GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Shewanella loihica PV-4

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate 5210397 Shew_2838 carbamoyl phosphate synthase large subunit (RefSeq)

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__PV4:5210397
          Length = 1073

 Score = 1770 bits (4585), Expect = 0.0
 Identities = 883/1073 (82%), Positives = 974/1073 (90%), Gaps = 1/1073 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPIHWEVVR II KERPDA+LPTMGGQTALNCAL LE +GVL EF V MIGATA
Sbjct: 61   ADATYIEPIHWEVVRNIIAKERPDAILPTMGGQTALNCALRLEAEGVLAEFNVDMIGATA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            DAIDKAEDR RFD AMKKIGLE  R+GIA +ME+A  V   VGFPCIIRPSFTMGGSGGG
Sbjct: 121  DAIDKAEDRSRFDAAMKKIGLECPRAGIARSMEDAYEVLEQVGFPCIIRPSFTMGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYN+EEFEEIC++GL+LSPT ELLIDESLIGWKEYEMEVVRD+NDN IIVCSIENFD M
Sbjct: 181  IAYNKEEFEEICSQGLELSPTNELLIDESLIGWKEYEMEVVRDRNDNSIIVCSIENFDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQ+MRNAS+AVLREIGVETGGSNVQF +NPK+GR+++IEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQLMRNASLAVLREIGVETGGSNVQFGINPKDGRMVIIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAK+AAKLAVG+TLDEL NDITGG TPASFEP+IDYVVTK+P
Sbjct: 301  NPRVSRSSALASKATGFPIAKIAAKLAVGFTLDELSNDITGGATPASFEPAIDYVVTKVP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RFNFEKFAGANDRLTTQMKSVGEVMAIGRT QESLQKALRGLEVG  G DP V ++D +A
Sbjct: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVNGLDPIVDVEDNDA 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            L++IR ELK+ GA+RIWYIADAFRAGLS+D +F LTNID WFLVQIEEL+ LE +V E G
Sbjct: 421  LSRIRHELKEPGAERIWYIADAFRAGLSLDAIFKLTNIDPWFLVQIEELLSLENQVKEAG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            +  ++ DFL +LKRKGF+DARLA L GV E+E+RKLR +++++PVYKRVDTCAAEF+TDT
Sbjct: 481  MASMDKDFLYKLKRKGFSDARLAALMGVSESEMRKLRYRHEVYPVYKRVDTCAAEFSTDT 540

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

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFE VTLEDVLEIVRIE+PKGVIVQYGGQTPLKLAR LEAAGVP
Sbjct: 600  CNPETVSTDYDTSDRLYFESVTLEDVLEIVRIEQPKGVIVQYGGQTPLKLARDLEAAGVP 659

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

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVYDE DLRRYF  AVSVSN +PVLLDHFLD+A EVD+DA+CDG  V++G IME
Sbjct: 720  GGRAMEIVYDEQDLRRYFNEAVSVSNASPVLLDHFLDNATEVDIDAVCDGTTVVVGAIME 779

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDS CSLP YTLSQEIQD MR+QV+KLA EL V GLMNVQFAV++N +Y+I
Sbjct: 780  HIEQAGVHSGDSGCSLPPYTLSQEIQDQMREQVRKLAMELGVVGLMNVQFAVQDNTIYMI 839

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRAARTVPFVSKATGVPLAK+AARVMAG+SL EQG TKEVIPP+YSVKEVVLPFNKF
Sbjct: 840  EVNPRAARTVPFVSKATGVPLAKIAARVMAGQSLEEQGFTKEVIPPFYSVKEVVLPFNKF 899

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDPLLGPEMRSTGEVMGVG TFAEA+AKA+LG+ S + K GRALLSVR  DK+RV DL
Sbjct: 900  PGVDPLLGPEMRSTGEVMGVGATFAEAYAKAELGATSEVPKSGRALLSVRNSDKKRVADL 959

