Alignments for a candidate for carB in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Marinobacter adhaerens HP15

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate GFF3135 HP15_3077 carbamoyl-phosphate synthase, large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Marino:GFF3135
          Length = 1072

 Score = 1574 bits (4076), Expect = 0.0
 Identities = 804/1071 (75%), Positives = 900/1071 (84%), Gaps = 2/1071 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDI+SILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP M
Sbjct: 1    MPKRTDIQSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPVM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI W+ V KIIEKE+PDA+LPTMGGQTALNCAL+LER G+LE+ GV MIGA A
Sbjct: 61   ADATYIEPITWKTVEKIIEKEQPDALLPTMGGQTALNCALDLERHGILEKHGVEMIGANA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            D IDKAEDR RFD AMKKIGLE  R+ IAH+MEEA  VA D+GFPCIIRPSFTMGGSGGG
Sbjct: 121  DTIDKAEDRDRFDKAMKKIGLECPRATIAHSMEEAWKVADDIGFPCIIRPSFTMGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNR+EFEEIC RGLDLSPT ELLIDESLIGWKEYEMEVVRDKNDNCIIVC+IENFDAM
Sbjct: 181  IAYNRDEFEEICTRGLDLSPTNELLIDESLIGWKEYEMEVVRDKNDNCIIVCAIENFDAM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQIMRNAS+AVLREIGVETGGSNVQF +NP  GR++VIEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQIMRNASLAVLREIGVETGGSNVQFGMNPDTGRMVVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL N+ITGG TPASFEPSIDYVVTKIP
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELRNEITGGVTPASFEPSIDYVVTKIP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKV-SLDDPE 419
            RF FEKF  A+ RLTTQMKSVGEVMAIGRT QESLQKALRGLEVG+ GFD K+  LD   
Sbjct: 361  RFTFEKFPQADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGSEGFDEKLEDLDSEN 420

Query: 420  ALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEV 479
            +   + REL   GADRIWYI DAFRAG++V+ +   T++D W+LVQIE+L+R E+ +   
Sbjct: 421  SRETLTRELNVPGADRIWYIGDAFRAGMTVEDLHEHTHVDPWYLVQIEDLIREEQALKSA 480

Query: 480  GITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATD 539
            G   ++   L +LKRKGF+DARLAKL G+ E  +RKLR   D+ PVYKRVDTCAAEFA+D
Sbjct: 481  GKADIDQATLFRLKRKGFSDARLAKLLGISEVSLRKLRHDLDIRPVYKRVDTCAAEFASD 540

Query: 540  TAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMV 599
            TAYMYSTYEEECE++ S DREKI+V+GGGPNRIGQGIEFDYCCVHA+LA+REDGYETIM+
Sbjct: 541  TAYMYSTYEEECESDAS-DREKIVVIGGGPNRIGQGIEFDYCCVHAALAMREDGYETIMI 599

Query: 600  NCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGV 659
            NCNPETVSTDYDTSDRLYFEP+TLEDVLEI+ +EKPKGVIVQYGGQTPLKLAR LEAAGV
Sbjct: 600  NCNPETVSTDYDTSDRLYFEPITLEDVLEIIHVEKPKGVIVQYGGQTPLKLARGLEAAGV 659

Query: 660  PVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYV 719
            P+IGTSPDAIDRAEDRERFQ  + RL LKQP NATV + E  +  A+EIGYPLVVRPSYV
Sbjct: 660  PIIGTSPDAIDRAEDRERFQQMITRLGLKQPENATVRSHEEGILAAREIGYPLVVRPSYV 719

Query: 720  LGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIM 779
            LGGRAMEIVYDE +L RY + AV VSND+PVLLDHFL+ A+EVD+DAI DG+ V+IGGIM
Sbjct: 720  LGGRAMEIVYDEEELVRYMRNAVLVSNDSPVLLDHFLNAAIEVDIDAISDGKDVVIGGIM 779

Query: 780  EHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYL 839
            +HIEQAGVHSGDSACSLP YTLSQ++QD MR  V+K+A EL V GLMNVQ A ++ E+Y+
Sbjct: 780  QHIEQAGVHSGDSACSLPPYTLSQQVQDEMRDAVKKMAIELDVVGLMNVQLAWQDGEIYV 839

