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

GapMind for Amino acid biosynthesis

Aligments 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)



>lcl|FitnessBrowser__PV4:5210397 Shew_2838 carbamoyl phosphate
            synthase large subunit (RefSeq)
          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.31094.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: 13.17
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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