Alignments for a candidate for carB in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Dechlorosoma suillum PS

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate Dsui_3064 Dsui_3064 carbamoyl-phosphate synthase, large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__PS:Dsui_3064
          Length = 1068

 Score = 1479 bits (3830), Expect = 0.0
 Identities = 756/1073 (70%), Positives = 873/1073 (81%), Gaps = 7/1073 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILI+GAGPI+IGQACEFDYSGAQACKAL+ EGYRVILVNSNPATIMTDPE 
Sbjct: 1    MPKRTDIKSILIIGAGPIIIGQACEFDYSGAQACKALKAEGYRVILVNSNPATIMTDPET 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            AD TYIEPI W+VV KIIEKERPDA+LPTMGGQTALNCAL+L + GVLE+FGV +IGA+ 
Sbjct: 61   ADVTYIEPISWKVVEKIIEKERPDALLPTMGGQTALNCALDLAKHGVLEKFGVELIGASE 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            +AIDKAEDR +F  AM KIGL +ARS +AH+MEEAL V A +GFP IIRPSFT+GGSGGG
Sbjct: 121  EAIDKAEDREKFKAAMTKIGLGSARSAVAHSMEEALQVQAMIGFPAIIRPSFTLGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYN+EEF  IC RGL+ SPTKELLI+ESLIGWKEYEMEVVRD  DNCII+CSIEN D M
Sbjct: 181  IAYNKEEFVTICERGLEASPTKELLIEESLIGWKEYEMEVVRDSKDNCIIICSIENLDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQIMRNAS+AVLREIGV+TGGSNVQFA++PK+GR+IVIEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQIMRNASIAVLREIGVDTGGSNVQFAISPKDGRMIVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL N+ITGG+TPASFEPSIDYVVTK+P
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELANEITGGKTPASFEPSIDYVVTKVP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RF FEKF  A+  LTTQMKSVGEVMAIGRT QESLQKALRGLEVG  GFD K +  D E 
Sbjct: 361  RFAFEKFPTADFHLTTQMKSVGEVMAIGRTLQESLQKALRGLEVGVDGFDEKTT--DREV 418

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
               I  EL + G +RIWY+ DAFR G+++D +  LT+ID WFL QIE+L    + +A   
Sbjct: 419  ---IETELAEPGPERIWYVGDAFRIGMTLDEIHRLTHIDPWFLAQIEDLHLKAKSLAGRS 475

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            +  L+ + L  LK+ GF+D RLAKL    +  +R+ R   ++ PV+KRVDTCAAEFAT+T
Sbjct: 476  VDSLSREELLVLKKCGFSDKRLAKLLATTQTAVRERRHALNVRPVFKRVDTCAAEFATNT 535

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AYMYSTYE+ECEA PS D++KIMVLGGGPNRIGQGIEFDYCCVHA++A+REDGYETIMVN
Sbjct: 536  AYMYSTYEDECEAQPS-DKKKIMVLGGGPNRIGQGIEFDYCCVHAAMAMREDGYETIMVN 594

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEP+TLEDVLE+V +EKP GVIVQYGGQTPLKLAR LEA GVP
Sbjct: 595  CNPETVSTDYDTSDRLYFEPLTLEDVLEVVNVEKPVGVIVQYGGQTPLKLARDLEANGVP 654

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            +IGTSPD ID AEDRERFQ  +  L LKQP N T      A+  A+EIGYPLVVRPSYVL
Sbjct: 655  IIGTSPDMIDAAEDRERFQKLLHELGLKQPPNRTARNEADALALAQEIGYPLVVRPSYVL 714

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIV+ ++DL RY + AV VSND+PVLLD FL+DA EVDVDA+ DG+ V+IGG+ME
Sbjct: 715  GGRAMEIVHQQSDLERYMREAVKVSNDSPVLLDRFLNDACEVDVDALSDGDEVIIGGVME 774

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDSACSLP Y+L++E+ D +R+Q + +A  L V GLMNVQFA++N+ VY++
Sbjct: 775  HIEQAGVHSGDSACSLPPYSLTKEVTDELRRQTKLMAKALNVCGLMNVQFAIQNDTVYVL 834

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRA+RTVPFVSKATG+ LAK+AAR MAG+SL  QG+TKEVIPPY+SVKE V PF KF
Sbjct: 835  EVNPRASRTVPFVSKATGLQLAKIAARCMAGQSLKSQGITKEVIPPYFSVKEAVFPFVKF 894

