GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Pseudomonas fluorescens FW300-N2E2

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate Pf6N2E2_3364 Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364
          Length = 1073

 Score = 1601 bits (4146), Expect = 0.0
 Identities = 808/1073 (75%), Positives = 918/1073 (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  DTIDKAEDRSRFDKAMKSIGLDCPRSGIAHSMEEANAVLERLGFPCIIRPSFTMGGTGGG 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 DPK+ L DPE+
Sbjct: 361  RFAFEKFAKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDPKLDLADPES 420

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

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            ++ ++ D + +LKRKGF+D RLAKL GV E  +R  R + ++ PVYKRVDTCAAEFATDT
Sbjct: 481  MSSIDRDTMFRLKRKGFSDMRLAKLLGVTEKSLRAHRHKLEVFPVYKRVDTCAAEFATDT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AY+YSTYEEECEA PST R+KIM+LGGGPNRIGQGIEFDYCCVHA+LALR+DGYETIMVN
Sbjct: 541  AYLYSTYEEECEAAPST-RDKIMILGGGPNRIGQGIEFDYCCVHAALALRDDGYETIMVN 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  IIGTSPDAIDRAEDRERFQQMVERLNLRQPPNATVRSEDEAIRAAAKIGYPLVVRPSYVL 719

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVY E +L+RY + AV VSND+PVLLDHFL+ A+E+DVDA+ DG+ V+IG IM+
Sbjct: 720  GGRAMEIVYQEDELKRYLREAVQVSNDSPVLLDHFLNCAIEMDVDAVSDGKDVVIGAIMQ 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   TKE+IP +YSVKE V PF KF
Sbjct: 840  EVNPRASRTVPFVSKCIGVSLAMIAARVMAGKTLKELNFTKEIIPNFYSVKEAVFPFAKF 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  ARDLINLGFEVVATAGTARLIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVTLIINTTEGR 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: 3125
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 Pf6N2E2_3364 (Carbamoyl-phosphate synthase large chain (EC 6.3.5.5))
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.19905.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 1574.3   0.0          0 1574.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  Carbamoyl-phosphate synthase lar


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1574.1   0.0         0         0       1    1052 []       2    1053 ..       2    1053 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1574.1 bits;  conditional E-value: 0
                                      TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladk 62  
                                                     pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+++ad+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364    2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPAMADA 63  
                                                     689*********************************************************** PP

                                      TIGR01369   63 vYiePltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikk 124 
                                                     +YieP+++++v+kiiekErpDa+l+t+GGqtaLn+a++le++GvLek+gv+++G++ ++i+k
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364   64 TYIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGVLEKFGVEMIGANADTIDK 125 
                                                     ************************************************************** PP

                                      TIGR01369  125 aedRekFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneee 186 
                                                     aedR +F++a+k i+++ ++s i++s+eea ++ e++g+P+i+R++ft+gGtG+gia+n+ee
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  126 AEDRSRFDKAMKSIGLDCPRSGIAHSMEEANAVLERLGFPCIIRPSFTMGGTGGGIAYNREE 187 
                                                     ************************************************************** PP

                                      TIGR01369  187 lkelvekalkaspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsiv 248 
                                                     ++e+++++l++sp+k++l+++sl gwkE+E+EvvRD+kdnciivc+iEn+Dp+GvHtGdsi+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  188 FEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPMGVHTGDSIT 249 
                                                     ************************************************************** PP

                                      TIGR01369  249 vaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALA 309 
                                                     vaP+qtLtdkeyq+lR+asl+++re+gve++ +nvqf++ P++ r+vviE+npRvsRssALA
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  250 VAPAQTLTDKEYQILRNASLAVLREIGVETGgSNVQFGICPNTGRMVVIEMNPRVSRSSALA 311 
                                                     *****************************988****************************** PP

                                      TIGR01369  310 skAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrk 370 
                                                     skAtG+PiAkvaaklavGy+Ldel+nd+t+ +t+AsfEPs+DYvv+k+Pr++++kf+k+d +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  312 SKATGFPIAKVAAKLAVGYTLDELSNDITGgKTPASFEPSIDYVVTKLPRFAFEKFAKADAR 373 
                                                     *****************************879****************************** PP

