Alignments for a candidate for carB in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Shewanella oneidensis MR-1

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate 200322 SO1142 carbamoyl-phosphate synthase, large subunit (NCBI ptt file)

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__MR1:200322
          Length = 1074

 Score = 1793 bits (4644), Expect = 0.0
 Identities = 895/1072 (83%), Positives = 974/1072 (90%), Gaps = 1/1072 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI WEVVR II KERPDA+LPTMGGQTALNCALELE +GVL EF V MIGATA
Sbjct: 61   ADATYIEPIQWEVVRNIIAKERPDAILPTMGGQTALNCALELEAKGVLAEFNVEMIGATA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            DAIDKAEDR RFD AMK IGLE  R+GIAH+MEEA  V   VGFPCIIRPSFTMGGSGGG
Sbjct: 121  DAIDKAEDRSRFDKAMKSIGLECPRAGIAHSMEEAYGVLEQVGFPCIIRPSFTMGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYN+EEFEEIC++GLDLSPTKELLIDESLIGWKEYEMEVVRD+NDNCIIVCSIENFD M
Sbjct: 181  IAYNKEEFEEICSQGLDLSPTKELLIDESLIGWKEYEMEVVRDRNDNCIIVCSIENFDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQF +NPK+GR+++IEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFGINPKDGRMVIIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAK+AAKLAVG+TLDELMNDITGGRTPASFEP+IDYVVTK+P
Sbjct: 301  NPRVSRSSALASKATGFPIAKIAAKLAVGFTLDELMNDITGGRTPASFEPAIDYVVTKVP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RFNFEKFAG+NDRLTTQMKSVGEVMAIGRT QESLQKALRGLEV   G DP   +  PEA
Sbjct: 361  RFNFEKFAGSNDRLTTQMKSVGEVMAIGRTFQESLQKALRGLEVNRHGLDPITDMSKPEA 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            + +IR ELK+ G DRIWYIADA RAGL++D +F LTNID WFLVQIEEL++LE +VAE G
Sbjct: 421  MARIRLELKEPGCDRIWYIADAMRAGLTLDEIFRLTNIDPWFLVQIEELIKLEGQVAEAG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            + GLN + LR+LKRKGFADARLA + GV E+E+RKLRD++D+HPVYKRVDTCAAEFATDT
Sbjct: 481  LAGLNEELLRKLKRKGFADARLAVVLGVNESEVRKLRDRFDIHPVYKRVDTCAAEFATDT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AYMYSTYEEECEANPS +R+KIMVLGGGPNRIGQGIEFDYCCVHA+LALREDGYETIMVN
Sbjct: 541  AYMYSTYEEECEANPS-NRDKIMVLGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVN 599

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP
Sbjct: 600  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 659

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            +IGTSPDAIDRAEDRERFQ A++RL++KQP N TVT +E AV  A+ IGYPLVVRPSYVL
Sbjct: 660  IIGTSPDAIDRAEDRERFQQAIQRLEMKQPENDTVTTVEGAVIAAERIGYPLVVRPSYVL 719

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVYD+ DL RYF  AVSVSN +PVLLDHFLDDA+EVD+DA+CDGE V+IG IME
Sbjct: 720  GGRAMEIVYDQQDLLRYFNEAVSVSNASPVLLDHFLDDAIEVDIDAVCDGETVVIGAIME 779

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDS CSLP YTLSQEIQD MR QV KLA EL V GLMNVQFAVKNNE+Y+I
Sbjct: 780  HIEQAGVHSGDSGCSLPPYTLSQEIQDRMRVQVGKLAMELGVVGLMNVQFAVKNNEIYMI 839

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRAARTVPFVSKATGVPLAK+AARVMAG+SL  Q  T+EVIPP+YSVKEVVLPFNKF
Sbjct: 840  EVNPRAARTVPFVSKATGVPLAKIAARVMAGQSLKAQNFTQEVIPPFYSVKEVVLPFNKF 899

