Alignments for a candidate for carB in Beijerinckia indica subsp. indica ATCC 9039

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Beijerinckia indica subsp. indica ATCC 9039

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_012383876.1 BIND_RS04420 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>NCBI__GCF_000019845.1:WP_012383876.1
          Length = 1107

 Score = 1266 bits (3277), Expect = 0.0
 Identities = 666/1095 (60%), Positives = 813/1095 (74%), Gaps = 43/1095 (3%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDI +I+I+GAGPI+IGQACEFDYSG QACKALR+EGYR++LVNSNPATIMTDP+M
Sbjct: 1    MPKRTDIGTIMIIGAGPIIIGQACEFDYSGTQACKALRQEGYRIVLVNSNPATIMTDPDM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDA-----VLPTMGGQTALNCALELERQGVLEEFGVTM 115
            AD TYIEPI  +VV KII KER  A     +LPTMGGQTALNCAL L++ GVLE++ V M
Sbjct: 61   ADRTYIEPITPDVVAKIIAKERHAAPGGFALLPTMGGQTALNCALSLKKMGVLEDYDVEM 120

Query: 116  IGATADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMG 175
            IGATA+AIDKAEDR  F  AM KIGL T RS    T+ +AL +  D+G P IIRPSFTMG
Sbjct: 121  IGATAEAIDKAEDRELFREAMTKIGLSTPRSHQIKTLTQALDILDDIGLPAIIRPSFTMG 180

Query: 176  GSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIE 235
            G+GGGIAYN+ EF +I  RG+D SPT E+L++ES++GWKEYEMEVVRD+NDNCIIVCSIE
Sbjct: 181  GTGGGIAYNKAEFIDIIERGIDASPTNEVLVEESVLGWKEYEMEVVRDRNDNCIIVCSIE 240

Query: 236  NFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRL 295
            N D MG+HTGDSITVAPA TLTDKEYQ+MR+AS+AVLREIGVETGGSNVQFAVNP +GR+
Sbjct: 241  NIDPMGVHTGDSITVAPALTLTDKEYQVMRDASLAVLREIGVETGGSNVQFAVNPSDGRM 300

Query: 296  IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYV 355
            IVIEMNPRVSRSSALASKATGFPIAKVAA+LAVGYTLDE+ NDITGG TPASFEP+IDYV
Sbjct: 301  IVIEMNPRVSRSSALASKATGFPIAKVAARLAVGYTLDEIANDITGGATPASFEPTIDYV 360

Query: 356  VTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSL 415
            VTKIPRF FEKF GA D LTT MKSVGE MAIGRT  ESLQKALR L+ G TG D ++++
Sbjct: 361  VTKIPRFAFEKFPGAEDTLTTAMKSVGESMAIGRTFAESLQKALRSLDTGLTGLD-EIAI 419

Query: 416  DD---PEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRL 472
            D     + +  +R  L     DR+  +A A R G+SV+ +     IDRWFL QIE +++L
Sbjct: 420  DGLGLGDDMNILRGALGRPTPDRLLIVAQAMREGMSVEEIHEACAIDRWFLEQIEGILKL 479

Query: 473  EEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTC 532
            E KV   G+   +A  LR LK  GF+D RL+ LA V   E+  LR + D+HPV+KR+DTC
Sbjct: 480  EAKVRAFGLPE-DAANLRLLKAAGFSDTRLSTLAKVTPQEVAALRAKLDVHPVFKRIDTC 538

Query: 533  AAEFATDTAYMYSTYEEE------CEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHAS 586
            AAEFA+ TAY+YSTY         CEA PS  R+K+++LGGGPNRIGQGIEFDYCC  A 
Sbjct: 539  AAEFASPTAYLYSTYAPPFAGAPVCEAKPS-PRDKVVILGGGPNRIGQGIEFDYCCCQAC 597

Query: 587  LALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKP----KGVIVQY 642
             AL + G+ETIM+NCNPETVSTDYDTSDRLYFEP+T EDVL I+  E+     KGVIVQ+
Sbjct: 598  FALHDAGFETIMINCNPETVSTDYDTSDRLYFEPLTPEDVLAILAKEQEAGTLKGVIVQF 657

Query: 643  GGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAV 702
            GGQTPLKLA  LE AG+P++GTS D+ID AEDR+RF+  ++++ LKQP N    ++E + 
Sbjct: 658  GGQTPLKLAHTLEKAGIPILGTSVDSIDLAEDRDRFKWLLDKVGLKQPMNGIAYSVEQSR 717

Query: 703  EKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAV-------------------- 742
              A ++G PLVVRPSYVLGGRAM I+ D A    Y    +                    
Sbjct: 718  LVASDLGLPLVVRPSYVLGGRAMAIIRDNASFDDYLLGTLPGLVPSDIKARYPNDKTGQI 777

