Alignments for a candidate for carB in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Pseudomonas stutzeri RCH2

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate GFF939 Psest_0968 carbamoyl-phosphate synthase, large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__psRCH2:GFF939
          Length = 1073

 Score = 1599 bits (4140), Expect = 0.0
 Identities = 813/1073 (75%), Positives = 911/1073 (84%), Gaps = 1/1073 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKAL+EEG+RVILVNSNPATIMTDP M
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALKEEGFRVILVNSNPATIMTDPSM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI W  V KIIEKERPDA+LPTMGGQTALNCAL+LE+ GVL +FGV MIGA A
Sbjct: 61   ADATYIEPIKWATVAKIIEKERPDALLPTMGGQTALNCALDLEKHGVLAKFGVEMIGANA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            D IDKAEDR RFD AMK IGL    SGIAH MEEA  V   VGFPCIIRPSFTMGG+GGG
Sbjct: 121  DTIDKAEDRSRFDKAMKDIGLACPVSGIAHNMEEAYGVLDKVGFPCIIRPSFTMGGTGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNREEFEEICARGLDLSPT ELLIDESLIGWKEYEMEVVRDK DNCIIVCSIENFD M
Sbjct: 181  IAYNREEFEEICARGLDLSPTSELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPM 240

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

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAK+AAKLAVGYTLDEL NDITGGRTPASFEP+IDYVVTKIP
Sbjct: 301  NPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELSNDITGGRTPASFEPAIDYVVTKIP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RF FEKF  A+ RLTTQMKSVGEVMAIGRT QES+QKALRGLEVGATGFDPK++L D EA
Sbjct: 361  RFAFEKFPKADARLTTQMKSVGEVMAIGRTFQESMQKALRGLEVGATGFDPKLNLADAEA 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
             + ++REL   GADRIW++ADAFRAG +V  VF LT ID WFLVQIE+LVR EE V  +G
Sbjct: 421  ESTLKRELTVPGADRIWFVADAFRAGKTVAEVFELTRIDEWFLVQIEDLVRDEEHVKTLG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            ++ ++ D + +LKRKGF+DARLAKL GV E  +R  R +  + PVYKRVDTCAAEFATDT
Sbjct: 481  LSSIDRDLMYKLKRKGFSDARLAKLLGVTEKNLRSHRHKLKVLPVYKRVDTCAAEFATDT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AYMYSTYEEECEANPS+ REKIM+LGGGPNRIGQGIEFDYCCVHA+LA+REDGYETIMVN
Sbjct: 541  AYMYSTYEEECEANPSS-REKIMILGGGPNRIGQGIEFDYCCVHAALAMREDGYETIMVN 599

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEPVTLEDVLEIVR+E+PKGVIVQYGGQTPLK+ RALE AGVP
Sbjct: 600  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEQPKGVIVQYGGQTPLKICRALEEAGVP 659

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            +IGTSPDAIDRAEDRERFQ  V+RL L+QP NAT  + E A+  +K IGYPLVVRPSYVL
Sbjct: 660  IIGTSPDAIDRAEDRERFQQMVQRLNLRQPQNATARSEEEAIAASKAIGYPLVVRPSYVL 719

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVY+E +L+RY + AV VSND+PVLLDHFL+ A+EVD+DA+CDG  V+IGGIM+
Sbjct: 720  GGRAMEIVYEEEELKRYMREAVQVSNDSPVLLDHFLNCAIEVDIDAVCDGTDVVIGGIMQ 779

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDSACSLPAY+L Q IQD +R QV+K+A EL V GLMNVQ AV+  ++Y++
Sbjct: 780  HIEQAGVHSGDSACSLPAYSLPQHIQDEIRDQVRKMALELDVIGLMNVQMAVQGEDIYVL 839

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRA+RTVPFVSK  G  LAKVAARVMAGK+L E G T+E+IP YYSVKE V PF KF
Sbjct: 840  EVNPRASRTVPFVSKCIGESLAKVAARVMAGKTLKEIGFTREIIPTYYSVKEAVFPFAKF 899

