Alignments for a candidate for carB in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Pseudomonas simiae WCS417

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate GFF4699 PS417_24040 carbamoyl phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__WCS417:GFF4699
          Length = 1073

 Score = 1602 bits (4148), Expect = 0.0
 Identities = 807/1073 (75%), Positives = 916/1073 (85%), Gaps = 1/1073 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP M
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPAM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI W+ V KIIEKERPDA+LPTMGGQTALNCAL+LER+GVLE+FGV MIGA A
Sbjct: 61   ADATYIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGVLEKFGVEMIGANA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            D IDKAEDR RFD AMK IGL   RSGIAH+MEEA AV   +GFPCIIRPSFTMGG+GGG
Sbjct: 121  DTIDKAEDRSRFDKAMKSIGLACPRSGIAHSMEEANAVLETLGFPCIIRPSFTMGGTGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDK DNCIIVCSIENFD M
Sbjct: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQI+RNAS+AVLREIGVETGGSNVQF + P  GR++VIEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQILRNASLAVLREIGVETGGSNVQFGICPNTGRMVVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL NDITGG+TPASFEPSIDYVVTK+P
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELSNDITGGKTPASFEPSIDYVVTKLP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RF FEKFA A+ RLTTQMKSVGEVMAIGRT QESLQKALRGLEVG  G D K+ L +PE+
Sbjct: 361  RFAFEKFAKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDEKLDLSNPES 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            ++ ++REL   GA+RIWY+ADAFRAG++V+ +F +  ID WFLVQIE+L++ EEKV  +G
Sbjct: 421  MSVLKRELTVPGAERIWYVADAFRAGMTVEDIFGMNMIDPWFLVQIEDLIKEEEKVKTLG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            +  ++ D + +LKRKGF+D RLAKL GV E  +R  R + ++ PVYKRVDTCAAEF+TDT
Sbjct: 481  LASIDRDMMFRLKRKGFSDQRLAKLLGVTEKNLRTHRHKLEIFPVYKRVDTCAAEFSTDT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AY+YSTYEEECEA PS  R+KIM+LGGGPNRIGQGIEFDYCCVHA+LALREDGYETIMVN
Sbjct: 541  AYLYSTYEEECEAAPS-GRDKIMILGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVN 599

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEPVTLEDVLEIVR+EKPKGVIVQYGGQTPLKLARALEAAGVP
Sbjct: 600  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEAAGVP 659

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            +IGTSPDAIDRAEDRERFQ  VERL L+QP NATV + + A+  A +IGYPLVVRPSYVL
Sbjct: 660  IIGTSPDAIDRAEDRERFQQMVERLNLRQPPNATVRSEDEAIRAASKIGYPLVVRPSYVL 719

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVY+E +L+RY + AV VSND+PVLLDHFL+ A+E+DVDA+CDG  V+IG IM+
Sbjct: 720  GGRAMEIVYEEEELKRYLRDAVKVSNDSPVLLDHFLNCAIEMDVDAVCDGTDVVIGAIMQ 779

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDSACSLP Y+L   IQD MR+QV+K+A EL V GLMNVQ A++  ++Y+I
Sbjct: 780  HIEQAGVHSGDSACSLPPYSLPAHIQDEMREQVKKMALELGVVGLMNVQLALQGEDIYVI 839

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRA+RTVPFVSK  GV LA +AARVMAGK+L E G TKE+IP +YSVKE V PF KF
Sbjct: 840  EVNPRASRTVPFVSKCIGVSLAMIAARVMAGKTLKEIGFTKEIIPNFYSVKEAVFPFAKF 899

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDP+LGPEM+STGEVMGVG TF EAFAKAQ+G++  +   G A +SVR+ DK  V  +
Sbjct: 900  PGVDPILGPEMKSTGEVMGVGDTFGEAFAKAQMGASEVLPTGGTAFISVRDDDKPLVAGV 959

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            A  L+  GFE+ AT GTA ++  AG+  R VNKV EGRPH+ D IKN E T IINTT GR
Sbjct: 960  ARDLINLGFEVVATAGTAKLIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVTLIINTTEGR 1019

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
            ++I DS  IRR+ALQ+K++  TT+  G A   AL     + V  +Q++HA +K
Sbjct: 1020 QSIADSYSIRRNALQHKIYCTTTIAAGEAICEALKFGPEKTVRRLQDLHAGLK 1072


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: 3184
Number of extensions: 135
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: 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 GFF4699 PS417_24040 (carbamoyl phosphate synthase large subunit)
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.27967.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 1575.9   0.0          0 1575.7   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4699  PS417_24040 carbamoyl phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4699  PS417_24040 carbamoyl phosphate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1575.7   0.0         0         0       1    1052 []       2    1053 ..       2    1053 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1575.7 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__WCS417:GFF4699    2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPAMADATYIEPIKWQTV 74  
                                          689********************************************************************** PP

                           TIGR01369   74 ekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakse 146 
                                          +kiiekErpDa+l+t+GGqtaLn+a++le++GvLek+gv+++G++ ++i+kaedR +F++a+k i++  ++s 
  lcl|FitnessBrowser__WCS417:GFF4699   75 AKIIEKERPDALLPTMGGQTALNCALDLEREGVLEKFGVEMIGANADTIDKAEDRSRFDKAMKSIGLACPRSG 147 
                                          ************************************************************************* 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__WCS417:GFF4699  148 IAHSMEEANAVLETLGFPCIIRPSFTMGGTGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEV 220 
                                          ************************************************************************* PP

