Alignments for a candidate for carB in Sulfurivirga caldicuralii DSM 17737

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Sulfurivirga caldicuralii DSM 17737

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_074200863.1 BUQ81_RS02835 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_900141795.1:WP_074200863.1
          Length = 1071

 Score = 1516 bits (3925), Expect = 0.0
 Identities = 757/1071 (70%), Positives = 895/1071 (83%), Gaps = 4/1071 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDI+SILI+GAGPI+IGQACEFDYSG QA KAL+EEGYRVILVNSNPATIMTDP++
Sbjct: 1    MPKRTDIESILIIGAGPIIIGQACEFDYSGVQAVKALKEEGYRVILVNSNPATIMTDPDL 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI W  + KIIEKERPDA+LPTMGGQTALN AL+L R GVLE++GV +IGA  
Sbjct: 61   ADATYIEPIEWRTIEKIIEKERPDAILPTMGGQTALNTALDLARHGVLEKYGVELIGANE 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            DAIDKAE+R RF  AM+KIGL+  +S +AH+MEEA A+  +VGFP IIRPSFT+GGSGGG
Sbjct: 121  DAIDKAENRDRFRAAMQKIGLDMPKSAVAHSMEEAWAILDEVGFPAIIRPSFTLGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNR+EFE+IC  GLDLSPT ELLI+ES+IGWKEYEMEV+RD+NDN IIVCSIEN D M
Sbjct: 181  IAYNRDEFEQICKFGLDLSPTNELLIEESIIGWKEYEMEVIRDRNDNAIIVCSIENLDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQIMRNAS+AVLREIGVETGGSNVQFAVNP+ GR+I+IEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQIMRNASLAVLREIGVETGGSNVQFAVNPETGRMIIIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL NDITGG TPASFEP+IDYVVTKIP
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELKNDITGGATPASFEPTIDYVVTKIP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKV---SLDD 417
            RF FEKF  A  RL+TQMKSVGEVMA+GR  QESLQKA+RGLE G TG +  +   +LD+
Sbjct: 361  RFTFEKFPQAEPRLSTQMKSVGEVMAMGRNFQESLQKAIRGLETGRTGLNEMLDLNTLDE 420

Query: 418  PEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVA 477
             E    +R EL+  G DR+WY+ADAFRAG +++ V +  +ID WFL QI+ELVR+E+++ 
Sbjct: 421  KEVRDTLRAELRHPGPDRLWYVADAFRAGWTLEEVHDACDIDPWFLAQIQELVRMEDELR 480

Query: 478  EVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFA 537
            ++G+ GL+A  LR+ K+KGF+DAR+A+L GV E  IRKLR   D+ PVYKRVDTCAAEFA
Sbjct: 481  QLGLDGLDAGTLRRYKQKGFSDARIAELLGVSEKSIRKLRHMLDIRPVYKRVDTCAAEFA 540

Query: 538  TDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETI 597
            T TAYMYS+Y+EECEA PS +R+KIMVLGGGPNRIGQGIEFDYCCVHA+ AL EDGYETI
Sbjct: 541  TKTAYMYSSYDEECEAEPS-ERKKIMVLGGGPNRIGQGIEFDYCCVHAAFALSEDGYETI 599

Query: 598  MVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAA 657
            MVNCNPETVSTDYDTSDRLYFEP+TLEDVLEIV +EKP GVIVQYGGQTPLKLAR LEAA
Sbjct: 600  MVNCNPETVSTDYDTSDRLYFEPLTLEDVLEIVEVEKPDGVIVQYGGQTPLKLARDLEAA 659

Query: 658  GVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPS 717
            GVP+IGT+P++ID AEDRERFQ  + RL LKQP N T  + E A+  AKEIGYPLVVRPS
Sbjct: 660  GVPIIGTTPESIDLAEDRERFQQLLHRLDLKQPPNRTARSEEEALALAKEIGYPLVVRPS 719

Query: 718  YVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGG 777
            YVLGGRAMEIVY E DL RY + AV VSND+PVLLD FLDDAVEVDVDA+ DGE V+IGG
Sbjct: 720  YVLGGRAMEIVYTEKDLERYMREAVKVSNDSPVLLDRFLDDAVEVDVDAVSDGEQVVIGG 779

Query: 778  IMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEV 837
            IMEHIEQAG+HSGDSACSLP Y++  E+QD +R+QV+K+A  L V GLMN QFA+K +E+
Sbjct: 780  IMEHIEQAGIHSGDSACSLPPYSIRPELQDRIREQVEKMAKALNVVGLMNTQFAIKEDEI 839

