Alignments for a candidate for carB in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Klebsiella michiganensis M5al

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate BWI76_RS04470 BWI76_RS04470 carbamoyl phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Koxy:BWI76_RS04470
          Length = 1074

 Score = 2053 bits (5318), Expect = 0.0
 Identities = 1042/1073 (97%), Positives = 1061/1073 (98%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVL EFGVTMIGATA
Sbjct: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLAEFGVTMIGATA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            DAIDKAEDRRRFDVAMKKIGL+TARSGIAHTMEEALAVAADVGFPCIIRPSFTMGG+GGG
Sbjct: 121  DAIDKAEDRRRFDVAMKKIGLDTARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGTGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNREEFEEIC RGLDLSPT ELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM
Sbjct: 181  IAYNREEFEEICERGLDLSPTNELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQF+VNPK+GRLIVIEM
Sbjct: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFSVNPKDGRLIVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RFNFEKF GANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA
Sbjct: 361  RFNFEKFVGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            LTKIRRELKDAGA+RIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG
Sbjct: 421  LTKIRRELKDAGAERIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            ITGL+ADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT
Sbjct: 481  ITGLDADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AYMYSTYE+ECEANPS DR+KIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN
Sbjct: 541  AYMYSTYEDECEANPSVDRDKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP
Sbjct: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            VIGTSPDAIDRAEDRERFQHAV+RLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL
Sbjct: 661  VIGTSPDAIDRAEDRERFQHAVDRLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVYDE DLRRYFQTAVSVSNDAPVLLD FLDDAVEVDVDAICDGEMVLIGGIME
Sbjct: 721  GGRAMEIVYDEIDLRRYFQTAVSVSNDAPVLLDRFLDDAVEVDVDAICDGEMVLIGGIME 780

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDSACSLPAYTLSQEIQDVMR+QVQKLAFELQVRGLMNVQFAVKNNEVYLI
Sbjct: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMREQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRAARTVPFVSKATGVPLAKVAARVM G++LA+QGVTKE+IPPYYSVKEVVLPFNKF
Sbjct: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMVGQTLAQQGVTKEIIPPYYSVKEVVLPFNKF 900

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKK GRALLSVREGDKERVVDL
Sbjct: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKQGRALLSVREGDKERVVDL 960

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            AAKLLK GFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTT+GR
Sbjct: 961  AAKLLKFGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTAGR 1020

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
            +AIEDS++IRRSALQYKVHYDTTLNGGFATAMALNA+A EKV SVQEMHAQIK
Sbjct: 1021 QAIEDSKLIRRSALQYKVHYDTTLNGGFATAMALNANAMEKVTSVQEMHAQIK 1073


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: 3520
Number of extensions: 137
Number of successful extensions: 11
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: 1074
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1029
Effective search space:  1057812
Effective search space used:  1057812
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 BWI76_RS04470 BWI76_RS04470 (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.3727.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 1615.7   0.0          0 1615.5   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04470  BWI76_RS04470 carbamoyl phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04470  BWI76_RS04470 carbamoyl phosphate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1615.5   0.0         0         0       1    1051 [.       2    1053 ..       2    1054 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1615.5 bits;  conditional E-value: 0
                               TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePlt 69  
                                              pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+e+ad++YieP++
  lcl|FitnessBrowser__Koxy:BWI76_RS04470    2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADATYIEPIH 70  
                                              689****************************************************************** PP

                               TIGR01369   70 veavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkei 138 
                                              +e+v+kiiekErpDa+l+t+GGqtaLn+a+ele++GvL+++gv+++G++ +ai+kaedR++F+ a+k+i
  lcl|FitnessBrowser__Koxy:BWI76_RS04470   71 WEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLAEFGVTMIGATADAIDKAEDRRRFDVAMKKI 139 
                                              ********************************************************************* PP

                               TIGR01369  139 neevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvek 207 
                                              ++++a+s i++++eeal++a+++g+P+i+R++ft+gGtG+gia+n+ee++e++e++l++sp++++l+++
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  140 GLDTARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGTGGGIAYNREEFEEICERGLDLSPTNELLIDE 208 
                                              ********************************************************************* PP

