Alignments for a candidate for carB in Thioalkalivibrio halophilus HL17

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Thioalkalivibrio halophilus HL17

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_018946366.1 B1A74_RS02470 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_001995255.1:WP_018946366.1
          Length = 1078

 Score = 1466 bits (3794), Expect = 0.0
 Identities = 746/1071 (69%), Positives = 871/1071 (81%), Gaps = 1/1071 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDI+S+LILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM
Sbjct: 1    MPKRTDIQSVLILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEP+ W+ V KII  E+PDA+LPTMGGQTALNCAL+L R+GVLE+ GV MIGA  
Sbjct: 61   ADATYIEPVEWKTVEKIIAAEQPDALLPTMGGQTALNCALDLSREGVLEKHGVEMIGANE 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
             AID AEDR  F  AM  IGL+T  + +AH+ EEA  +   +GFP IIRPSFT+GGSGGG
Sbjct: 121  AAIDMAEDRDHFKAAMADIGLDTPTAELAHSWEEAQQIQPRIGFPVIIRPSFTLGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNREEFE I   GLDLSP  ++L++ES +GWKE+EMEVVRD+ DN II+CSIEN D M
Sbjct: 181  IAYNREEFEYIVKNGLDLSPVNQVLLEESALGWKEFEMEVVRDQADNAIIICSIENVDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            GIHTGDSITVAPAQTLTDKEYQIMR+AS+AVLR+IGVETGGSNVQFA+NP+NGR+IVIEM
Sbjct: 241  GIHTGDSITVAPAQTLTDKEYQIMRDASLAVLRKIGVETGGSNVQFAINPENGRMIVIEM 300

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

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RF FEKF  A  +LTTQMK+VGE MAIGRT QESLQKALR +E G  G D ++ LD  + 
Sbjct: 361  RFTFEKFPQAEAQLTTQMKAVGEAMAIGRTFQESLQKALRSMETGMDGLDERIDLDAQDV 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            + ++R  L +   D++ Y+ADAFR G SV  +F LT ID WFL QI+ELV LE+ V +  
Sbjct: 421  VERLRTALANPTPDQLLYVADAFRHGFSVQDIFELTAIDPWFLAQIQELVDLEKAVRDRI 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            +  ++A+ + +LK++GF+D RLA+L    E  +RK R +  + PVYKRVDTCAAEFAT T
Sbjct: 481  LGEIDAEEMYRLKQRGFSDLRLARLLNETEKAVRKHRHRLGVRPVYKRVDTCAAEFATTT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AYMYS+YEEE EA P TDR+KIMVLGGGPNRIGQGIEFDYCCVHA+LA+RED YETIMVN
Sbjct: 541  AYMYSSYEEENEAEP-TDRQKIMVLGGGPNRIGQGIEFDYCCVHAALAMREDQYETIMVN 599

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEP+TLEDVLE+V  E+P GVIVQYGGQTPLKLAR LE AGVP
Sbjct: 600  CNPETVSTDYDTSDRLYFEPLTLEDVLEVVETERPTGVIVQYGGQTPLKLARDLEDAGVP 659

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            +IGTSPD+ID AEDRERFQ  + +L LKQP N T  + E A + A EIGYPLVVRPSYVL
Sbjct: 660  IIGTSPDSIDLAEDRERFQALLNKLGLKQPPNRTARSEEEAEKLADEIGYPLVVRPSYVL 719

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIV D  DLR Y Q+AVSVSN+APVLLD FLDDA+EVD+DA+CDG+ V IGG+ME
Sbjct: 720  GGRAMEIVRDREDLRGYMQSAVSVSNEAPVLLDRFLDDAIEVDIDAVCDGQDVFIGGVME 779

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDSACSLP ++LS E+Q+ M  QV+K+A  L+V GLMN QFAVK +++Y++
Sbjct: 780  HIEQAGVHSGDSACSLPPFSLSLELQERMVDQVRKMAVGLRVVGLMNTQFAVKGDDIYVL 839

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRA+RTVP+VSK+ G+PLAK+AAR MAG SLAEQGV   V P YYSVKE V PF KF
Sbjct: 840  EVNPRASRTVPYVSKSVGLPLAKIAARCMAGTSLAEQGVGGAVFPDYYSVKEAVFPFAKF 899

