Alignments for a candidate for carB in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Burkholderia phytofirmans PsJN

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate BPHYT_RS14190 BPHYT_RS14190 carbamoyl phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__BFirm:BPHYT_RS14190
          Length = 1084

 Score = 1460 bits (3780), Expect = 0.0
 Identities = 747/1089 (68%), Positives = 876/1089 (80%), Gaps = 23/1089 (2%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILI+GAGPI+IGQACEFDYSGAQACKALREEGY+VILVNSNPATIMTDP  
Sbjct: 1    MPKRTDIKSILIIGAGPIIIGQACEFDYSGAQACKALREEGYKVILVNSNPATIMTDPNT 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            AD TYIEPI WEVV +II KERPDA+LPTMGGQTALNCAL+L   GVLE++ V +IGA+ 
Sbjct: 61   ADVTYIEPITWEVVERIIAKERPDAILPTMGGQTALNCALDLHAHGVLEKYKVELIGASP 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADV-------GFPCIIRPSFT 173
            +AIDKAEDR++F  AM KIGL +A+SG AH+MEEALAV AD+       G+P +IRPSFT
Sbjct: 121  EAIDKAEDRQKFKDAMTKIGLGSAKSGTAHSMEEALAVQADIASQTGSGGYPVVIRPSFT 180

Query: 174  MGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCS 233
            +GGSGGGIAYNR+EFEEIC RGLDLSPT+ELLI+ESL+GWKEYEMEVVRDK DNCIIVCS
Sbjct: 181  LGGSGGGIAYNRDEFEEICKRGLDLSPTRELLIEESLLGWKEYEMEVVRDKKDNCIIVCS 240

Query: 234  IENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNG 293
            IEN D MGIHTGDSITVAPAQTLTDKEYQI+RNAS+AVLREIGV+TGGSNVQF++NPK+G
Sbjct: 241  IENLDPMGIHTGDSITVAPAQTLTDKEYQILRNASLAVLREIGVDTGGSNVQFSINPKDG 300

Query: 294  RLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSID 353
            R++VIEMNPRVSRSSALASKATGFPIAK+AAKLAVGY+LDEL N+ITGG+TPASFEP+ID
Sbjct: 301  RMVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYSLDELKNEITGGQTPASFEPTID 360

Query: 354  YVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKV 413
            YVVTKIPRF FEKF  A+ RLTTQMKSVGEVMAIGRT QES QKALRGLEVG  G D K 
Sbjct: 361  YVVTKIPRFAFEKFREADSRLTTQMKSVGEVMAIGRTFQESFQKALRGLEVGVDGLDEKT 420

Query: 414  SLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLE 473
               D     +I RE+ +AG DRIWY+ DAFR G++ + +F  T+ID WFL QIE+++  E
Sbjct: 421  DNRD-----EIIREIGEAGPDRIWYVGDAFRVGMTAEEIFEETSIDPWFLAQIEQIILKE 475

Query: 474  EKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCA 533
            + +A   +  L+ + L+ LK+ GF+D RLAKL G + AE+R+ R + ++ PVYKRVDTCA
Sbjct: 476  KALAGRTLASLSKEELKYLKQSGFSDRRLAKLLGAKPAEVRQRRIELNVRPVYKRVDTCA 535

Query: 534  AEFATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDG 593
            AEFAT TAYMYSTYEEECEANP T  +KIMVLGGGPNRIGQGIEFDYCCVHA+LA+REDG
Sbjct: 536  AEFATKTAYMYSTYEEECEANP-TSNKKIMVLGGGPNRIGQGIEFDYCCVHAALAMREDG 594

Query: 594  YETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARA 653
            YETIMVNCNPETVSTDYDTSDRLYFE +TLEDVLEIV  EKP GVIVQYGGQTPLKLA  
Sbjct: 595  YETIMVNCNPETVSTDYDTSDRLYFESLTLEDVLEIVDKEKPVGVIVQYGGQTPLKLALD 654

Query: 654  LEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLV 713
            LEA GVP++GTSPD ID AEDRERFQ  ++ L L+QP N T  A + A++ A EIGYPLV
Sbjct: 655  LEANGVPIVGTSPDMIDAAEDRERFQKLLQDLGLRQPPNRTARAEDEALKLADEIGYPLV 714

Query: 714  VRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMV 773
            VRPSYVLGGRAMEIV++  DL RY + AV VSND+PVLLD FL+DA+E DVD I DGE V
Sbjct: 715  VRPSYVLGGRAMEIVHEPRDLERYMREAVKVSNDSPVLLDRFLNDAIECDVDCISDGEAV 774