Query: 840  IEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNK 899
            IEVNPRA+RTVPFVSKA GV LAKVAARVMAGK+L E   T+E+IP YY+VKE V PFNK
Sbjct: 840  IEVNPRASRTVPFVSKAIGVSLAKVAARVMAGKTLKELEFTQEIIPSYYAVKESVFPFNK 899

Query: 900  FPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVD 959
            FP VDP+LGPEM+STGEVMG+G +F EAFAKA L     +   G A +SVR+ DK     
Sbjct: 900  FPAVDPILGPEMKSTGEVMGLGDSFDEAFAKAALAVGERLPAKGTAFMSVRDVDKPGAAK 959

Query: 960  LAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSG 1019
            +A  L+  GF+L AT GTA  L EAGI    VNKV EGRPHI D IKNG+   IINTT G
Sbjct: 960  VARDLVDAGFKLVATTGTAKALKEAGIEVDRVNKVREGRPHIVDAIKNGQVQLIINTTEG 1019

Query: 1020 RRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHA 1070
            R+AI DS  IR+SALQ KV Y TTL GG A   A+       V  +Q++HA
Sbjct: 1020 RKAISDSAQIRQSALQTKVTYTTTLAGGEAFCRAIKFGPERTVRRLQDLHA 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: 3265
Number of extensions: 140
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: 1072
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1027
Effective search space:  1055756
Effective search space used:  1055756
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 GFF3135 HP15_3077 (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.20854.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 1585.6   0.0          0 1585.4   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3135  HP15_3077 carbamoyl-phosphate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3135  HP15_3077 carbamoyl-phosphate synthase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1585.4   0.0         0         0       1    1052 []       2    1054 ..       2    1054 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1585.4 bits;  conditional E-value: 0
                           TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveav 73  
                                          pkr+di+++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+ +ad++YieP+t+++v
  lcl|FitnessBrowser__Marino:GFF3135    2 PKRTDIQSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPVMADATYIEPITWKTV 74  
                                          689********************************************************************** PP

                           TIGR01369   74 ekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakse 146 
                                          ekiiekE+pDa+l+t+GGqtaLn+a++le++G+Lek+gv+++G++ ++i+kaedR++F++a+k+i++e ++++
  lcl|FitnessBrowser__Marino:GFF3135   75 EKIIEKEQPDALLPTMGGQTALNCALDLERHGILEKHGVEMIGANADTIDKAEDRDRFDKAMKKIGLECPRAT 147 
                                          ************************************************************************* PP

                           TIGR01369  147 ivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEv 219 
                                          i++s+eea ++a++ig+P+i+R++ft+gG+G+gia+n++e++e++ ++l++sp++++l+++sl gwkE+E+Ev
  lcl|FitnessBrowser__Marino:GFF3135  148 IAHSMEEAWKVADDIGFPCIIRPSFTMGGSGGGIAYNRDEFEEICTRGLDLSPTNELLIDESLIGWKEYEMEV 220 
                                          ************************************************************************* PP

                           TIGR01369  220 vRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPesk 291 
                                          vRD++dnciivc+iEn+D++GvHtGdsi+vaP+qtLtdkeyq++R+asl+++re+gve++ +nvqf+++P++ 
  lcl|FitnessBrowser__Marino:GFF3135  221 VRDKNDNCIIVCAIENFDAMGVHTGDSITVAPAQTLTDKEYQIMRNASLAVLREIGVETGgSNVQFGMNPDTG 293 
                                          **********************************************************988************ PP

                           TIGR01369  292 ryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldk 363 
                                          r+vviE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldel+n++t+  t+AsfEPs+DYvv+kiPr+ ++k
  lcl|FitnessBrowser__Marino:GFF3135  294 RMVVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELRNEITGgVTPASFEPSIDYVVTKIPRFTFEK 366 
                                          ***********************************************868*********************** PP

                           TIGR01369  364 fekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkek...eaesdeeleealkkpndrRlfa 433 
                                          f ++d +l+tqmksvGEvmaigrtf+e+lqkalr le +  g+++k +   +++s+e+l+++l+ p ++R+++
  lcl|FitnessBrowser__Marino:GFF3135  367 FPQADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGSEGFDEKLEdldSENSRETLTRELNVPGADRIWY 439 
                                          ******************************************8876441114556678899************ PP

