Alignments for a candidate for carB in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Phaeobacter inhibens BS107

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate GFF2425 PGA1_c24560 carbamoyl-phosphate synthase large chain

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Phaeo:GFF2425
          Length = 1119

 Score = 1251 bits (3238), Expect = 0.0
 Identities = 673/1111 (60%), Positives = 805/1111 (72%), Gaps = 56/1111 (5%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDI+SI+I+GAGPI+IGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP +
Sbjct: 1    MPKRTDIQSIMIIGAGPIIIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGL 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI  EVV KIIEKERPDA+LPTMGGQT LN AL LE  GVL +F V MIGA  
Sbjct: 61   ADATYIEPITPEVVAKIIEKERPDALLPTMGGQTGLNTALALEEMGVLAKFDVEMIGAKR 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHT-------------MEEALAVAADVGFPCI 167
            +AI+ AEDR+ F  AM ++GLE  R+ I                ++ AL    D+G P I
Sbjct: 121  EAIEMAEDRKLFREAMDRLGLENPRATIITAPKKDNGNADLDAGVQMALDELEDIGLPAI 180

Query: 168  IRPSFTMGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDN 227
            IRP+FT+GG+GGG+AYNRE++   C  G+D SP  ++L+DESL+GWKEYEMEVVRD  DN
Sbjct: 181  IRPAFTLGGTGGGVAYNREDYIHFCRSGMDASPVNQILVDESLLGWKEYEMEVVRDTADN 240

Query: 228  CIIVCSIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFA 287
             IIVCSIEN D MG+HTGDSITVAPA TLTDKEYQ+MR+AS+AVLREIGVETGGSNVQ+A
Sbjct: 241  AIIVCSIENIDPMGVHTGDSITVAPALTLTDKEYQMMRSASIAVLREIGVETGGSNVQWA 300

Query: 288  VNPKNGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPAS 347
            VNP +GR++VIEMNPRVSRSSALASKATGFPIAK+AAKLAVG+TLDEL NDIT G TPAS
Sbjct: 301  VNPADGRMVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGFTLDELDNDIT-GVTPAS 359

Query: 348  FEPSIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGAT 407
            FEP+IDYVVTKIPRF FEKFAG+   LTT MKSVGE MAIGRT  ESLQKAL  +E G T
Sbjct: 360  FEPTIDYVVTKIPRFAFEKFAGSEPYLTTAMKSVGETMAIGRTIHESLQKALASMETGLT 419

Query: 408  GFDPKV---SLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLV 464
            GFD      + D+ +    + + +     DR+  IA A R GLS D +  +T  D WFL 
Sbjct: 420  GFDEVAIPGAEDETDGKAAVIKAISQQTPDRMRTIAQAMRHGLSDDDIHAVTKFDPWFLA 479

Query: 465  QIEELVRLEEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHP 524
            +I E+V  E K+   G+   +   LR +K  GF DARLA L   RE +IR  R    ++ 
Sbjct: 480  RIREIVEAEAKIRAEGLP-QDEHGLRAIKMLGFTDARLAMLTDQREGDIRAARRALGVNA 538

Query: 525  VYKRVDTCAAEFATDTAYMYSTYEE------ECEANPSTDREKIMVLGGGPNRIGQGIEF 578
            V+KR+DTCAAEF   T YMYSTYE       ECEA PS D++K+++LGGGPNRIGQGIEF
Sbjct: 539  VFKRIDTCAAEFEAQTPYMYSTYEAPAFGDVECEARPS-DKKKVVILGGGPNRIGQGIEF 597

Query: 579  DYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPK-- 636
            DYCC HA  AL + GYETIM+NCNPETVSTDYDTSDRLYFEP+T E V+EI+  E     
Sbjct: 598  DYCCCHACFALTDAGYETIMINCNPETVSTDYDTSDRLYFEPLTFEHVMEILTKELENGT 657

Query: 637  --GVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANAT 694
              GVIVQ+GGQTPLKLA ALE  G+P++GTSPDAID AEDRERFQ  V +L LKQP N  
Sbjct: 658  LHGVIVQFGGQTPLKLANALEEEGIPILGTSPDAIDLAEDRERFQALVNQLGLKQPHNGI 717

Query: 695  VTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDH 754
             +    A+E A+EIG+PLV+RPSYVLGGRAMEIV D   L+RY   AV VS D+PVLLD 
Sbjct: 718  ASTDAQALEIAEEIGFPLVIRPSYVLGGRAMEIVRDMDQLKRYIAEAVVVSGDSPVLLDS 777

Query: 755  FLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQ 814
            +L  AVE+DVDAICDG  V + GIM+HIE+AGVHSGDSACSLP Y+LS+E+   ++ Q  
Sbjct: 778  YLSGAVELDVDAICDGTEVHVAGIMQHIEEAGVHSGDSACSLPPYSLSKEVIAEVKTQTN 837