                           TIGR01369  220 vRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPesk 291 
                                          vRD+kdnciivc+iEn+Dp+GvHtGdsi+vaP+qtLtdkeyq+lR+asl+++re+gve++ +nvqf++ P++ 
  lcl|FitnessBrowser__WCS417:GFF4699  221 VRDKKDNCIIVCSIENFDPMGVHTGDSITVAPAQTLTDKEYQILRNASLAVLREIGVETGgSNVQFGICPNTG 293 
                                          **********************************************************988************ PP

                           TIGR01369  292 ryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldk 363 
                                          r+vviE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldel+nd+t+ +t+AsfEPs+DYvv+k+Pr++++k
  lcl|FitnessBrowser__WCS417:GFF4699  294 RMVVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELSNDITGgKTPASFEPSIDYVVTKLPRFAFEK 366 
                                          ***********************************************879*********************** PP

                           TIGR01369  364 fekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkeke..aesdeeleealkkpndrRlfai 434 
                                          f+k+d +l+tqmksvGEvmaigrtf+e+lqkalr le ++ gl++k +    es + l+++l+ p ++R++++
  lcl|FitnessBrowser__WCS417:GFF4699  367 FAKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDEKLDLsnPESMSVLKRELTVPGAERIWYV 439 
                                          ******************************************887755400455667899************* PP

                           TIGR01369  435 aealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseae 507 
                                          a+a+r+g++ve+++ +  id +fl ++++l++ e+++++  l  ++++++ ++k++Gfsd+++akl++v+e++
  lcl|FitnessBrowser__WCS417:GFF4699  440 ADAFRAGMTVEDIFGMNMIDPWFLVQIEDLIKEEEKVKTLGLASIDRDMMFRLKRKGFSDQRLAKLLGVTEKN 512 
                                          ************************************************************************* PP

                           TIGR01369  508 vrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavha 580 
                                          +r+ r++l+i pv+krvDt+aaEf+++t+YlYstyeee++ +++ ++ k+++lG+Gp+Rigqg+EFDyc+vha
  lcl|FitnessBrowser__WCS417:GFF4699  513 LRTHRHKLEIFPVYKRVDTCAAEFSTDTAYLYSTYEEECEAAPSGRD-KIMILGGGPNRIGQGIEFDYCCVHA 584 
                                          **************************************766666665.************************* PP

                           TIGR01369  581 vlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeag 653 
                                          +lalre gy+ti++n+nPEtvstDyd++drLyFe++t+edvl+i++ ek++gvivq+gGqt+l+la++le+ag
  lcl|FitnessBrowser__WCS417:GFF4699  585 ALALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEAAG 657 
                                          ************************************************************************* PP

                           TIGR01369  654 vkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameivene 726 
                                          v+i+Gts+++idraEdRe+F++++++l++ qp +++++s +ea ++a++igyP++vRpsyvlgGrameiv++e
  lcl|FitnessBrowser__WCS417:GFF4699  658 VPIIGTSPDAIDRAEDRERFQQMVERLNLRQPPNATVRSEDEAIRAASKIGYPLVVRPSYVLGGRAMEIVYEE 730 
                                          ************************************************************************* PP

                           TIGR01369  727 eeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklsee 799 
                                          eel+ryl++av+vs+++Pvl+d++l+ a+E+dvDav+dg++v+i +i++HiE+aGvHsGDs+++lpp +l ++
  lcl|FitnessBrowser__WCS417:GFF4699  731 EELKRYLRDAVKVSNDSPVLLDHFLNCAIEMDVDAVCDGTDVVIGAIMQHIEQAGVHSGDSACSLPPYSLPAH 803 
                                          ************************************************************************* PP

                           TIGR01369  800 vkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleel 872 
                                          ++++++e+vkk+a el v+Gl+n+q+++++e++yviEvn+RasRtvPfvsk +gv+l+ +a++v++gk+l+e 
  lcl|FitnessBrowser__WCS417:GFF4699  804 IQDEMREQVKKMALELGVVGLMNVQLALQGEDIYVIEVNPRASRTVPFVSKCIGVSLAMIAARVMAGKTLKE- 875 
                                          ************************************************************************. PP

                           TIGR01369  873 ekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvlls 945 
                                            g +ke  +++++vk+avf+f+k+ gvd++lgpemkstGEvmg+g+++ ea++ka++ +++++++ g++++s
  lcl|FitnessBrowser__WCS417:GFF4699  876 -IGFTKEIIPNFYSVKEAVFPFAKFPGVDPILGPEMKSTGEVMGVGDTFGEAFAKAQMGASEVLPTGGTAFIS 947 
                                          .6789******************************************************************** PP

                           TIGR01369  946 vkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkk 1018
                                          v+d dk  +  +a+ l ++g++v+at+gtak +e ag k++ v+kv+e ++++++++k++e++l+in+t+ ++
  lcl|FitnessBrowser__WCS417:GFF4699  948 VRDDDKPLVAGVARDLINLGFEVVATAGTAKLIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVTLIINTTE-GR 1019
                                          *******************************************************************997.77 PP

                           TIGR01369 1019 kaaekgykirreaveykvplvteletaealleal 1052
                                          ++  ++y+irr+a+++k+ + t++++ ea++eal
  lcl|FitnessBrowser__WCS417:GFF4699 1020 QSIADSYSIRRNALQHKIYCTTTIAAGEAICEAL 1053
                                          788899***********************99986 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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 12.85
//
[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