                           TIGR01369  434 iaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvsea 506 
                                          i +a+r+g++ve+++e t++d ++l ++++l++ e++l++  + ++++ +l ++k++Gfsd+++akl++ se 
  lcl|FitnessBrowser__Marino:GFF3135  440 IGDAFRAGMTVEDLHEHTHVDPWYLVQIEDLIREEQALKSAGKADIDQATLFRLKRKGFSDARLAKLLGISEV 512 
                                          ************************************************************************* PP

                           TIGR01369  507 evrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavh 579 
                                          ++rklr++l+i pv+krvDt+aaEf ++t+Y+Ystyeee  +++ ++++k++v+G+Gp+Rigqg+EFDyc+vh
  lcl|FitnessBrowser__Marino:GFF3135  513 SLRKLRHDLDIRPVYKRVDTCAAEFASDTAYMYSTYEEE-CESDASDREKIVVIGGGPNRIGQGIEFDYCCVH 584 
                                          ***************************************.677888888************************ PP

                           TIGR01369  580 avlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleea 652 
                                          a+la+re gy+ti+in+nPEtvstDyd++drLyFe++t+edvl+ii+ ek++gvivq+gGqt+l+la+ le+a
  lcl|FitnessBrowser__Marino:GFF3135  585 AALAMREDGYETIMINCNPETVSTDYDTSDRLYFEPITLEDVLEIIHVEKPKGVIVQYGGQTPLKLARGLEAA 657 
                                          ************************************************************************* PP

                           TIGR01369  653 gvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiven 725 
                                          gv+i+Gts+++idraEdRe+F++++ +lg+kqp++++++s ee   +a+eigyP++vRpsyvlgGrameiv++
  lcl|FitnessBrowser__Marino:GFF3135  658 GVPIIGTSPDAIDRAEDRERFQQMITRLGLKQPENATVRSHEEGILAAREIGYPLVVRPSYVLGGRAMEIVYD 730 
                                          ************************************************************************* PP

                           TIGR01369  726 eeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklse 798 
                                          eeel ry+++av vs+++Pvl+d++l+ a+Evd+Da++dg++v+i gi++HiE+aGvHsGDs+++lpp +ls+
  lcl|FitnessBrowser__Marino:GFF3135  731 EEELVRYMRNAVLVSNDSPVLLDHFLNAAIEVDIDAISDGKDVVIGGIMQHIEQAGVHSGDSACSLPPYTLSQ 803 
                                          ************************************************************************* PP

                           TIGR01369  799 evkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkklee 871 
                                          +v+++++++vkk+a el+v+Gl+n+q++ +d+e+yviEvn+RasRtvPfvska+gv+l+k+a++v++gk+l+e
  lcl|FitnessBrowser__Marino:GFF3135  804 QVQDEMRDAVKKMAIELDVVGLMNVQLAWQDGEIYVIEVNPRASRTVPFVSKAIGVSLAKVAARVMAGKTLKE 876 
                                          ************************************************************************* PP

                           TIGR01369  872 lekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvll 944 
                                          le   ++e  ++++avk++vf+f+k+  vd++lgpemkstGEvmg+g++++ea++ka la++++++ kg++++
  lcl|FitnessBrowser__Marino:GFF3135  877 LEF--TQEIIPSYYAVKESVFPFNKFPAVDPILGPEMKSTGEVMGLGDSFDEAFAKAALAVGERLPAKGTAFM 947 
                                          775..89999*************************************************************** PP

                           TIGR01369  945 svkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskk 1017
                                          sv+d dk  + ++a+ l+++g+k++at+gtak+l+eagi+++ v+kv+e +++i++++k+++++l+in+t+ +
  lcl|FitnessBrowser__Marino:GFF3135  948 SVRDVDKPGAAKVARDLVDAGFKLVATTGTAKALKEAGIEVDRVNKVREGRPHIVDAIKNGQVQLIINTTE-G 1019
                                          ********************************************************************997.7 PP

                           TIGR01369 1018 kkaaekgykirreaveykvplvteletaealleal 1052
                                          +ka +++ +ir++a+++kv++ t+l++ ea+++a+
  lcl|FitnessBrowser__Marino:GFF3135 1020 RKAISDSAQIRQSALQTKVTYTTTLAGGEAFCRAI 1054
                                          7799999************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1072 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: 12.05
//
[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