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            AAKL++ G+E+DATHGTA+VLGEAGINPRLVNKVHEGRPHI DRIKN EYTYI+NTT GR
Sbjct: 960  AAKLIELGYEIDATHGTAVVLGEAGINPRLVNKVHEGRPHILDRIKNDEYTYIVNTTEGR 1019

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
            +AIEDSR +RR AL+YKV+Y TTLN  FAT MA +AD+   V SVQE+H +IK
Sbjct: 1020 QAIEDSRQLRRGALRYKVNYTTTLNAAFATCMAHSADSRTNVTSVQELHQRIK 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: 3284
Number of extensions: 127
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 5210397 Shew_2838 (carbamoyl phosphate synthase large subunit (RefSeq))
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.25549.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 1576.5   0.0          0 1576.3   0.0    1.0  1  lcl|FitnessBrowser__PV4:5210397  Shew_2838 carbamoyl phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210397  Shew_2838 carbamoyl phosphate synthase large subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1576.3   0.0         0         0       1    1051 [.       2    1052 ..       2    1053 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1576.3 bits;  conditional E-value: 0
                        TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveaveki 76  
                                       pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+e+ad++YieP+++e+v++i
  lcl|FitnessBrowser__PV4:5210397    2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADATYIEPIHWEVVRNI 77  
                                       689************************************************************************* PP

                        TIGR01369   77 iekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseivesve 152 
                                       i kErpDail+t+GGqtaLn+a+ le +GvL++++v ++G++ +ai+kaedR +F++a+k+i++e +++ i++s+e
  lcl|FitnessBrowser__PV4:5210397   78 IAKERPDAILPTMGGQTALNCALRLEAEGVLAEFNVDMIGATADAIDKAEDRSRFDAAMKKIGLECPRAGIARSME 153 
                                       **************************************************************************** PP

                        TIGR01369  153 ealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskdnci 228 
                                       +a e+ e++g+P+i+R++ft+gG+G+gia+n+ee++e+++++l++sp++++l+++sl gwkE+E+EvvRD++dn+i
  lcl|FitnessBrowser__PV4:5210397  154 DAYEVLEQVGFPCIIRPSFTMGGSGGGIAYNKEEFEEICSQGLELSPTNELLIDESLIGWKEYEMEVVRDRNDNSI 229 
                                       **************************************************************************** PP

                        TIGR01369  229 ivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvs 303 
                                       ivc+iEn+Dp+GvHtGdsi+vaP+qtLtdkeyql+R+asl+++re+gve++ +nvqf+++P++ r+v+iE+npRvs
  lcl|FitnessBrowser__PV4:5210397  230 IVCSIENFDPMGVHTGDSITVAPAQTLTDKEYQLMRNASLAVLREIGVETGgSNVQFGINPKDGRMVIIEMNPRVS 305 
                                       *************************************************988************************ PP

                        TIGR01369  304 RssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksv 378 
                                       RssALAskAtG+PiAk+aaklavG++Ldel+nd+t+  t+AsfEP++DYvv+k+Pr++++kf++++++l+tqmksv
  lcl|FitnessBrowser__PV4:5210397  306 RSSALASKATGFPIAKIAAKLAVGFTLDELSNDITGgATPASFEPAIDYVVTKVPRFNFEKFAGANDRLTTQMKSV 381 
                                       ***********************************878************************************** PP

                        TIGR01369  379 GEvmaigrtfeealqkalrsleekllglk..lkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltk 452 
                                       GEvmaigrtf+e+lqkalr le ++ gl+  ++ + + + ++++++lk+p ++R+++ia+a+r+g+s++++++lt+
  lcl|FitnessBrowser__PV4:5210397  382 GEVMAIGRTFQESLQKALRGLEVGVNGLDpiVDVEDNDALSRIRHELKEPGAERIWYIADAFRAGLSLDAIFKLTN 457 
                                       ***************************6521333445556778899****************************** PP