Query: 815  KLAFELQVRGLMNVQFAVK-----NNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVM 869
             LA  L V GLMN+QFAVK      + +YLIEVNPRA+RTVPFV+K+T   +A +AARVM
Sbjct: 838  ALAKALNVVGLMNIQFAVKPDADGKDVIYLIEVNPRASRTVPFVAKSTDSAIASIAARVM 897

Query: 870  AGKSL---------------------AEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLG 908
            AG+ L                     A+     +   P++SVKE VLPF +FPGVD LLG
Sbjct: 898  AGEPLSNFPKRAPYEPDAGYDVNVPMADPMTLADPDMPWFSVKEAVLPFARFPGVDTLLG 957

Query: 909  PEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLL-KQ 967
            PEMRSTGEVMG  R+FA AF KAQ+G+   +   GRA +S+++ DK  ++  AAK+L +Q
Sbjct: 958  PEMRSTGEVMGWDRSFARAFLKAQMGAGMVLPSEGRAFISIKDADKGTLMLDAAKILVEQ 1017

Query: 968  GFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSR 1027
            GF L AT GT   L   G+   LVNKV+EGRPH+ D +K+G    ++NTT G +A++DS+
Sbjct: 1018 GFTLVATRGTQSWLDGHGVPCELVNKVYEGRPHVVDMLKDGNVQLLMNTTEGAQAVQDSK 1077

Query: 1028 VIRRSALQYKVHYDTTLNGGFATAMALNADA 1058
             +R  AL  K+ Y TT  G  A A A+ A A
Sbjct: 1078 DMRSVALYDKIPYFTTAAGANAAARAIKAQA 1108


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: 3105
Number of extensions: 157
Number of successful extensions: 23
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: 1119
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1073
Effective search space:  1101971
Effective search space used:  1101971
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 GFF2425 PGA1_c24560 (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.21086.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 1436.0   0.0          0 1435.8   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2425  PGA1_c24560 carbamoyl-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2425  PGA1_c24560 carbamoyl-phosphate synthase large chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1435.8   0.0         0         0       1    1051 [.       2    1103 ..       2    1104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1435.8 bits;  conditional E-value: 0
                          TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveave 74  
                                         pkr+di+++++iG+Gpi+igqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+ lad++YieP+t+e+v+
  lcl|FitnessBrowser__Phaeo:GFF2425    2 PKRTDIQSIMIIGAGPIIIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGLADATYIEPITPEVVA 75  
                                         689*********************************************************************** PP

                          TIGR01369   75 kiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseiv 148 
                                         kiiekErpDa+l+t+GGqt+Ln a+ lee+GvL+k++v+++G+k eai+ aedR++F+ea++ +++e ++++i+
  lcl|FitnessBrowser__Phaeo:GFF2425   76 KIIEKERPDALLPTMGGQTGLNTALALEEMGVLAKFDVEMIGAKREAIEMAEDRKLFREAMDRLGLENPRATII 149 
                                         *********************************************************************99998 PP

                          TIGR01369  149 es.............veealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlveksl 209 
                                         +              v+ al+  e+ig+P i+R+aftlgGtG+g+a+n+e+  + ++++++asp++q+lv++sl
  lcl|FitnessBrowser__Phaeo:GFF2425  150 TApkkdngnadldagVQMALDELEDIGLPAIIRPAFTLGGTGGGVAYNREDYIHFCRSGMDASPVNQILVDESL 223 
                                         752222222222222456788889************************************************** PP

                          TIGR01369  210 agwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnv 282 
                                          gwkE+E+EvvRD++dn+iivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++R+as++++re+gve++ +nv
  lcl|FitnessBrowser__Phaeo:GFF2425  224 LGWKEYEMEVVRDTADNAIIVCSIENIDPMGVHTGDSITVAPALTLTDKEYQMMRSASIAVLREIGVETGgSNV 297 
                                         ********************************************************************988*** PP

                          TIGR01369  283 qfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvki 356 
                                         q+a++P + r+vviE+npRvsRssALAskAtG+PiAk+aaklavG++Ldel nd+t+ t+AsfEP++DYvv+ki
  lcl|FitnessBrowser__Phaeo:GFF2425  298 QWAVNPADGRMVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGFTLDELDNDITGVTPASFEPTIDYVVTKI 371 
                                         ************************************************************************** PP

                          TIGR01369  357 PrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglkl.....kekeaesdeeleealkk 425 
                                         Pr++++kf++ +  l+t mksvGE maigrt++e+lqkal+s+e++l+g+++      e+e+  + ++ +a+ +
  lcl|FitnessBrowser__Phaeo:GFF2425  372 PRFAFEKFAGSEPYLTTAMKSVGETMAIGRTIHESLQKALASMETGLTGFDEvaipgAEDETDGKAAVIKAISQ 445 
                                         *************************************************6541111134445556678899*** PP