Query: 838  YLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPF 897
            +++EVNPRA+RTVPFVSKA G PLAK+AAR M G++LA+Q   +E++P +YSVKE V PF
Sbjct: 840  FVLEVNPRASRTVPFVSKAIGHPLAKIAARCMVGQTLAQQQFEREIVPRHYSVKEAVFPF 899

Query: 898  NKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERV 957
             KF GVDP+LGPEM+STGEVMG+G TF +A+AKA++ + + + + G A LSVR+ D+E+ 
Sbjct: 900  IKFLGVDPILGPEMKSTGEVMGIGETFPQAYAKAEMAAGTVLPRSGTAFLSVRKADREKA 959

Query: 958  VDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTT 1017
             +LA +L+++GF L AT GTA  L EAGI   +VNKV EGRP+I D IKNGE   I+NT+
Sbjct: 960  TELARRLIERGFRLVATRGTAAALKEAGIEVDVVNKVTEGRPNIVDLIKNGEIDLIVNTS 1019

Query: 1018 SGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEM 1068
             G  +I+DS  IRR AL +KV Y TT+ G FA   A++    + V  +Q++
Sbjct: 1020 DGSVSIKDSADIRREALMHKVCYTTTIAGAFAMVAAMDYLDPQPVYRLQDL 1070


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: 3167
Number of extensions: 128
Number of successful extensions: 13
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: 1071
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1026
Effective search space:  1054728
Effective search space used:  1054728
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 WP_074200863.1 BUQ81_RS02835 (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.4175670.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 1577.1   0.0          0 1576.9   0.0    1.0  1  NCBI__GCF_900141795.1:WP_074200863.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900141795.1:WP_074200863.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1576.9   0.0         0         0       1    1051 [.       2    1055 ..       2    1056 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1576.9 bits;  conditional E-value: 0
                             TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71  
                                            pkr+di+++l+iG+Gpi+igqA+EFDYsG qa+kalkeeg++v+Lvnsn+At+mtd++lad++YieP++++
  NCBI__GCF_900141795.1:WP_074200863.1    2 PKRTDIESILIIGAGPIIIGQACEFDYSGVQAVKALKEEGYRVILVNSNPATIMTDPDLADATYIEPIEWR 72  
                                            689******************************************************************** PP

                             TIGR01369   72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142 
                                            ++ekiiekErpDail+t+GGqtaLn a++l ++GvLekygv+l+G++ +ai+kae+R++F++a+++i++++
  NCBI__GCF_900141795.1:WP_074200863.1   73 TIEKIIEKERPDAILPTMGGQTALNTALDLARHGVLEKYGVELIGANEDAIDKAENRDRFRAAMQKIGLDM 143 
                                            *********************************************************************** PP

                             TIGR01369  143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213 
                                            +ks++++s+eea ++ +e+g+P i+R++ftlgG+G+gia+n++e++++++ +l++sp++++l+e+s+ gwk
  NCBI__GCF_900141795.1:WP_074200863.1  144 PKSAVAHSMEEAWAILDEVGFPAIIRPSFTLGGSGGGIAYNRDEFEQICKFGLDLSPTNELLIEESIIGWK 214 
                                            *********************************************************************** PP

                             TIGR01369  214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvq 283 
                                            E+E+Ev+RD++dn+iivc+iEnlDp+GvHtGdsi+vaP+qtLtdkeyq++R+asl+++re+gve++ +nvq
  NCBI__GCF_900141795.1:WP_074200863.1  215 EYEMEVIRDRNDNAIIVCSIENLDPMGVHTGDSITVAPAQTLTDKEYQIMRNASLAVLREIGVETGgSNVQ 285 
                                            ****************************************************************988**** PP

                             TIGR01369  284 faldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvv 353 
                                            fa++Pe+ r+++iE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldelknd+t+  t+AsfEP++DYvv
  NCBI__GCF_900141795.1:WP_074200863.1  286 FAVNPETGRMIIIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELKNDITGgATPASFEPTIDYVV 356 
                                            *******************************************************878************* PP

                             TIGR01369  354 vkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllg....lklkek.eaesdeel 419 
                                            +kiPr+ ++kf +++ +l+tqmksvGEvma+gr+f+e+lqka+r le++ +g    l+l++  e+e +++l
  NCBI__GCF_900141795.1:WP_074200863.1  357 TKIPRFTFEKFPQAEPRLSTQMKSVGEVMAMGRNFQESLQKAIRGLETGRTGlnemLDLNTLdEKEVRDTL 427 
                                            ****************************************************4333233333133444567 PP