                                      TIGR01369  371 lgtqmksvGEvmaigrtfeealqkalrsleekllglklk..ekeaesdeeleealkkpndrR 430 
                                                     l+tqmksvGEvmaigrtf+e+lqkalr le ++ gl+ k   +  es + l+++l+ p ++R
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  374 LTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDPKldLADPESMSVLKRELTVPGAER 435 
                                                     ***********************************76551045556677889********** PP

                                      TIGR01369  431 lfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGf 492 
                                                     ++++a+a+r+g++ve+++ +  id +fl ++++l++ e+++++  ++ ++++++ ++k++Gf
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  436 IWYVADAFRAGMTVEQIFGMNMIDPWFLVQIEDLIKEEEKVKTLGMSSIDRDTMFRLKRKGF 497 
                                                     ************************************************************** PP

                                      TIGR01369  493 sdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtek 554 
                                                     sd ++akl++v+e+++r+ r++l++ pv+krvDt+aaEf ++t+YlYstyeee++ +++t++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  498 SDMRLAKLLGVTEKSLRAHRHKLEVFPVYKRVDTCAAEFATDTAYLYSTYEEECEAAPSTRD 559 
                                                     *****************************************************877777777 PP

                                      TIGR01369  555 kkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeel 616 
                                                      k+++lG+Gp+Rigqg+EFDyc+vha+lalr+ gy+ti++n+nPEtvstDyd++drLyFe++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  560 -KIMILGGGPNRIGQGIEFDYCCVHAALALRDDGYETIMVNCNPETVSTDYDTSDRLYFEPV 620 
                                                     .************************************************************* PP

                                      TIGR01369  617 tvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklld 678 
                                                     t+edvl+i++ ek++gvivq+gGqt+l+la++le+agv+i+Gts+++idraEdRe+F+++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  621 TLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEAAGVPIIGTSPDAIDRAEDRERFQQMVE 682 
                                                     ************************************************************** PP

                                      TIGR01369  679 elgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevs 740 
                                                     +l++ qp +++++s +ea ++a++igyP++vRpsyvlgGrameiv++e+el+ryl+eav+vs
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  683 RLNLRQPPNATVRSEDEAIRAAAKIGYPLVVRPSYVLGGRAMEIVYQEDELKRYLREAVQVS 744 
                                                     ************************************************************** PP

                                      TIGR01369  741 kekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkk 802 
                                                     +++Pvl+d++l+ a+E+dvDav+dg++v+i +i++HiE+aGvHsGDs+++lpp +l +++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  745 NDSPVLLDHFLNCAIEMDVDAVSDGKDVVIGAIMQHIEQAGVHSGDSACSLPPYSLPAHIQD 806 
                                                     ************************************************************** PP

                                      TIGR01369  803 kikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvl 864 
                                                     +++e+vkk+a el v+Gl+n+q+++++e++yviEvn+RasRtvPfvsk +gv+l+ +a++v+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  807 EMREQVKKMALELGVVGLMNVQLALQGEDIYVIEVNPRASRTVPFVSKCIGVSLAMIAARVM 868 
                                                     ************************************************************** PP

                                      TIGR01369  865 lgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeall 926 
                                                     +gk+l+el+   +ke  +++++vk+avf+f+k+ gvd++lgpemkstGEvmg+g+++ ea++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  869 AGKTLKELNF--TKEIIPNFYSVKEAVFPFAKFPGVDPILGPEMKSTGEVMGVGDTFGEAFA 928 
                                                     *******775..999*********************************************** PP

                                      TIGR01369  927 kallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevv 988 
                                                     ka++ +++++++ g++++sv+d dk  +  +a+ l ++g++v+at+gta+ +e ag k++ v
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  929 KAQMGASEVLPTGGTAFISVRDDDKPLVAGVARDLINLGFEVVATAGTARLIEAAGLKVRRV 990 
                                                     ************************************************************** PP

                                      TIGR01369  989 lkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaealle 1050
                                                     +kv+e ++++++++k++e++l+in+t+ ++++  ++y+irr+a+++k+ + t++++ ea++e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364  991 NKVTEGRPHVVDMIKNDEVTLIINTTE-GRQSIADSYSIRRNALQHKIYCTTTIAAGEAICE 1051
                                                     ************************997.77788899***********************999 PP

                                      TIGR01369 1051 al 1052
                                                     al
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364 1052 AL 1053
                                                     86 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: 13.37
//
[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:

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:

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:

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:

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