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVD +LGPEM+STGEVMGVG TFAEAF K+QL +   +   G+  LSV++ DK + VD+
Sbjct: 895  PGVDTILGPEMKSTGEVMGVGTTFAEAFVKSQLAAGVKLPTGGKVFLSVKDSDKTKAVDV 954

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            A  L   GF + AT GT   +  AGI   +VNKV EGRPHI D IKN E   IINT   +
Sbjct: 955  ARDLHAAGFTILATRGTGAAMEAAGIPVTVVNKVTEGRPHIVDMIKNNEIALIINTVDEK 1014

Query: 1021 R-AIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQI 1072
            R AI DSR IR S L  +V   TT+ G  A A  +       V  +Q +HAQI
Sbjct: 1015 RQAINDSRSIRTSGLAARVTMYTTIWGAEAAAAGIRQGGELVVYPIQALHAQI 1067


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: 3039
Number of extensions: 109
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: 1068
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1023
Effective search space:  1051644
Effective search space used:  1051644
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 Dsui_3064 Dsui_3064 (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.25191.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 1562.8   0.0          0 1562.6   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_3064  Dsui_3064 carbamoyl-phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3064  Dsui_3064 carbamoyl-phosphate synthase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1562.6   0.0         0         0       1    1048 [.       2    1045 ..       2    1049 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1562.6 bits;  conditional E-value: 0
                         TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveavek 75  
                                        pkr+dik++l+iG+Gpi+igqA+EFDYsG+qa+kalk eg++v+Lvnsn+At+mtd+e ad +YieP+ +++vek
  lcl|FitnessBrowser__PS:Dsui_3064    2 PKRTDIKSILIIGAGPIIIGQACEFDYSGAQACKALKAEGYRVILVNSNPATIMTDPETADVTYIEPISWKVVEK 76  
                                        689************************************************************************ PP

                         TIGR01369   76 iiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseives 150 
                                        iiekErpDa+l+t+GGqtaLn+a++l ++GvLek+gv+l+G++ eai+kaedRekFk+a+++i++  a+s++++s
  lcl|FitnessBrowser__PS:Dsui_3064   77 IIEKERPDALLPTMGGQTALNCALDLAKHGVLEKFGVELIGASEEAIDKAEDREKFKAAMTKIGLGSARSAVAHS 151 
                                        *************************************************************************** PP

                         TIGR01369  151 veealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskd 225 
                                        +eeal++++ ig+P i+R++ftlgG+G+gia+n+ee+ +++e++l+asp+k++l+e+sl gwkE+E+EvvRDskd
  lcl|FitnessBrowser__PS:Dsui_3064  152 MEEALQVQAMIGFPAIIRPSFTLGGSGGGIAYNKEEFVTICERGLEASPTKELLIEESLIGWKEYEMEVVRDSKD 226 
                                        *************************************************************************** PP

                         TIGR01369  226 nciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvn 299 
                                        ncii+c+iEnlDp+GvHtGdsi+vaP+qtLtdkeyq++R+as++++re+gv+++ +nvqfa++P++ r++viE+n
  lcl|FitnessBrowser__PS:Dsui_3064  227 NCIIICSIENLDPMGVHTGDSITVAPAQTLTDKEYQIMRNASIAVLREIGVDTGgSNVQFAISPKDGRMIVIEMN 301 
                                        ***************************************************9988******************** PP

                         TIGR01369  300 pRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgt 373 
                                        pRvsRssALAskAtG+PiAkvaaklavGy+Ldel n++t+ +t+AsfEPs+DYvv+k+Pr++++kf ++d +l+t
  lcl|FitnessBrowser__PS:Dsui_3064  302 PRVSRSSALASKATGFPIAKVAAKLAVGYTLDELANEITGgKTPASFEPSIDYVVTKVPRFAFEKFPTADFHLTT 376 
                                        ***************************************879********************************* PP

                         TIGR01369  374 qmksvGEvmaigrtfeealqkalrsleekllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevy 448 
                                        qmksvGEvmaigrt++e+lqkalr le ++ g+++k   ++++e +e++l +p ++R++++ +a+r g++++e++
  lcl|FitnessBrowser__PS:Dsui_3064  377 QMKSVGEVMAIGRTLQESLQKALRGLEVGVDGFDEK---TTDREVIETELAEPGPERIWYVGDAFRIGMTLDEIH 448 
                                        ********************************9987...677777889*************************** PP

