSACSLPPYSLSKEVQDEVRVQVKKMALELGVVGLMNVQLALQGDKIYVI 842

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRA+RTVPFVSK  G  LA +AARVMAGK+L E G T+E+IP +YSVKE V PF KF
Sbjct: 843  EVNPRASRTVPFVSKCIGTSLAMIAARVMAGKTLKELGFTQEIIPNFYSVKEAVFPFAKF 902

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDP+LGPEM+STGEVMGVG +F EAFAKAQ+G++  +   G A +SVR+ DK +V  +
Sbjct: 903  PGVDPILGPEMKSTGEVMGVGDSFGEAFAKAQMGASEVLPTGGTAFISVRDDDKPQVAGV 962

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            A  L+  GFE+ AT GTA V+  AG+  R VNKV EGRPH+ D IKN E + IINTT GR
Sbjct: 963  ARDLIALGFEVVATAGTAKVIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVSLIINTTEGR 1022

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
            ++I DS  IRR+ALQ+K++  TT+  G A   AL     + V  +Q++HA +K
Sbjct: 1023 QSIADSYSIRRNALQHKIYCTTTIAAGEAICEALKFGPEKTVRRLQDLHAGLK 1075


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: 3200
Number of extensions: 127
Number of successful extensions: 12
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: 1076
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1031
Effective search space:  1059868
Effective search space used:  1059868
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 PP_4723 PP_4723 (Carbamoyl-phosphate synthase large chain)
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.5386.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 1566.9   0.0          0 1566.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4723  PP_4723 Carbamoyl-phosphate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4723  PP_4723 Carbamoyl-phosphate synthase large chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1566.7   0.0         0         0       1    1052 []       5    1056 ..       5    1056 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1566.7 bits;  conditional E-value: 0
                           TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveav 73  
                                          pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+++ad++YieP+++++v
  lcl|FitnessBrowser__Putida:PP_4723    5 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGFRVILVNSNPATIMTDPAMADATYIEPIKWQSV 77  
                                          689********************************************************************** PP

                           TIGR01369   74 ekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakse 146 
                                          +kiiekErpDa+l+t+GGqtaLn+a++le++GvLek+gv+++G++ ++i+kaedR +F++a+k+i++e ++s 
  lcl|FitnessBrowser__Putida:PP_4723   78 AKIIEKERPDAVLPTMGGQTALNCALDLERHGVLEKFGVEMIGANADTIDKAEDRSRFDKAMKDIGLECPRSG 150 
                                          ************************************************************************* PP

                           TIGR01369  147 ivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEv 219 
                                          i++s+eea ++ e++g+P+i+R++ft+gGtG+gia+n+ee++e++ ++l++sp+k++l+++sl gwkE+E+Ev
  lcl|FitnessBrowser__Putida:PP_4723  151 IAHSMEEANAVLEKLGFPCIIRPSFTMGGTGGGIAYNREEFEEICTRGLDLSPTKELLIDESLIGWKEYEMEV 223 
                                          ************************************************************************* PP

                           TIGR01369  220 vRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPesk 291 
                                          vRD+kdnciivc+iEn+Dp+GvHtGdsi+vaP+qtLtdkeyq++R+asl+++re+gve++ +nvqf++ P++ 
  lcl|FitnessBrowser__Putida:PP_4723  224 VRDKKDNCIIVCSIENFDPMGVHTGDSITVAPAQTLTDKEYQIMRNASLAVLREIGVETGgSNVQFGICPNTG 296 
                                          **********************************************************988************ PP

                           TIGR01369  292 ryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldk 363 
                                          r+vviE+npRvsRssALAskAtG+PiAk+aakla+Gy+Ldel+nd+t+ +t+AsfEPs+DYvv+k+Pr++++k
  lcl|FitnessBrowser__Putida:PP_4723  297 RMVVIEMNPRVSRSSALASKATGFPIAKIAAKLAIGYTLDELQNDITGgRTPASFEPSIDYVVTKLPRFAFEK 369 
                                          ***********************************************879*********************** PP

                           TIGR01369  364 fekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklk..ekeaesdeeleealkkpndrRlfai 434 
                                          f k+d +l+tqmksvGEvmaigrtf+e+lqkalr le ++ gl+ k   ++ e+ + l+++l+ p ++R++++
  lcl|FitnessBrowser__Putida:PP_4723  370 FPKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGACGLDPKvdLASPEAASILKRELTVPGAERIWYV 442 
                                          ******************************************76551045566777899************** PP