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDPLLGPEMRSTGEVMGVG TFAEA+AKAQLG+ S + K GRALLSVR  DK+RV DL
Sbjct: 900  PGVDPLLGPEMRSTGEVMGVGDTFAEAYAKAQLGATSEVPKSGRALLSVRNSDKKRVADL 959

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            AAKL++ G+++DATHGTA++LGEAGINPRLVNKVHEGRPHI DRIKNGEYTYI+NTT GR
Sbjct: 960  AAKLIELGYQIDATHGTAVILGEAGINPRLVNKVHEGRPHILDRIKNGEYTYIVNTTEGR 1019

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQI 1072
            +AIEDSR +RR AL+YKV+Y TT+N  FAT MA  AD    V SVQE+H +I
Sbjct: 1020 QAIEDSRQLRRGALRYKVNYTTTMNAAFATCMAHAADDRTNVTSVQELHKRI 1071


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: 3363
Number of extensions: 120
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: 1074
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1029
Effective search space:  1057812
Effective search space used:  1057812
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 200322 SO1142 (carbamoyl-phosphate synthase, large subunit (NCBI ptt file))
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.5075.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 1578.7   0.0          0 1578.5   0.0    1.0  1  lcl|FitnessBrowser__MR1:200322  SO1142 carbamoyl-phosphate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200322  SO1142 carbamoyl-phosphate synthase, large subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1578.5   0.0         0         0       1    1051 [.       2    1052 ..       2    1053 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1578.5 bits;  conditional E-value: 0
                       TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveavekii 77  
                                      pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+e+ad++YieP+++e+v++ii
  lcl|FitnessBrowser__MR1:200322    2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADATYIEPIQWEVVRNII 78  
                                      689************************************************************************** PP

                       TIGR01369   78 ekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseivesveea 154 
                                       kErpDail+t+GGqtaLn+a+ele kGvL++++v+++G++ +ai+kaedR +F++a+k i++e +++ i++s+eea
  lcl|FitnessBrowser__MR1:200322   79 AKERPDAILPTMGGQTALNCALELEAKGVLAEFNVEMIGATADAIDKAEDRSRFDKAMKSIGLECPRAGIAHSMEEA 155 
                                      ***************************************************************************** PP

                       TIGR01369  155 leaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskdnciivc 231 
                                        + e++g+P+i+R++ft+gG+G+gia+n+ee++e+++++l++sp+k++l+++sl gwkE+E+EvvRD++dnciivc
  lcl|FitnessBrowser__MR1:200322  156 YGVLEQVGFPCIIRPSFTMGGSGGGIAYNKEEFEEICSQGLDLSPTKELLIDESLIGWKEYEMEVVRDRNDNCIIVC 232 
                                      ***************************************************************************** PP

                       TIGR01369  232 niEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssA 307 
                                      +iEn+Dp+GvHtGdsi+vaP+qtLtdkeyq++R+as++++re+gve++ +nvqf+++P++ r+v+iE+npRvsRssA
  lcl|FitnessBrowser__MR1:200322  233 SIENFDPMGVHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGgSNVQFGINPKDGRMVIIEMNPRVSRSSA 309 
                                      **********************************************988**************************** PP

                       TIGR01369  308 LAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvma 383 
                                      LAskAtG+PiAk+aaklavG++Ldel+nd+t+ +t+AsfEP++DYvv+k+Pr++++kf++ +++l+tqmksvGEvma
  lcl|FitnessBrowser__MR1:200322  310 LASKATGFPIAKIAAKLAVGFTLDELMNDITGgRTPASFEPAIDYVVTKVPRFNFEKFAGSNDRLTTQMKSVGEVMA 386 
                                      *******************************879******************************************* PP

                       TIGR01369  384 igrtfeealqkalrsleekllglklkek..eaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffl 458 
                                      igrtf+e+lqkalr le + +gl+  ++  + e+  +++ +lk+p  +R+++ia+a+r+g++++e+++lt+id +fl
  lcl|FitnessBrowser__MR1:200322  387 IGRTFQESLQKALRGLEVNRHGLDPITDmsKPEAMARIRLELKEPGCDRIWYIADAMRAGLTLDEIFRLTNIDPWFL 463 
                                      **********************7654330034455667789************************************ PP