Query: 743  -SVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTL 801
             +V    P+L D +L DAVEVDVDA+CDG+ V I GIMEHIE+AG+HSGDSACSLP  +L
Sbjct: 778  NTVLGKNPLLFDRYLSDAVEVDVDALCDGKDVFICGIMEHIEEAGIHSGDSACSLPPRSL 837

Query: 802  SQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPL 861
              +    + +Q +KLA  L+V G MNVQ+A+K+ E+Y++EVNPRAARTVPFV+K  G+PL
Sbjct: 838  GPDKIAALEEQTRKLALALKVGGFMNVQYALKDGEIYVLEVNPRAARTVPFVAKVIGIPL 897

Query: 862  AKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVG 921
            AK+A+R+MAG++LA   +  + +  +  VKE V PF +FPGVD +LGPEMRSTGEVMG+ 
Sbjct: 898  AKIASRIMAGENLASFRLEPKKL-RHVGVKEAVFPFARFPGVDTVLGPEMRSTGEVMGID 956

Query: 922  RTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVL 981
             +FA AFAK+QLG  + +   G   +SVR+ DK R VD    L+  GF++ AT GT+  L
Sbjct: 957  FSFAIAFAKSQLGGGTKVPTKGTVFVSVRDEDKPRAVDTIKLLINLGFKICATGGTSRFL 1016

Query: 982  GEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYD 1041
               GI  + +NKV EGRPH+ D IKNG    ++NTT G +A+ DSR +RR+AL +KV Y 
Sbjct: 1017 EGEGIEAQRLNKVSEGRPHVVDAIKNGAIQLVLNTTEGAQALADSRSLRRAALLHKVPYY 1076

Query: 1042 TTLNGGFATAMALNA 1056
            TTL G  A A  + A
Sbjct: 1077 TTLAGAIAAAQGIRA 1091


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: 3138
Number of extensions: 158
Number of successful extensions: 19
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: 1107
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1061
Effective search space:  1089647
Effective search space used:  1089647
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_012383876.1 BIND_RS04420 (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.2574183.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 1437.1   0.0          0 1436.3   0.0    1.3  1  NCBI__GCF_000019845.1:WP_012383876.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019845.1:WP_012383876.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1436.3   0.0         0         0       1    1049 [.       2    1086 ..       2    1089 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1436.3 bits;  conditional E-value: 0
                             TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71  
                                            pkr+di ++++iG+Gpi+igqA+EFDYsG+qa+kal++eg+++vLvnsn+At+mtd+++ad++YieP+t+ 
  NCBI__GCF_000019845.1:WP_012383876.1    2 PKRTDIGTIMIIGAGPIIIGQACEFDYSGTQACKALRQEGYRIVLVNSNPATIMTDPDMADRTYIEPITPD 72  
                                            689******************************************************************** PP

                             TIGR01369   72 avekiiekErpD.....ailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealke 137 
                                            +v+kii kEr       a+l+t+GGqtaLn+a++l+++GvLe y+v+++G++ eai+kaedRe+F+ea+++
  NCBI__GCF_000019845.1:WP_012383876.1   73 VVAKIIAKERHAapggfALLPTMGGQTALNCALSLKKMGVLEDYDVEMIGATAEAIDKAEDRELFREAMTK 143 
                                            **********763334469**************************************************** PP

                             TIGR01369  138 ineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlveks 208 
                                            i++++++s+ +++ ++al++ ++ig+P i+R++ft+gGtG+gia+n++e+  ++e++++asp+++vlve+s
  NCBI__GCF_000019845.1:WP_012383876.1  144 IGLSTPRSHQIKTLTQALDILDDIGLPAIIRPSFTMGGTGGGIAYNKAEFIDIIERGIDASPTNEVLVEES 214 
                                            *********************************************************************** PP

                             TIGR01369  209 lagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege 279 
                                            + gwkE+E+EvvRD++dnciivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq +Rdasl+++re+gve++
  NCBI__GCF_000019845.1:WP_012383876.1  215 VLGWKEYEMEVVRDRNDNCIIVCSIENIDPMGVHTGDSITVAPALTLTDKEYQVMRDASLAVLREIGVETG 285 
                                            *********************************************************************98 PP

                             TIGR01369  280 .cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPs 348 
                                             +nvqfa++P++ r++viE+npRvsRssALAskAtG+PiAkvaa+lavGy+Lde+ nd+t+  t+AsfEP+
  NCBI__GCF_000019845.1:WP_012383876.1  286 gSNVQFAVNPSDGRMIVIEMNPRVSRSSALASKATGFPIAKVAARLAVGYTLDEIANDITGgATPASFEPT 356 
                                            8***********************************************************878******** PP

                             TIGR01369  349 lDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllg...lklkekeaesd 416 
                                            +DYvv+kiPr++++kf +++++l+t mksvGE maigrtf e+lqkalrsl+++l+g   + ++     +d
  NCBI__GCF_000019845.1:WP_012383876.1  357 IDYVVTKIPRFAFEKFPGAEDTLTTAMKSVGESMAIGRTFAESLQKALRSLDTGLTGldeIAIDGLGLGDD 427 
                                            *********************************************************43333444445555 PP