                           TIGR01369  435 aealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseae 507 
                                          a+a+r+g++ ee+++lt id +fl ++++l++ e+++++ +l+ ++k+ + ++k++Gfsd+++a l++ ++++
  lcl|FitnessBrowser__Putida:PP_4723  443 ADAMRSGMTCEEIFNLTGIDMWFLVQMEDLIKEEEKVKTLALSAIDKDYMLRLKRKGFSDQRLAVLLGITDKN 515 
                                          ************************************************************************* PP

                           TIGR01369  508 vrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavha 580 
                                          +r+ r++l++ pv+krvDt+aaEf ++t+YlYstyeee++ +++t++ k+++lG+Gp+Rigqg+EFDyc+vha
  lcl|FitnessBrowser__Putida:PP_4723  516 LRRHRHKLEVFPVYKRVDTCAAEFATDTAYLYSTYEEECEANPSTRD-KIMILGGGPNRIGQGIEFDYCCVHA 587 
                                          **************************************888877777.************************* PP

                           TIGR01369  581 vlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeag 653 
                                          +lalre gy+ti++n+nPEtvstDyd++drLyFe+lt+edvl++++ ek++gviv++gGqt+l+la++leeag
  lcl|FitnessBrowser__Putida:PP_4723  588 ALALREDGYETIMVNCNPETVSTDYDTSDRLYFEPLTLEDVLEVCRVEKPKGVIVHYGGQTPLKLARALEEAG 660 
                                          ************************************************************************* PP

                           TIGR01369  654 vkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameivene 726 
                                          v+i+Gts+++idraEdRe+F++++++l + qp +++++s eea ++a +igyP++vRpsyvlgGrameiv++ 
  lcl|FitnessBrowser__Putida:PP_4723  661 VPIIGTSPDAIDRAEDRERFQQMVQRLSLLQPPNATVRSEEEAIRAAGSIGYPLVVRPSYVLGGRAMEIVYEL 733 
                                          ************************************************************************* PP

                           TIGR01369  727 eeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklsee 799 
                                          +el+ryl+eav+vs+++Pvl+d++l+ a+E+dvDav+dg++v+i +i++HiE+aGvHsGDs+++lpp +ls+e
  lcl|FitnessBrowser__Putida:PP_4723  734 DELKRYLREAVQVSNDSPVLLDHFLNCAIEMDVDAVCDGTDVVIGAIMQHIEQAGVHSGDSACSLPPYSLSKE 806 
                                          ************************************************************************* PP

                           TIGR01369  800 vkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleel 872 
                                          v+++++ +vkk+a el v+Gl+n+q++++++++yviEvn+RasRtvPfvsk +g +l+ +a++v++gk+l+e 
  lcl|FitnessBrowser__Putida:PP_4723  807 VQDEVRVQVKKMALELGVVGLMNVQLALQGDKIYVIEVNPRASRTVPFVSKCIGTSLAMIAARVMAGKTLKE- 878 
                                          ************************************************************************. PP

                           TIGR01369  873 ekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvlls 945 
                                            g ++e  +++++vk+avf+f+k+ gvd++lgpemkstGEvmg+g+++ ea++ka++ +++++++ g++++s
  lcl|FitnessBrowser__Putida:PP_4723  879 -LGFTQEIIPNFYSVKEAVFPFAKFPGVDPILGPEMKSTGEVMGVGDSFGEAFAKAQMGASEVLPTGGTAFIS 950 
                                          .56799******************************************************************* PP

                           TIGR01369  946 vkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkk 1018
                                          v+d dk ++  +a+ l ++g++v+at+gtakv+e ag k++ v+kv+e ++++++++k++e++l+in+t+ ++
  lcl|FitnessBrowser__Putida:PP_4723  951 VRDDDKPQVAGVARDLIALGFEVVATAGTAKVIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVSLIINTTE-GR 1022
                                          *******************************************************************997.77 PP

                           TIGR01369 1019 kaaekgykirreaveykvplvteletaealleal 1052
                                          ++  ++y+irr+a+++k+ + t++++ ea++eal
  lcl|FitnessBrowser__Putida:PP_4723 1023 QSIADSYSIRRNALQHKIYCTTTIAAGEAICEAL 1056
                                          788899***********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1076 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.10
# Mc/sec: 11.25
//
[ok]

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

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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
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