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVD +LGPEM+STGEVMGVG +FAEAFAKAQLG++  +   G A LSVRE DK  V  +
Sbjct: 900  PGVDTILGPEMKSTGEVMGVGDSFAEAFAKAQLGASEILPTSGCAFLSVREDDKPYVEQV 959

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

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
            ++I DS  IRR+ALQ+K+   TT+ GG A   AL     + V  +Q++HA IK
Sbjct: 1020 QSIADSYSIRRNALQHKICITTTIAGGQAICEALKFGPEKTVRRLQDLHAGIK 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: 3195
Number of extensions: 127
Number of successful extensions: 14
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 GFF939 Psest_0968 (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.21060.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 1572.6   0.0          0 1572.4   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF939  Psest_0968 carbamoyl-phosphate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF939  Psest_0968 carbamoyl-phosphate synthase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1572.4   0.0         0         0       1    1052 []       2    1053 ..       2    1053 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1572.4 bits;  conditional E-value: 0
                          TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveave 74  
                                         pkr+dik++l++G+GpivigqA+EFDYsG+qa+kalkeeg++v+Lvnsn+At+mtd+++ad++YieP+++++v+
  lcl|FitnessBrowser__psRCH2:GFF939    2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALKEEGFRVILVNSNPATIMTDPSMADATYIEPIKWATVA 75  
                                         689*********************************************************************** PP

                          TIGR01369   75 kiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseiv 148 
                                         kiiekErpDa+l+t+GGqtaLn+a++le++GvL+k+gv+++G++ ++i+kaedR +F++a+k+i++  + s i+
  lcl|FitnessBrowser__psRCH2:GFF939   76 KIIEKERPDALLPTMGGQTALNCALDLEKHGVLAKFGVEMIGANADTIDKAEDRSRFDKAMKDIGLACPVSGIA 149 
                                         ************************************************************************** PP

                          TIGR01369  149 esveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRD 222 
                                         +++eea  + +++g+P+i+R++ft+gGtG+gia+n+ee++e+++++l++sp++++l+++sl gwkE+E+EvvRD
  lcl|FitnessBrowser__psRCH2:GFF939  150 HNMEEAYGVLDKVGFPCIIRPSFTMGGTGGGIAYNREEFEEICARGLDLSPTSELLIDESLIGWKEYEMEVVRD 223 
                                         ************************************************************************** PP

                          TIGR01369  223 skdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvv 295 
                                         +kdnciivc+iEn+Dp+GvHtGdsi+vaP+qtLtdkeyq+lR+asl+++re+gve++ +nvqf++ P++ r+vv
  lcl|FitnessBrowser__psRCH2:GFF939  224 KKDNCIIVCSIENFDPMGVHTGDSITVAPAQTLTDKEYQILRNASLAVLREIGVETGgSNVQFGICPNTGRMVV 297 
                                         *******************************************************988**************** PP

                          TIGR01369  296 iEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvd 368 
                                         iE+npRvsRssALAskAtG+PiAk+aaklavGy+Ldel+nd+t+ +t+AsfEP++DYvv+kiPr++++kf k+d
  lcl|FitnessBrowser__psRCH2:GFF939  298 IEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELSNDITGgRTPASFEPAIDYVVTKIPRFAFEKFPKAD 371 
                                         *******************************************879**************************** PP

                          TIGR01369  369 rklgtqmksvGEvmaigrtfeealqkalrsleekllglk..lkekeaesdeeleealkkpndrRlfaiaealrr 440 
                                          +l+tqmksvGEvmaigrtf+e++qkalr le +++g++  l+ + ae++++l+++l+ p ++R++ +a+a+r+
  lcl|FitnessBrowser__psRCH2:GFF939  372 ARLTTQMKSVGEVMAIGRTFQESMQKALRGLEVGATGFDpkLNLADAEAESTLKRELTVPGADRIWFVADAFRA 445 
                                         *************************************7511556677888999********************* PP