                               TIGR01369  208 slagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgv 276 
                                              sl gwkE+E+EvvRD++dnciivc+iEn+D++G+HtGdsi+vaP+qtLtdkeyq++R+as++++re+gv
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  209 SLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGV 277 
                                              ********************************************************************* PP

                               TIGR01369  277 ege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvA 343 
                                              e++ +nvqf+++P++ r++viE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldel+nd+t+ +t+A
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  278 ETGgSNVQFSVNPKDGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGgRTPA 346 
                                              *988***********************************************************879*** PP

                               TIGR01369  344 sfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklk..e 410 
                                              sfEPs+DYvv+kiPr++++kf +++++l+tqmksvGEvmaigrt +e+lqkalr le +++g++ k   
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  347 SFEPSIDYVVTKIPRFNFEKFVGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKvsL 415 
                                              **************************************************************7655105 PP

                               TIGR01369  411 keaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkel 479 
                                              +  e+ ++++++lk++ ++R+++ia+a+r+g+sv+ v++lt+idr+fl ++++lv+le++++e+ ++ l
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  416 DDPEALTKIRRELKDAGAERIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGL 484 
                                              5677889999*********************************************************** PP

                               TIGR01369  480 kkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekdd 548 
                                              +++ l+++k++Gf+d+++akl++v+eae+rklr++++++pv+krvDt+aaEf ++t+Y+Ystye+e++ 
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  485 DADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEDECEA 553 
                                              ********************************************************************* PP

                               TIGR01369  549 vevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeelt 617 
                                              +++ +++k++vlG+Gp+Rigqg+EFDyc+vha+lalre gy+ti++n+nPEtvstDyd++drLyFe++t
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  554 NPSVDRDKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVT 622 
                                              ********************************************************************* PP

                               TIGR01369  618 vedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpk 686 
                                              +edvl+i++ ek++gvivq+gGqt+l+la++le+agv+++Gts+++idraEdRe+F++++d+l++kqp+
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  623 LEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVDRLKLKQPA 691 
                                              ********************************************************************* PP

                               TIGR01369  687 gkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledav 755 
                                              ++++t++e+a+e+akeigyP++vRpsyvlgGrameiv++e +l+ry+++av+vs+++Pvl+d++l+dav
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  692 NATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEIDLRRYFQTAVSVSNDAPVLLDRFLDDAV 760 
                                              ********************************************************************* PP

                               TIGR01369  756 EvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniq 824 
                                              EvdvDa++dge+vli gi+eHiE+aGvHsGDs+++lp+ +ls+e+++ ++e+v+k+a el+v+Gl+n+q
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  761 EVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMREQVQKLAFELQVRGLMNVQ 829 
                                              ********************************************************************* PP

                               TIGR01369  825 fvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfs 893 
                                              f+vk++evy+iEvn+Ra+RtvPfvska+gvpl+k+a++v++g++l++  +gv+ke  + +++vk++v++
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  830 FAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMVGQTLAQ--QGVTKEIIPPYYSVKEVVLP 896 
                                              **********************************************9..889***************** PP

                               TIGR01369  894 fsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakkla 962 
                                              f+k+ gvd++lgpem+stGEvmg+gr+++ea++ka+l s++++kk+g++llsv++ dke++++la+kl 
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  897 FNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKQGRALLSVREGDKERVVDLAAKLL 965 
                                              ********************************************************************* PP

                               TIGR01369  963 ekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirrea 1031
                                              ++g+++ at+gta vl eagi+ ++v+kv+e +++i++ +k++e++++in+t+ +++a e+++ irr+a
  lcl|FitnessBrowser__Koxy:BWI76_RS04470  966 KFGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTA-GRQAIEDSKLIRRSA 1033
                                              **************************************************997.88899999******* PP

                               TIGR01369 1032 veykvplvteletaeallea 1051
                                              ++ykv++ t+l++  a+++a
  lcl|FitnessBrowser__Koxy:BWI76_RS04470 1034 LQYKVHYDTTLNGGFATAMA 1053
                                              ***********998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1074 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: 13.48
//
[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