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDP+LGPEM+STGEVMGVGR+FAEAFAK+QLG+   +   G+A +SVR+ DK  V  +
Sbjct: 900  PGVDPILGPEMKSTGEVMGVGRSFAEAFAKSQLGAGVLLPSTGKAFVSVRDIDKPEVTGI 959

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            A +L++ GFE+ AT GTA +L E GI    VNKV EGRPHI D IKN E ++IINT  G+
Sbjct: 960  ARRLVELGFEVLATRGTAGLLEEQGIAVTRVNKVTEGRPHIVDMIKNDEVSFIINTVEGK 1019

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQ 1071
            ++  DS  IRR AL +KV Y TT+ G  AT  AL+     +V  +Q +H +
Sbjct: 1020 QSTADSYTIRREALMHKVGYTTTIAGARATVQALDHLEGSEVFRLQSLHQE 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: 3114
Number of extensions: 119
Number of successful extensions: 12
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: 1078
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1033
Effective search space:  1061924
Effective search space used:  1061924
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_018946366.1 B1A74_RS02470 (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.2575350.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 1565.4   0.0          0 1565.2   0.0    1.0  1  NCBI__GCF_001995255.1:WP_018946366.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001995255.1:WP_018946366.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1565.2   0.0         0         0       1    1052 []       2    1053 ..       2    1053 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1565.2 bits;  conditional E-value: 0
                             TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71  
                                            pkr+di++vl++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+e+ad++YieP++++
  NCBI__GCF_001995255.1:WP_018946366.1    2 PKRTDIQSVLILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADATYIEPVEWK 72  
                                            689******************************************************************** PP

                             TIGR01369   72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142 
                                            +vekii  E+pDa+l+t+GGqtaLn+a++l+++GvLek+gv+++G++  ai+ aedR++Fk+a+++i++++
  NCBI__GCF_001995255.1:WP_018946366.1   73 TVEKIIAAEQPDALLPTMGGQTALNCALDLSREGVLEKHGVEMIGANEAAIDMAEDRDHFKAAMADIGLDT 143 
                                            *********************************************************************** PP

                             TIGR01369  143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213 
                                            +++e ++s eea++++ +ig+Pvi+R++ftlgG+G+gia+n+ee++ +v+++l++sp++qvl+e+s  gwk
  NCBI__GCF_001995255.1:WP_018946366.1  144 PTAELAHSWEEAQQIQPRIGFPVIIRPSFTLGGSGGGIAYNREEFEYIVKNGLDLSPVNQVLLEESALGWK 214 
                                            *********************************************************************** PP

                             TIGR01369  214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvq 283 
                                            E+E+EvvRD++dn+ii+c+iEn+Dp+G+HtGdsi+vaP+qtLtdkeyq++Rdasl+++r++gve++ +nvq
  NCBI__GCF_001995255.1:WP_018946366.1  215 EFEMEVVRDQADNAIIICSIENVDPMGIHTGDSITVAPAQTLTDKEYQIMRDASLAVLRKIGVETGgSNVQ 285 
                                            ****************************************************************988**** PP

                             TIGR01369  284 faldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvv 353 
                                            fa++Pe+ r++viE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldelkn++t+  t+AsfEPs+DYvv
  NCBI__GCF_001995255.1:WP_018946366.1  286 FAINPENGRMIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELKNEITGgLTPASFEPSIDYVV 356 
                                            *******************************************************867************* PP

                             TIGR01369  354 vkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkek..eaesdeeleea 422 
                                            +kiPr+ ++kf +++ +l+tqmk+vGE maigrtf+e+lqkalrs+e+++ gl+++ +  ++   e+l++a
  NCBI__GCF_001995255.1:WP_018946366.1  357 TKIPRFTFEKFPQAEAQLTTQMKAVGEAMAIGRTFQESLQKALRSMETGMDGLDERIDldAQDVVERLRTA 427 
                                            ****************************************************8776441044556788999 PP