                         TIGR01369  449 eltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkr 523 
                                        +lt+id +fl ++++l   +k+l+  +++ l++e+l  +kk Gfsd+++akl+ +++++vr+ r++l++ pv+kr
  lcl|FitnessBrowser__PS:Dsui_3064  449 RLTHIDPWFLAQIEDLHLKAKSLAGRSVDSLSREELLVLKKCGFSDKRLAKLLATTQTAVRERRHALNVRPVFKR 523 
                                        *************************************************************************** PP

                         TIGR01369  524 vDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynP 598 
                                        vDt+aaEf ++t+Y+Ystye+e  +++ ++kkk++vlG+Gp+Rigqg+EFDyc+vha++a+re gy+ti++n+nP
  lcl|FitnessBrowser__PS:Dsui_3064  524 VDTCAAEFATNTAYMYSTYEDE-CEAQPSDKKKIMVLGGGPNRIGQGIEFDYCCVHAAMAMREDGYETIMVNCNP 597 
                                        **********************.667777888******************************************* PP

                         TIGR01369  599 EtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekF 673 
                                        EtvstDyd++drLyFe+lt+edvl++++ ek+ gvivq+gGqt+l+la++le++gv+i+Gts++ id aEdRe+F
  lcl|FitnessBrowser__PS:Dsui_3064  598 ETVSTDYDTSDRLYFEPLTLEDVLEVVNVEKPVGVIVQYGGQTPLKLARDLEANGVPIIGTSPDMIDAAEDRERF 672 
                                        *************************************************************************** PP

                         TIGR01369  674 sklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlid 748 
                                        +kll+elg+kqp +++a++  +a  +a+eigyP++vRpsyvlgGrameiv+++ +lery++eav+vs+++Pvl+d
  lcl|FitnessBrowser__PS:Dsui_3064  673 QKLLHELGLKQPPNRTARNEADALALAQEIGYPLVVRPSYVLGGRAMEIVHQQSDLERYMREAVKVSNDSPVLLD 747 
                                        *************************************************************************** PP

                         TIGR01369  749 kyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllni 823 
                                        ++l+da EvdvDa++dg+ev+i g++eHiE+aGvHsGDs+++lpp +l++ev++++++++k +ak+l+v Gl+n+
  lcl|FitnessBrowser__PS:Dsui_3064  748 RFLNDACEVDVDALSDGDEVIIGGVMEHIEQAGVHSGDSACSLPPYSLTKEVTDELRRQTKLMAKALNVCGLMNV 822 
                                        *************************************************************************** PP

                         TIGR01369  824 qfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfskla 898 
                                        qf++++++vyv+Evn+RasRtvPfvska+g++l+k+a+++++g++l++  +g++ke  + +++vk+avf+f k+ 
  lcl|FitnessBrowser__PS:Dsui_3064  823 QFAIQNDTVYVLEVNPRASRTVPFVSKATGLQLAKIAARCMAGQSLKS--QGITKEVIPPYFSVKEAVFPFVKFP 895 
                                        ***********************************************9..789********************** PP

                         TIGR01369  899 gvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyateg 973 
                                        gvd +lgpemkstGEvmg+g++++ea++k++la++ k+++ g+v+lsvkd+dk++++++a+ l+++g++++at+g
  lcl|FitnessBrowser__PS:Dsui_3064  896 GVDTILGPEMKSTGEVMGVGTTFAEAFVKSQLAAGVKLPTGGKVFLSVKDSDKTKAVDVARDLHAAGFTILATRG 970 
                                        *************************************************************************** PP

                         TIGR01369  974 takvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeal 1048
                                        t +++e agi ++vv+kv+e +++i++++k++ei l+in+ ++k++a +++ +ir + +  +v++ t++ +aea+
  lcl|FitnessBrowser__PS:Dsui_3064  971 TGAAMEAAGIPVTVVNKVTEGRPHIVDMIKNNEIALIINTVDEKRQAINDSRSIRTSGLAARVTMYTTIWGAEAA 1045
                                        *******************************************************************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1068 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 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 12.61
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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