                       TIGR01369  459 eklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeakt 535 
                                       ++++l++le +++e  l  l++ell+k+k++Gf+d+++a +++v+e+evrklr++ +i+pv+krvDt+aaEf ++t
  lcl|FitnessBrowser__MR1:200322  464 VQIEELIKLEGQVAEAGLAGLNEELLRKLKRKGFADARLAVVLGVNESEVRKLRDRFDIHPVYKRVDTCAAEFATDT 540 
                                      ***************************************************************************** PP

                       TIGR01369  536 pYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLy 612 
                                      +Y+Ystyeee++ ++++++ k++vlG+Gp+Rigqg+EFDyc+vha+lalre gy+ti++n+nPEtvstDyd++drLy
  lcl|FitnessBrowser__MR1:200322  541 AYMYSTYEEECEANPSNRD-KIMVLGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVNCNPETVSTDYDTSDRLY 616 
                                      **********777766666.********************************************************* PP

                       TIGR01369  613 FeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgke 689 
                                      Fe++t+edvl+i++ ek++gvivq+gGqt+l+la++le+agv+i+Gts+++idraEdRe+F++++++l++kqp++ +
  lcl|FitnessBrowser__MR1:200322  617 FEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVPIIGTSPDAIDRAEDRERFQQAIQRLEMKQPENDT 693 
                                      ***************************************************************************** PP

                       TIGR01369  690 atsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadge 766 
                                      +t+ve a+ +a++igyP++vRpsyvlgGrameiv+++++l ry++eav+vs+ +Pvl+d++l+da+Evd+Dav+dge
  lcl|FitnessBrowser__MR1:200322  694 VTTVEGAVIAAERIGYPLVVRPSYVLGGRAMEIVYDQQDLLRYFNEAVSVSNASPVLLDHFLDDAIEVDIDAVCDGE 770 
                                      ***************************************************************************** PP

                       TIGR01369  767 evliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasR 843 
                                      +v+i +i+eHiE+aGvHsGDs ++lpp +ls+e++++++ +v k+a el v+Gl+n+qf+vk++e+y+iEvn+Ra+R
  lcl|FitnessBrowser__MR1:200322  771 TVVIGAIMEHIEQAGVHSGDSGCSLPPYTLSQEIQDRMRVQVGKLAMELGVVGLMNVQFAVKNNEIYMIEVNPRAAR 847 
                                      ***************************************************************************** PP

                       TIGR01369  844 tvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrd 920 
                                      tvPfvska+gvpl+k+a++v++g++l+ ++   ++e  + +++vk++v++f+k+ gvd++lgpem+stGEvmg+g++
  lcl|FitnessBrowser__MR1:200322  848 TVPFVSKATGVPLAKIAARVMAGQSLKAQN--FTQEVIPPFYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGDT 922 
                                      ****************************55..6999***************************************** PP

                       TIGR01369  921 leeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaek 997 
                                      ++ea++ka+l ++++++k g++llsv+++dk+++ +la+kl e+g+++ at+gta +l eagi+ ++v+kv+e +++
  lcl|FitnessBrowser__MR1:200322  923 FAEAYAKAQLGATSEVPKSGRALLSVRNSDKKRVADLAAKLIELGYQIDATHGTAVILGEAGINPRLVNKVHEGRPH 999 
                                      ***************************************************************************** PP

                       TIGR01369  998 ilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
                                      il+ +k++e+++++n+t+ +++a e++ ++rr a++ykv++ t++++a a+++a
  lcl|FitnessBrowser__MR1:200322 1000 ILDRIKNGEYTYIVNTTE-GRQAIEDSRQLRRGALRYKVNYTTTMNAAFATCMA 1052
                                      ***************997.88899999*******************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1074 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: 00:00:00.09
# Mc/sec: 11.61
//
[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