                             TIGR01369  423 lkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfs 493 
                                            l +p+++ l+++a+a+r+g+sv++++elt id +fl ++++lv+lek++++  l e+++e++ ++k+ Gfs
  NCBI__GCF_001995255.1:WP_018946366.1  428 LANPTPDQLLYVADAFRHGFSVQDIFELTAIDPWFLAQIQELVDLEKAVRDRILGEIDAEEMYRLKQRGFS 498 
                                            *********************************************************************** PP

                             TIGR01369  494 deqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGp 564 
                                            d ++a+l++ +e++vrk r++lg+ pv+krvDt+aaEf ++t+Y+Ys+yeee +++e t+++k++vlG+Gp
  NCBI__GCF_001995255.1:WP_018946366.1  499 DLRLARLLNETEKAVRKHRHRLGVRPVYKRVDTCAAEFATTTAYMYSSYEEE-NEAEPTDRQKIMVLGGGP 568 
                                            ****************************************************.99**************** PP

                             TIGR01369  565 iRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegviv 635 
                                            +Rigqg+EFDyc+vha+la+re +y+ti++n+nPEtvstDyd++drLyFe+lt+edvl+++e+e+++gviv
  NCBI__GCF_001995255.1:WP_018946366.1  569 NRIGQGIEFDYCCVHAALAMREDQYETIMVNCNPETVSTDYDTSDRLYFEPLTLEDVLEVVETERPTGVIV 639 
                                            *********************************************************************** PP

                             TIGR01369  636 qlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyP 706 
                                            q+gGqt+l+la++le+agv+i+Gts++sid aEdRe+F++ll++lg+kqp +++a+s eea+++a+eigyP
  NCBI__GCF_001995255.1:WP_018946366.1  640 QYGGQTPLKLARDLEDAGVPIIGTSPDSIDLAEDRERFQALLNKLGLKQPPNRTARSEEEAEKLADEIGYP 710 
                                            *********************************************************************** PP

                             TIGR01369  707 vlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHi 777 
                                            ++vRpsyvlgGrameiv+++e+l+ y+++av+vs+e+Pvl+d++l+da+Evd+Dav+dg++v+i g++eHi
  NCBI__GCF_001995255.1:WP_018946366.1  711 LVVRPSYVLGGRAMEIVRDREDLRGYMQSAVSVSNEAPVLLDRFLDDAIEVDIDAVCDGQDVFIGGVMEHI 781 
                                            *********************************************************************** PP

                             TIGR01369  778 EeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfv 848 
                                            E+aGvHsGDs+++lpp +ls e+++++ ++v+k+a  l+v+Gl+n qf+vk++++yv+Evn+RasRtvP+v
  NCBI__GCF_001995255.1:WP_018946366.1  782 EQAGVHSGDSACSLPPFSLSLELQERMVDQVRKMAVGLRVVGLMNTQFAVKGDDIYVLEVNPRASRTVPYV 852 
                                            *********************************************************************** PP

                             TIGR01369  849 skalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigr 919 
                                            sk +g+pl+k+a+++++g++l+e  +gv     +++++vk+avf+f+k+ gvd++lgpemkstGEvmg+gr
  NCBI__GCF_001995255.1:WP_018946366.1  853 SKSVGLPLAKIAARCMAGTSLAE--QGVGGAVFPDYYSVKEAVFPFAKFPGVDPILGPEMKSTGEVMGVGR 921 
                                            ***********************..789999**************************************** PP

                             TIGR01369  920 dleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlk 990 
                                            +++ea++k++l ++  +++ g++++sv+d dk e++ +a++l+e+g++v+at+gta  lee+gi ++ v+k
  NCBI__GCF_001995255.1:WP_018946366.1  922 SFAEAFAKSQLGAGVLLPSTGKAFVSVRDIDKPEVTGIARRLVELGFEVLATRGTAGLLEEQGIAVTRVNK 992 
                                            *********************************************************************** PP

                             TIGR01369  991 vseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaealleal 1052
                                            v+e +++i++++k++e++++in+ + +k+++ ++y+irrea+++kv + t++++a+a+++al
  NCBI__GCF_001995255.1:WP_018946366.1  993 VTEGRPHIVDMIKNDEVSFIINTVE-GKQSTADSYTIRREALMHKVGYTTTIAGARATVQAL 1053
                                            **********************987.77788899***********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1078 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 22.79
//
[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)
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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 2024 update 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 original 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