                          TIGR01369  441 gvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrke 514 
                                         g +v ev+elt+id++fl ++++lv+ e+++++  l+ ++++l+ k+k++Gfsd+++akl++v+e+++r+ r++
  lcl|FitnessBrowser__psRCH2:GFF939  446 GKTVAEVFELTRIDEWFLVQIEDLVRDEEHVKTLGLSSIDRDLMYKLKRKGFSDARLAKLLGVTEKNLRSHRHK 519 
                                         ************************************************************************** PP

                          TIGR01369  515 lgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreag 588 
                                         l+++pv+krvDt+aaEf ++t+Y+Ystyeee++ ++++++ k+++lG+Gp+Rigqg+EFDyc+vha+la+re g
  lcl|FitnessBrowser__psRCH2:GFF939  520 LKVLPVYKRVDTCAAEFATDTAYMYSTYEEECEANPSSRE-KIMILGGGPNRIGQGIEFDYCCVHAALAMREDG 592 
                                         *******************************776666665.********************************* PP

                          TIGR01369  589 yktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsae 662 
                                         y+ti++n+nPEtvstDyd++drLyFe++t+edvl+i++ e+++gvivq+gGqt+l++ ++leeagv+i+Gts++
  lcl|FitnessBrowser__psRCH2:GFF939  593 YETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEQPKGVIVQYGGQTPLKICRALEEAGVPIIGTSPD 666 
                                         ************************************************************************** PP

                          TIGR01369  663 sidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleea 736 
                                         +idraEdRe+F++++++l++ qp++++a+s eea  + k igyP++vRpsyvlgGrameiv++eeel+ry++ea
  lcl|FitnessBrowser__psRCH2:GFF939  667 AIDRAEDRERFQQMVQRLNLRQPQNATARSEEEAIAASKAIGYPLVVRPSYVLGGRAMEIVYEEEELKRYMREA 740 
                                         ************************************************************************** PP

                          TIGR01369  737 vevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkk 810 
                                         v+vs+++Pvl+d++l+ a+Evd+Dav+dg++v+i gi++HiE+aGvHsGDs+++lp+ +l ++++++i+++v+k
  lcl|FitnessBrowser__psRCH2:GFF939  741 VQVSNDSPVLLDHFLNCAIEVDIDAVCDGTDVVIGGIMQHIEQAGVHSGDSACSLPAYSLPQHIQDEIRDQVRK 814 
                                         ************************************************************************** PP

                          TIGR01369  811 iakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekkskl 884 
                                         +a el+v Gl+n+q++v++e++yv+Evn+RasRtvPfvsk +g +l+k+a++v++gk+l+e   g ++e  +++
  lcl|FitnessBrowser__psRCH2:GFF939  815 MALELDVIGLMNVQMAVQGEDIYVLEVNPRASRTVPFVSKCIGESLAKVAARVMAGKTLKE--IGFTREIIPTY 886 
                                         *************************************************************..6679******* PP

                          TIGR01369  885 vavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellela 958 
                                         ++vk+avf+f+k+ gvd +lgpemkstGEvmg+g++++ea++ka+l +++++++ g ++lsv++ dk ++ ++a
  lcl|FitnessBrowser__psRCH2:GFF939  887 YSVKEAVFPFAKFPGVDTILGPEMKSTGEVMGVGDSFAEAFAKAQLGASEILPTSGCAFLSVREDDKPYVEQVA 960 
                                         ************************************************************************** PP

                          TIGR01369  959 kklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreav 1032
                                         + l+ +g++v+at+gta+++e ag  ++ v+kv+e ++++++++k++e++lvin+t+ ++++  ++y+irr+a+
  lcl|FitnessBrowser__psRCH2:GFF939  961 RDLVGLGFEVVATAGTARIIEAAGLPVRRVNKVTEGRPHVVDMIKNDEVTLVINTTE-GRQSIADSYSIRRNAL 1033
                                         ******************************************************997.77788899******** PP

                          TIGR01369 1033 eykvplvteletaealleal 1052
                                         ++k+ + t++++ +a++eal
  lcl|FitnessBrowser__psRCH2:GFF939 1034 QHKICITTTIAGGQAICEAL 1053
                                         ***************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: 12.98
//
[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