Query: 774  LIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAV- 832
             IGG+MEHIEQAGVHSGDSACSLP Y+LS+E    +++Q   +A  L V GLMNVQFA+ 
Sbjct: 775  FIGGVMEHIEQAGVHSGDSACSLPPYSLSKETVAELKRQTGAMAKALNVIGLMNVQFAIQ 834

Query: 833  --------KNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVI 884
                    K + +Y++EVNPRA+RTVP+VSKAT +PLAK+AAR M G+ LA+QGVTKE+ 
Sbjct: 835  QVPQADGSKEDVIYVLEVNPRASRTVPYVSKATSLPLAKIAARAMVGQKLADQGVTKEID 894

Query: 885  PPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGR 944
            PPY+SVKE V PF KFP VDP+LGPEMRSTGEVMGVG+TF EA  K+QL + S + + G 
Sbjct: 895  PPYFSVKEAVFPFVKFPAVDPVLGPEMRSTGEVMGVGQTFGEALFKSQLAAGSRLPESGT 954

Query: 945  ALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDR 1004
             LL+V + DK + V++A  L + G+ + AT GTA  +  AG+  ++VNKV +GRPHI D 
Sbjct: 955  VLLTVMDADKPKAVEVARMLHELGYPIVATKGTAAAIEAAGVPVKVVNKVKDGRPHIVDM 1014

Query: 1005 IKNGEYTYIINTT-SGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVI 1063
            IKNGE   +  T    R AI DSR IR SA   KV Y TT++G  A    L      +V 
Sbjct: 1015 IKNGEIALVFTTVDETRAAIADSRSIRMSAQANKVTYYTTMSGARAAVEGLRYLKDLEVY 1074

Query: 1064 SVQEMHAQI 1072
             +Q +HA++
Sbjct: 1075 DLQGLHARL 1083


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: 3146
Number of extensions: 132
Number of successful extensions: 18
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: 1084
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1038
Effective search space:  1066026
Effective search space used:  1066026
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 BPHYT_RS14190 BPHYT_RS14190 (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.31299.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 1539.5   0.0          0 1539.3   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  BPHYT_RS14190 carbamoyl phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS14190  BPHYT_RS14190 carbamoyl phosphate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1539.3   0.0         0         0       1    1050 [.       2    1063 ..       2    1065 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1539.3 bits;  conditional E-value: 0
                                TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePl 68  
                                               pkr+dik++l+iG+Gpi+igqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd++ ad +YieP+
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190    2 PKRTDIKSILIIGAGPIIIGQACEFDYSGAQACKALREEGYKVILVNSNPATIMTDPNTADVTYIEPI 69  
                                               689***************************************************************** PP

                                TIGR01369   69 tveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealk 136 
                                               t+e+ve+ii kErpDail+t+GGqtaLn+a++l+ +GvLeky v+l+G++ eai+kaedR+kFk+a++
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190   70 TWEVVERIIAKERPDAILPTMGGQTALNCALDLHAHGVLEKYKVELIGASPEAIDKAEDRQKFKDAMT 137 
                                               ******************************************************************** PP

                                TIGR01369  137 eineevakseivesveealeaaeei.......gyPvivRaaftlgGtGsgiaeneeelkelvekalka 197 
                                               +i++  aks +++s+eeal+++++i       gyPv++R++ftlgG+G+gia+n++e++e+++++l++
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  138 KIGLGSAKSGTAHSMEEALAVQADIasqtgsgGYPVVIRPSFTLGGSGGGIAYNRDEFEEICKRGLDL 205 
                                               *******************99887766666668*********************************** PP

                                TIGR01369  198 spikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRd 265 
                                               sp++++l+e+sl gwkE+E+EvvRD+kdnciivc+iEnlDp+G+HtGdsi+vaP+qtLtdkeyq+lR+
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  206 SPTRELLIEESLLGWKEYEMEVVRDKKDNCIIVCSIENLDPMGIHTGDSITVAPAQTLTDKEYQILRN 273 
                                               ******************************************************************** PP

                                TIGR01369  266 aslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLde 332 
                                               asl+++re+gv+++ +nvqf+++P++ r+vviE+npRvsRssALAskAtG+PiAk+aaklavGysLde
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  274 ASLAVLREIGVDTGgSNVQFSINPKDGRMVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYSLDE 341 
                                               ***********9988***************************************************** PP

                                TIGR01369  333 lkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsl 399 
                                               lkn++t+ +t+AsfEP++DYvv+kiPr++++kf+++d++l+tqmksvGEvmaigrtf+e++qkalr l
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  342 LKNEITGgQTPASFEPTIDYVVTKIPRFAFEKFREADSRLTTQMKSVGEVMAIGRTFQESFQKALRGL 409 
                                               ******879*********************************************************** PP