                        TIGR01369  453 idrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtva 528 
                                       id +fl ++++l++le++++e  +  ++k+ l k+k++Gfsd+++a+l++vse+e+rklr + ++ pv+krvDt+a
  lcl|FitnessBrowser__PV4:5210397  458 IDPWFLVQIEELLSLENQVKEAGMASMDKDFLYKLKRKGFSDARLAALMGVSESEMRKLRYRHEVYPVYKRVDTCA 533 
                                       **************************************************************************** PP

                        TIGR01369  529 aEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstD 604 
                                       aEf+++t+Y+Ystyeee++ ++++++ k++vlG+Gp+Rigqg+EFDyc+vha+lalre gy+ti++n+nPEtvstD
  lcl|FitnessBrowser__PV4:5210397  534 AEFSTDTAYMYSTYEEECEANPSNRD-KIMVLGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVNCNPETVSTD 608 
                                       *****************777766666.************************************************* PP

                        TIGR01369  605 ydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldel 680 
                                       yd++drLyFe++t+edvl+i++ e+++gvivq+gGqt+l+la++le+agv+i+Gts+++idraEdRe+F++++++l
  lcl|FitnessBrowser__PV4:5210397  609 YDTSDRLYFESVTLEDVLEIVRIEQPKGVIVQYGGQTPLKLARDLEAAGVPIIGTSPDAIDRAEDRERFQQAIQRL 684 
                                       **************************************************************************** PP

                        TIGR01369  681 gikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavE 756 
                                       ++kqp++ ++t+ve a+  a++igyP++vRpsyvlgGrameiv++e++l+ry++eav+vs+ +Pvl+d++l++a+E
  lcl|FitnessBrowser__PV4:5210397  685 EMKQPENDTVTTVEGAVISAERIGYPLVVRPSYVLGGRAMEIVYDEQDLRRYFNEAVSVSNASPVLLDHFLDNATE 760 
                                       **************************************************************************** PP

                        TIGR01369  757 vdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeev 832 
                                       vd+Dav+dg++v++ +i+eHiE+aGvHsGDs ++lpp +ls+e++++++e+v+k+a el v+Gl+n+qf+v+d+++
  lcl|FitnessBrowser__PV4:5210397  761 VDIDAVCDGTTVVVGAIMEHIEQAGVHSGDSGCSLPPYTLSQEIQDQMREQVRKLAMELGVVGLMNVQFAVQDNTI 836 
                                       **************************************************************************** PP

                        TIGR01369  833 yviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpem 908 
                                       y+iEvn+Ra+RtvPfvska+gvpl+k+a++v++g++lee  +g +ke  + +++vk++v++f+k+ gvd++lgpem
  lcl|FitnessBrowser__PV4:5210397  837 YMIEVNPRAARTVPFVSKATGVPLAKIAARVMAGQSLEE--QGFTKEVIPPFYSVKEVVLPFNKFPGVDPLLGPEM 910 
                                       ***************************************..788******************************** PP

                        TIGR01369  909 kstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagik 984 
                                       +stGEvmg+g +++ea++ka l ++++++k g++llsv+++dk+++ +la+kl e+g+++ at+gta vl eagi+
  lcl|FitnessBrowser__PV4:5210397  911 RSTGEVMGVGATFAEAYAKAELGATSEVPKSGRALLSVRNSDKKRVADLAAKLIELGYEIDATHGTAVVLGEAGIN 986 
                                       **************************************************************************** PP

                        TIGR01369  985 aevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
                                        ++v+kv+e +++il+ +k++e+++++n+t+ +++a e++ ++rr a++ykv++ t+l++a a+++a
  lcl|FitnessBrowser__PV4:5210397  987 PRLVNKVHEGRPHILDRIKNDEYTYIVNTTE-GRQAIEDSRQLRRGALRYKVNYTTTLNAAFATCMA 1052
                                       ****************************997.88899999*******************99988765 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: 13.12
//
[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