                             TIGR01369  420 eealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakkl 490 
                                            + +l++p ++Rl+++a+a+r+g ++eev+++++id +fl ++++lv++e el++  l+ l++ +l+++k++
  NCBI__GCF_900141795.1:WP_074200863.1  428 RAELRHPGPDRLWYVADAFRAGWTLEEVHDACDIDPWFLAQIQELVRMEDELRQLGLDGLDAGTLRRYKQK 498 
                                            789******************************************************************** PP

                             TIGR01369  491 GfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlG 561 
                                            Gfsd++ia+l++vse+++rklr+ l+i pv+krvDt+aaEf +kt+Y+Ys+y ee  ++e +e+kk++vlG
  NCBI__GCF_900141795.1:WP_074200863.1  499 GFSDARIAELLGVSEKSIRKLRHMLDIRPVYKRVDTCAAEFATKTAYMYSSYDEE-CEAEPSERKKIMVLG 568 
                                            *******************************************************.667777788****** PP

                             TIGR01369  562 sGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekveg 632 
                                            +Gp+Rigqg+EFDyc+vha+ al+e gy+ti++n+nPEtvstDyd++drLyFe+lt+edvl+i+e ek++g
  NCBI__GCF_900141795.1:WP_074200863.1  569 GGPNRIGQGIEFDYCCVHAAFALSEDGYETIMVNCNPETVSTDYDTSDRLYFEPLTLEDVLEIVEVEKPDG 639 
                                            *********************************************************************** PP

                             TIGR01369  633 vivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakei 703 
                                            vivq+gGqt+l+la++le+agv+i+Gt++esid aEdRe+F++ll++l++kqp +++a+s eea  +akei
  NCBI__GCF_900141795.1:WP_074200863.1  640 VIVQYGGQTPLKLARDLEAAGVPIIGTTPESIDLAEDRERFQQLLHRLDLKQPPNRTARSEEEALALAKEI 710 
                                            *********************************************************************** PP

                             TIGR01369  704 gyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagil 774 
                                            gyP++vRpsyvlgGrameiv+ e++lery++eav+vs+++Pvl+d++l+davEvdvDav+dge+v+i gi+
  NCBI__GCF_900141795.1:WP_074200863.1  711 GYPLVVRPSYVLGGRAMEIVYTEKDLERYMREAVKVSNDSPVLLDRFLDDAVEVDVDAVSDGEQVVIGGIM 781 
                                            *********************************************************************** PP

                             TIGR01369  775 eHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtv 845 
                                            eHiE+aG+HsGDs+++lpp +++ e++++i+e+v+k+ak+l+v+Gl+n qf++k++e+ v+Evn+RasRtv
  NCBI__GCF_900141795.1:WP_074200863.1  782 EHIEQAGIHSGDSACSLPPYSIRPELQDRIREQVEKMAKALNVVGLMNTQFAIKEDEIFVLEVNPRASRTV 852 
                                            *********************************************************************** PP

                             TIGR01369  846 PfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmg 916 
                                            Pfvska+g+pl+k+a+++++g++l++++   ++e  +++++vk+avf+f k+ gvd++lgpemkstGEvmg
  NCBI__GCF_900141795.1:WP_074200863.1  853 PFVSKAIGHPLAKIAARCMVGQTLAQQQ--FEREIVPRHYSVKEAVFPFIKFLGVDPILGPEMKSTGEVMG 921 
                                            **************************55..699999*********************************** PP

                             TIGR01369  917 igrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaev 987 
                                            ig+++ +a++ka +a+++++++ g+++lsv+++d+e+++ela++l e+g++++at+gta++l+eagi+++v
  NCBI__GCF_900141795.1:WP_074200863.1  922 IGETFPQAYAKAEMAAGTVLPRSGTAFLSVRKADREKATELARRLIERGFRLVATRGTAAALKEAGIEVDV 992 
                                            *********************************************************************** PP

                             TIGR01369  988 vlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
                                            v+kv+e +++i++l+k++ei+l++n+++ ++ + +++  irrea+++kv + t++++a a++ a
  NCBI__GCF_900141795.1:WP_074200863.1  993 VNKVTEGRPNIVDLIKNGEIDLIVNTSD-GSVSIKDSADIRREALMHKVCYTTTIAGAFAMVAA 1055
                                            *************************887.77799999********************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1071 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 26.24
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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