Alignments for a candidate for carB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Echinicola vietnamensis KMM 6221, DSM 17526

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate Echvi_0768 Echvi_0768 carbamoyl-phosphate synthase, large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Cola:Echvi_0768
          Length = 939

 Score =  920 bits (2378), Expect = 0.0
 Identities = 487/926 (52%), Positives = 640/926 (69%), Gaps = 19/926 (2%)

Query: 1   MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
           MPK   IK +LI+G+GPIVIGQACEFDYSG+QA ++LREEG  V L+NSNPATIMTDP  
Sbjct: 1   MPKDNSIKHVLIIGSGPIVIGQACEFDYSGSQAARSLREEGITVTLINSNPATIMTDPVT 60

Query: 61  ADATYIEPIHWEVVRKIIEKERPD--AVLPTMGGQTALNCALELERQGVLEEFGVTMIGA 118
           AD  Y+ P+  + + KI+E E PD   VLPTMGGQTALN A+E ++ G+ + F V MIG 
Sbjct: 61  ADNVYLLPLEKKSLVKILE-EHPDIDCVLPTMGGQTALNLAIEADKAGIWDRFKVRMIGV 119

Query: 119 TADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSG 178
             DAI+ AE+R +F   ++++ +       A +  +   +A ++GFP +IRPS+T+GG+G
Sbjct: 120 DIDAIETAENREKFKALLEELNVGVCIGKTATSFLQGKEIAQEIGFPLVIRPSYTLGGTG 179

Query: 179 GGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFD 238
           GG     EEFE     GL  SPT E+LI++S++GWKEYE+EV+RD   N +++CSIENFD
Sbjct: 180 GGFVEKEEEFENALMSGLKASPTHEVLIEQSILGWKEYELEVLRDSLGNMVVICSIENFD 239

Query: 239 AMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVI 298
            MG+HTGDSITVAPA TL D  YQ MRN ++ ++  IG   GG NVQF+V+P N  +I I
Sbjct: 240 PMGVHTGDSITVAPAMTLPDTVYQEMRNLAIKMMNGIGNFAGGCNVQFSVSPDNQTIIGI 299

Query: 299 EMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTK 358
           E+NPRVSRSSALASKATG+PIAKVAAKLA+GY LDEL N ITG  T A FEP+IDYV+ K
Sbjct: 300 EINPRVSRSSALASKATGYPIAKVAAKLAIGYNLDELKNSITGS-TSAFFEPAIDYVIVK 358

Query: 359 IPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGF--DPKVSLD 416
           IPR+NF+KF G++ RL   MK+VGEVM IG   QE+LQKA + LE+   G   D K  L 
Sbjct: 359 IPRWNFDKFKGSDRRLGLSMKAVGEVMGIGGNFQEALQKACQSLEIKRNGLGADGK-ELK 417

Query: 417 DPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKV 476
           + E   +I   L+    +R+++I DAF+ G+S   + +LT ID+WFL QIEELV L+  +
Sbjct: 418 NQE---QILYSLEHPSWNRLFHIYDAFKLGISFRTIHDLTKIDKWFLKQIEELVHLDITL 474

Query: 477 AEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEI-RKLRDQYDLHPVYKRVDTCAAE 535
            +  +  +  D +   K KG+AD ++A L G  E+E+  K RD+  +  VYK VDTCAAE
Sbjct: 475 DKYTLDTIPKDLMMLAKHKGYADRQIAHLLGCLESEVFNKRRDEMGIKRVYKLVDTCAAE 534

Query: 536 FATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYE 595
           F   T Y YS++ EE E+  S DR+K++VLG GPNR+GQGIEFDY CVH  LA +E GYE
Sbjct: 535 FEAQTPYYYSSFGEENESQVS-DRKKVIVLGSGPNRVGQGIEFDYSCVHGVLAAKECGYE 593