                          TIGR01369  426 pndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiak 499 
                                         ++++R+ +ia+a+r+g+s ++++ +tk+d +fl +++++ve+e +++ e l   +++ l+ +k lGf+d+++a 
  lcl|FitnessBrowser__Phaeo:GFF2425  446 QTPDRMRTIAQAMRHGLSDDDIHAVTKFDPWFLARIREIVEAEAKIRAEGLP-QDEHGLRAIKMLGFTDARLAM 518 
                                         **********************************************977776.78999**************** PP

                          TIGR01369  500 lvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee.....kddvevtekkkvlvlGsGpiRig 568 
                                         l++++e ++r++r++lg+  v+kr+Dt+aaEfea+tpY+Ystye+      + +++ ++kkkv++lG+Gp+Rig
  lcl|FitnessBrowser__Phaeo:GFF2425  519 LTDQREGDIRAARRALGVNAVFKRIDTCAAEFEAQTPYMYSTYEAPafgdvECEARPSDKKKVVILGGGPNRIG 592 
                                         ********************************************87555545566778889************* PP

                          TIGR01369  569 qgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiieke....kvegvivqlg 638 
                                         qg+EFDyc+ ha+ al +agy+ti+in+nPEtvstDyd++drLyFe+lt+e+v++i++ke      +gvivq+g
  lcl|FitnessBrowser__Phaeo:GFF2425  593 QGIEFDYCCCHACFALTDAGYETIMINCNPETVSTDYDTSDRLYFEPLTFEHVMEILTKElengTLHGVIVQFG 666 
                                         ********************************************************988744445789****** PP

                          TIGR01369  639 GqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRps 712 
                                         Gqt+l+la++lee+g++ilGts+++id aEdRe+F++l+++lg+kqp++ +a++  +a eia+eig+P+++Rps
  lcl|FitnessBrowser__Phaeo:GFF2425  667 GQTPLKLANALEEEGIPILGTSPDAIDLAEDRERFQALVNQLGLKQPHNGIASTDAQALEIAEEIGFPLVIRPS 740 
                                         ************************************************************************** PP

                          TIGR01369  713 yvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGD 786 
                                         yvlgGrameiv+++++l+ry+ eav vs ++Pvl+d yl+ avE+dvDa++dg+ev +agi++HiEeaGvHsGD
  lcl|FitnessBrowser__Phaeo:GFF2425  741 YVLGGRAMEIVRDMDQLKRYIAEAVVVSGDSPVLLDSYLSGAVELDVDAICDGTEVHVAGIMQHIEEAGVHSGD 814 
                                         ************************************************************************** PP

                          TIGR01369  787 stlvlppqklseevkkkikeivkkiakelkvkGllniqfvvk.....deevyviEvnvRasRtvPfvskalgvp 855 
                                         s+++lpp +ls+ev  ++k++++++ak+l+v+Gl+niqf+vk     ++ +y+iEvn+RasRtvPfv+k ++  
  lcl|FitnessBrowser__Phaeo:GFF2425  815 SACSLPPYSLSKEVIAEVKTQTNALAKALNVVGLMNIQFAVKpdadgKDVIYLIEVNPRASRTVPFVAKSTDSA 888 
                                         ****************************************98433222569*********************** PP

                          TIGR01369  856 lvklavkvllgkkleele...................kgvkkekksklvavkaavfsfsklagvdvvlgpemks 910 
                                         ++++a++v++g+ l++                          ++++  ++vk+av++f+++ gvd +lgpem+s
  lcl|FitnessBrowser__Phaeo:GFF2425  889 IASIAARVMAGEPLSNFPkrapyepdagydvnvpmadPMTLADPDMPWFSVKEAVLPFARFPGVDTLLGPEMRS 962 
                                         ****************9899************999985567889999*************************** PP

                          TIGR01369  911 tGEvmgigrdleeallkallaskakikkkgsvllsvkdkdk.eellelakklaekglkvyategtakvleeagi 983 
                                         tGEvmg +r++++a+lka++ ++++++++g++++s+kd+dk + +l++ak l+e+g++++at+gt++ l  +g+
  lcl|FitnessBrowser__Phaeo:GFF2425  963 TGEVMGWDRSFARAFLKAQMGAGMVLPSEGRAFISIKDADKgTLMLDAAKILVEQGFTLVATRGTQSWLDGHGV 1036
                                         ****************************************95567899************************** PP

                          TIGR01369  984 kaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
                                          +e+v+kv e +++++++lk+++++l++n+t+ +++a+++++ +r  a+  k+p++t++++a+a+++a
  lcl|FitnessBrowser__Phaeo:GFF2425 1037 PCELVNKVYEGRPHVVDMLKDGNVQLLMNTTE-GAQAVQDSKDMRSVALYDKIPYFTTAAGANAAARA 1103
                                         *****************************997.88899999*********************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1119 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: 00:00:00.09
# Mc/sec: 12.96
//
[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