                             TIGR01369  417 ee.leealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkk 486 
                                            ++ l+ al +p+++Rl+++a+a+r+g+svee++e++ idr+fle+++ +++le +++   l   ++ +l+ 
  NCBI__GCF_000019845.1:WP_012383876.1  428 MNiLRGALGRPTPDRLLIVAQAMREGMSVEEIHEACAIDRWFLEQIEGILKLEAKVRAFGLP-EDAANLRL 497 
                                            551566899************************************************99888.68899*** PP

                             TIGR01369  487 akklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee.....kddvevt 552 
                                            +k+ Gfsd+++++l+kv+ +ev +lr +l+++pv+kr+Dt+aaEf + t+YlYsty+         +++ +
  NCBI__GCF_000019845.1:WP_012383876.1  498 LKAAGFSDTRLSTLAKVTPQEVAALRAKLDVHPVFKRIDTCAAEFASPTAYLYSTYAPPfagapVCEAKPS 568 
                                            ********************************************************988555554455555 PP

                             TIGR01369  553 ekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvld 623 
                                             ++kv++lG+Gp+Rigqg+EFDyc+ +a+ al++ag++ti+in+nPEtvstDyd++drLyFe+lt edvl 
  NCBI__GCF_000019845.1:WP_012383876.1  569 PRDKVVILGGGPNRIGQGIEFDYCCCQACFALHDAGFETIMINCNPETVSTDYDTSDRLYFEPLTPEDVLA 639 
                                            567******************************************************************** PP

                             TIGR01369  624 iiekek....vegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkea 690 
                                            i+ ke+     +gvivq+gGqt+l+la++le+ag++ilGts++sid aEdR++F+ lld++g+kqp + +a
  NCBI__GCF_000019845.1:WP_012383876.1  640 ILAKEQeagtLKGVIVQFGGQTPLKLAHTLEKAGIPILGTSVDSIDLAEDRDRFKWLLDKVGLKQPMNGIA 710 
                                            **99983333579********************************************************** PP

                             TIGR01369  691 tsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryle.....................eavevs 740 
                                             sve+ + +a+++g+P++vRpsyvlgGram+i+++++++ +yl                      ++++v 
  NCBI__GCF_000019845.1:WP_012383876.1  711 YSVEQSRLVASDLGLPLVVRPSYVLGGRAMAIIRDNASFDDYLLgtlpglvpsdikarypndktgQINTVL 781 
                                            *****************************************997788888899998988888777778888 PP

                             TIGR01369  741 kekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkki 811 
                                             ++P+l d+yl+davEvdvDa++dg++v+i+gi+eHiEeaG+HsGDs+++lpp++l  +   +++e+++k+
  NCBI__GCF_000019845.1:WP_012383876.1  782 GKNPLLFDRYLSDAVEVDVDALCDGKDVFICGIMEHIEEAGIHSGDSACSLPPRSLGPDKIAALEEQTRKL 852 
                                            9********************************************************************** PP

                             TIGR01369  812 akelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekks 882 
                                            a +lkv G +n+q+++kd+e+yv+Evn+Ra+RtvPfv+k++g+pl+k+a ++++g++l++      + kk 
  NCBI__GCF_000019845.1:WP_012383876.1  853 ALALKVGGFMNVQYALKDGEIYVLEVNPRAARTVPFVAKVIGIPLAKIASRIMAGENLASFRL---EPKKL 920 
                                            ************************************************************876...9999* PP

                             TIGR01369  883 klvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkee 953 
                                            ++v+vk+avf+f+++ gvd vlgpem+stGEvmgi+ +++ a++k++l  ++k+++kg+v++sv+d+dk +
  NCBI__GCF_000019845.1:WP_012383876.1  921 RHVGVKEAVFPFARFPGVDTVLGPEMRSTGEVMGIDFSFAIAFAKSQLGGGTKVPTKGTVFVSVRDEDKPR 991 
                                            *********************************************************************** PP

                             TIGR01369  954 llelakklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekg 1024
                                            +++++k l ++g+k++at gt+++le +gi+a+ ++kvse ++++++++k++ i+lv+n+t+ +++a  ++
  NCBI__GCF_000019845.1:WP_012383876.1  992 AVDTIKLLINLGFKICATGGTSRFLEGEGIEAQRLNKVSEGRPHVVDAIKNGAIQLVLNTTE-GAQALADS 1061
                                            ***********************************************************997.88899999 PP

                             TIGR01369 1025 ykirreaveykvplvteletaeall 1049
                                             ++rr+a+ +kvp+ t+l++a a++
  NCBI__GCF_000019845.1:WP_012383876.1 1062 RSLRRAALLHKVPYYTTLAGAIAAA 1086
                                            *****************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1107 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 0.02s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 13.01
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 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