Query: 596 TIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALE 655
           TIM+NCNPETVSTD+D +D+LYFEPV  E + EI+  EKP+GVIVQ GGQT LKLA  LE
Sbjct: 594 TIMINCNPETVSTDFDIADKLYFEPVFWEHIYEIILHEKPEGVIVQLGGQTALKLAEKLE 653

Query: 656 AAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVR 715
             G+ ++GTS +A+D AEDR  F   ++   +  P   T+ + + A+E  K IG+PL+VR
Sbjct: 654 KYGIKILGTSFEALDLAEDRGEFSSLLKENDVPYPEFGTIHSTDEALELCKTIGFPLLVR 713

Query: 716 PSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLI 775
           PSYVLGG+ M+IV +E +L ++    +    D  +LLDHFL+ A+E + DAICDGE V I
Sbjct: 714 PSYVLGGQGMKIVINEKELEQHVVEVLKDIPDNEILLDHFLEGAIEAEADAICDGENVYI 773

Query: 776 GGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNN 835
            GIM+HIE AG+HSGDS   LP Y L   +   +    +K+A  L+ +GL+N+QFAVK++
Sbjct: 774 IGIMQHIEPAGIHSGDSYAVLPPYNLGDLVVRQIETFTEKIALALKTKGLINIQFAVKDD 833

Query: 836 EVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPY---YSVKE 892
           +VY+IE NPRA+RTVPF+ KA   P    A +VM G    E  VT     PY   Y++KE
Sbjct: 834 KVYVIEANPRASRTVPFICKAYKEPYVNYAVKVMLG----ENKVTDFEFKPYKKGYAIKE 889

Query: 893 VVLPFNKFPGVDPLLGPEMRSTGEVM 918
            V  F+KFP V+  LGPEM+STGE +
Sbjct: 890 PVFSFHKFPNVNKELGPEMKSTGEAI 915



 Score =  213 bits (542), Expect = 5e-59
 Identities = 145/391 (37%), Positives = 207/391 (52%), Gaps = 23/391 (5%)

Query: 562 IMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPV 621
           ++++G GP  IGQ  EFDY    A+ +LRE+G    ++N NP T+ TD  T+D +Y  P+
Sbjct: 10  VLIIGSGPIVIGQACEFDYSGSQAARSLREEGITVTLINSNPATIMTDPVTADNVYLLPL 69

Query: 622 TLEDVLEIVRIEKPK--GVIVQYGGQTPLKLARALEAAG------VPVIGTSPDAIDRAE 673
             + +++I+  E P    V+   GGQT L LA   + AG      V +IG   DAI+ AE
Sbjct: 70  EKKSLVKILE-EHPDIDCVLPTMGGQTALNLAIEADKAGIWDRFKVRMIGVDIDAIETAE 128

Query: 674 DRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEAD 733
           +RE+F+  +E L +      T T+     E A+EIG+PLV+RPSY LGG     V  E +
Sbjct: 129 NREKFKALLEELNVGVCIGKTATSFLQGKEIAQEIGFPLVIRPSYTLGGTGGGFVEKEEE 188

Query: 734 LRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICD--GEMVLIGGIMEHIEQAGVHSGD 791
                 + +  S    VL++  +    E +++ + D  G MV+I  I E+ +  GVH+GD
Sbjct: 189 FENALMSGLKASPTHEVLIEQSILGWKEYELEVLRDSLGNMVVICSI-ENFDPMGVHTGD 247

Query: 792 SACSLPAYTLSQEIQDVMRQQVQKLAFEL-QVRGLMNVQFAVK--NNEVYLIEVNPRAAR 848
           S    PA TL   +   MR    K+   +    G  NVQF+V   N  +  IE+NPR +R
Sbjct: 248 SITVAPAMTLPDTVYQEMRNLAIKMMNGIGNFAGGCNVQFSVSPDNQTIIGIEINPRVSR 307