                                TIGR01369  400 eekllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvel 467 
                                               e ++ gl++k   + +++e+ +++ ++ ++R++++ +a+r g++ ee++e t id +fl ++++++  
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  410 EVGVDGLDEK---TDNRDEIIREIGEAGPDRIWYVGDAFRVGMTAEEIFEETSIDPWFLAQIEQIILK 474 
                                               **99998886...667778899********************************************** PP

                                TIGR01369  468 ekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeakt 535 
                                               ek+l+  +l  l+ke+lk +k+ Gfsd+++akl++ + aevr+ r el++ pv+krvDt+aaEf +kt
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  475 EKALAGRTLASLSKEELKYLKQSGFSDRRLAKLLGAKPAEVRQRRIELNVRPVYKRVDTCAAEFATKT 542 
                                               ******************************************************************** PP

                                TIGR01369  536 pYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvst 603 
                                               +Y+Ystyeee++ +++++k k++vlG+Gp+Rigqg+EFDyc+vha+la+re gy+ti++n+nPEtvst
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  543 AYMYSTYEEECEANPTSNK-KIMVLGGGPNRIGQGIEFDYCCVHAALAMREDGYETIMVNCNPETVST 609 
                                               **********766666655.************************************************ PP

                                TIGR01369  604 DydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRe 671 
                                               Dyd++drLyFe+lt+edvl+i++kek+ gvivq+gGqt+l+la +le++gv+i+Gts++ id aEdRe
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  610 DYDTSDRLYFESLTLEDVLEIVDKEKPVGVIVQYGGQTPLKLALDLEANGVPIVGTSPDMIDAAEDRE 677 
                                               ******************************************************************** PP

                                TIGR01369  672 kFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavev 739 
                                               +F+kll++lg+ qp +++a++ +ea ++a+eigyP++vRpsyvlgGrameiv++  +lery++eav+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  678 RFQKLLQDLGLRQPPNRTARAEDEALKLADEIGYPLVVRPSYVLGGRAMEIVHEPRDLERYMREAVKV 745 
                                               ******************************************************************** PP

                                TIGR01369  740 skekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikei 807 
                                               s+++Pvl+d++l+da+E+dvD ++dge v+i g++eHiE+aGvHsGDs+++lpp +ls+e++ ++k++
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  746 SNDSPVLLDRFLNDAIECDVDCISDGEAVFIGGVMEHIEQAGVHSGDSACSLPPYSLSKETVAELKRQ 813 
                                               ******************************************************************** PP

                                TIGR01369  808 vkkiakelkvkGllniqfvv.........kdeevyviEvnvRasRtvPfvskalgvplvklavkvllg 866 
                                               + ++ak+l+v Gl+n+qf++         k++ +yv+Evn+RasRtvP+vska+++pl+k+a+++++g
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  814 TGAMAKALNVIGLMNVQFAIqqvpqadgsKEDVIYVLEVNPRASRTVPYVSKATSLPLAKIAARAMVG 881 
                                               ******************9833333222234679********************************** PP

                                TIGR01369  867 kkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaska 934 
                                               +kl++  +gv+ke ++ +++vk+avf+f k+  vd+vlgpem+stGEvmg+g+++ eal+k++la+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  882 QKLAD--QGVTKEIDPPYFSVKEAVFPFVKFPAVDPVLGPEMRSTGEVMGVGQTFGEALFKSQLAAGS 947 
                                               ****9..889********************************************************** PP

                                TIGR01369  935 kikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaekilell 1002
                                               ++++ g+vll+v d+dk +++e+a++l+e+g+ ++at+gta+++e ag+ ++vv+kv++ +++i++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190  948 RLPESGTVLLTVMDADKPKAVEVARMLHELGYPIVATKGTAAAIEAAGVPVKVVNKVKDGRPHIVDMI 1015
                                               ******************************************************************** PP

                                TIGR01369 1003 keeeielvinltskkkkaaekgykirreaveykvplvteletaealle 1050
                                               k++ei lv+++ +++++a  ++ +ir +a  +kv++ t++++a+a++e
  lcl|FitnessBrowser__BFirm:BPHYT_RS14190 1016 KNGEIALVFTTVDETRAAIADSRSIRMSAQANKVTYYTTMSGARAAVE 1063
                                               ******************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1084 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: 0.09u 0.04s 00:00:00.13 Elapsed: 00:00:00.12
# Mc/sec: 9.10
//
[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