Query: 849 TVPFVSKATGVPLAKVAARVMAGKSLAE-----QGVTKEVIPPYYSVKEVVLP---FNKF 900
           +    SKATG P+AKVAA++  G +L E      G T     P      V +P   F+KF
Sbjct: 308 SSALASKATGYPIAKVAAKLAIGYNLDELKNSITGSTSAFFEPAIDYVIVKIPRWNFDKF 367

Query: 901 PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKA 931
            G D  LG  M++ GEVMG+G  F EA  KA
Sbjct: 368 KGSDRRLGLSMKAVGEVMGIGGNFQEALQKA 398


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: 2556
Number of extensions: 144
Number of successful extensions: 19
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1073
Length of database: 939
Length adjustment: 44
Effective length of query: 1029
Effective length of database: 895
Effective search space:   920955
Effective search space used:   920955
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: 57 (26.6 bits)

Align candidate Echvi_0768 Echvi_0768 (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.25469.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 1299.0   0.0          0 1298.7   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0768  Echvi_0768 carbamoyl-phosphate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0768  Echvi_0768 carbamoyl-phosphate synthase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1298.7   0.0         0         0       1     926 [.       2     926 ..       2     938 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1298.7 bits;  conditional E-value: 0
                            TIGR01369   1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveave 74 
                                          pk+++ik+vl+iGsGpivigqA+EFDYsGsqa ++l+eegi+v L+nsn+At+mtd+  ad+vY++Pl+++++ 
  lcl|FitnessBrowser__Cola:Echvi_0768   2 PKDNSIKHVLIIGSGPIVIGQACEFDYSGSQAARSLREEGITVTLINSNPATIMTDPVTADNVYLLPLEKKSLV 75 
                                          57899********************************************************************* PP

                            TIGR01369  75 kiiekE.rpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevaksei 147
                                          ki+e+   +D +l+t+GGqtaLnla+e +++G+ +++ v+++G++++ai++ae+RekFk++l+e+n+ v  +++
  lcl|FitnessBrowser__Cola:Echvi_0768  76 KILEEHpDIDCVLPTMGGQTALNLAIEADKAGIWDRFKVRMIGVDIDAIETAENREKFKALLEELNVGVCIGKT 149
                                          **98642789**************************************************************** PP

                            TIGR01369 148 vesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvR 221
                                          ++s  +  e+a+eig+P+++R+++tlgGtG+g++e+eee+++   ++lkasp+++vl+e+s+ gwkE+E+Ev+R
  lcl|FitnessBrowser__Cola:Echvi_0768 150 ATSFLQGKEIAQEIGFPLVIRPSYTLGGTGGGFVEKEEEFENALMSGLKASPTHEVLIEQSILGWKEYELEVLR 223
                                          ************************************************************************** PP

                            TIGR01369 222 DskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelg.vegecnvqfaldPeskryv 294
                                          Ds +n +++c+iEn+Dp+GvHtGdsi+vaP+ tL d+ yq +R+ ++k+++ +g  +g+cnvqf+++P+++ ++
  lcl|FitnessBrowser__Cola:Echvi_0768 224 DSLGNMVVICSIENFDPMGVHTGDSITVAPAMTLPDTVYQEMRNLAIKMMNGIGnFAGGCNVQFSVSPDNQTII 297
                                          *****************************************************836777*************** PP

                            TIGR01369 295 viEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvkiPrwdldkfekvd 368
                                           iE+npRvsRssALAskAtGyPiAkvaakla+Gy+Ldelkn++t++t+A+fEP++DYv+vkiPrw++dkf++ d
  lcl|FitnessBrowser__Cola:Echvi_0768 298 GIEINPRVSRSSALASKATGYPIAKVAAKLAIGYNLDELKNSITGSTSAFFEPAIDYVIVKIPRWNFDKFKGSD 371
                                          ************************************************************************** PP

                            TIGR01369 369 rklgtqmksvGEvmaigrtfeealqkalrsleekllglklkekeaesdeeleealkkpndrRlfaiaealrrgv 442
                                          r+lg +mk+vGEvm+ig +f+ealqka +sle+k  gl  + ke +++e++  +l++p+ +Rlf i +a++ g+
  lcl|FitnessBrowser__Cola:Echvi_0768 372 RRLGLSMKAVGEVMGIGGNFQEALQKACQSLEIKRNGLGADGKELKNQEQILYSLEHPSWNRLFHIYDAFKLGI 445
                                          ************************************************************************** PP

                            TIGR01369 443 sveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaev.rklrkel 515
                                          s  ++++ltkid++fl+++++lv+l  +l++ +l+ ++k+l+  ak++G++d+qia+l++  e+ev +k r+e+
  lcl|FitnessBrowser__Cola:Echvi_0768 446 SFRTIHDLTKIDKWFLKQIEELVHLDITLDKYTLDTIPKDLMMLAKHKGYADRQIAHLLGCLESEVfNKRRDEM 519
                                          ************************************************************9999984678899* PP

                            TIGR01369 516 givpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagy 589
                                          gi  v+k vDt+aaEfea+tpY+Ys++ ee ++++v+++kkv+vlGsGp+R+gqg+EFDy++vh+vla +e gy
  lcl|FitnessBrowser__Cola:Echvi_0768 520 GIKRVYKLVDTCAAEFEAQTPYYYSSFGEE-NESQVSDRKKVIVLGSGPNRVGQGIEFDYSCVHGVLAAKECGY 592
                                          ****************************99.******************************************* PP

                            TIGR01369 590 ktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaes 663
                                          +ti+in+nPEtvstD+diad+LyFe++  e++ +ii +ek+egvivqlgGqtal+la++le+ g+kilGts+e+
  lcl|FitnessBrowser__Cola:Echvi_0768 593 ETIMINCNPETVSTDFDIADKLYFEPVFWEHIYEIILHEKPEGVIVQLGGQTALKLAEKLEKYGIKILGTSFEA 666
                                          ************************************************************************** PP

                            TIGR01369 664 idraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeav 737
                                          +d aEdR +Fs+ll+e +++ p++ +++s++ea e++k+ig+P+lvRpsyvlgG++m+iv ne+ele+ + e++
  lcl|FitnessBrowser__Cola:Echvi_0768 667 LDLAEDRGEFSSLLKENDVPYPEFGTIHSTDEALELCKTIGFPLLVRPSYVLGGQGMKIVINEKELEQHVVEVL 740
                                          ************************************************************************** PP

                            TIGR01369 738 evskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkki 811
                                          +  +++ +l+d++le a+E++ Da++dge+v+i+gi++HiE aG+HsGDs +vlpp +l + v+++i++ ++ki
  lcl|FitnessBrowser__Cola:Echvi_0768 741 KDIPDNEILLDHFLEGAIEAEADAICDGENVYIIGIMQHIEPAGIHSGDSYAVLPPYNLGDLVVRQIETFTEKI 814
                                          ************************************************************************** PP

                            TIGR01369 812 akelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklv 885
                                          a +lk kGl+niqf+vkd++vyviE+n+RasRtvPf+ ka + p+v++avkv+lg++        + ++ +k +
  lcl|FitnessBrowser__Cola:Echvi_0768 815 ALALKTKGLINIQFAVKDDKVYVIEANPRASRTVPFICKAYKEPYVNYAVKVMLGENKVT---DFEFKPYKKGY 885
                                          *******************************************************98777...345788889** PP

                            TIGR01369 886 avkaavfsfsklagvdvvlgpemkstGEvmgigrdleeall 926
                                          a+k++vfsf+k+ +v+  lgpemkstGE++++ +dl + ++
  lcl|FitnessBrowser__Cola:Echvi_0768 886 AIKEPVFSFHKFPNVNKELGPEMKSTGEAIYFIDDLMDDYF 926
                                          ******************************99888876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (939 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: 11.54
//
[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