GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metE in Enterococcus termitis LMG 8895

Align homocysteine methyltransferase Met26; EC 2.1.1.14 (characterized)
to candidate WP_069664705.1 BCR25_RS16550 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase

Query= CharProtDB::CH_124367
         (764 letters)



>NCBI__GCF_001730305.1:WP_069664705.1
          Length = 754

 Score =  648 bits (1672), Expect = 0.0
 Identities = 351/767 (45%), Positives = 498/767 (64%), Gaps = 24/767 (3%)

Query: 2   VKSAVLGFPRIGKNRELKKATEAYWSGKTSAEELLATAKQLRLEHWKLQKAQGVDIIPSN 61
           +K++++GFPR+G+ RELK ATE Y+  + +A+EL AT   LR +HW+L   Q +D IPS 
Sbjct: 1   MKTSIIGFPRVGELRELKFATEKYFRKEITADELEATGYALRKKHWQLLVNQELDFIPSG 60

Query: 62  DFSLYDQIMDHSFSFNVIPPRYRLSGLSSLDTYFAMGRGMQRAATADKAAVDVPAGEMVK 121
           DFS +D  +D + S N++P +Y+   LS L+TYFA+ RG Q  A       DV A  M K
Sbjct: 61  DFSFFDTTLDTAVSLNLVPKKYQDLHLSPLETYFALARGYQGEAG------DVTALAMKK 114

Query: 122 WFDSNYHFLRPEVSEETDFKLSSTKALDEFLEAKEAGIITRPVLVGPVTYLFIAKAAKGS 181
           WF++NYH++ PE+ +ET+ +L     ++ F EA  AG+ TRP ++GP T L +A      
Sbjct: 115 WFNTNYHYMVPEIDDETNLELVGHTLVETFKEAAAAGVKTRPTILGPFTLLKLATYHGEK 174

Query: 182 SIKPIELLPKLLPVYVELIKKLTEAGAEYIQIDEPILTLDLPQEILASYKEAYETL---- 237
             +  +     +  Y +L  +L+EAG E++QIDEP L LDL Q+ +  ++  Y++L    
Sbjct: 175 QAE--DFYQAAISAYSQLFTELSEAGCEWLQIDEPALVLDLSQKEIQQFEALYQSLLSEK 232

Query: 238 GKIGKLILTTYFGSLQSNADVLKGLPIAGVHVDVVRAPENLDRALAV-LGENQIISVGVV 296
           G + K+++ TYFG ++     L  LP  G+ +D V   +  D        +++I+  G+V
Sbjct: 233 GTL-KILVQTYFGDVRDVYQELIRLPFDGIGLDFVEGRKTRDLIEQYGFPKDKILFAGIV 291

Query: 297 SGRNIWKTDFQKATAIIEKAISAVGSERVQVASSSSILHIPHSLSGEDQINPEIKRWFAF 356
           +G+NIW  D+Q++  ++E   S      V + +S S+LH+P +L+ E  +  E+K +FAF
Sbjct: 292 NGKNIWINDYQQSLNLLENLGSVA---EVVLNTSCSLLHVPFTLTNETSLTSEVKDYFAF 348

Query: 357 AVEKCAELAILTKAANDGPASVRAELEANAADCKARAESPITNVEAVRERQSKVTPQMHE 416
           AVEK AEL  L K + D  AS +A +E N A  K   +   T  E ++++  K+T     
Sbjct: 349 AVEKLAELNDLKKISEDKVAS-QAIVEKNRALFK---KERFTKNERLKQQLEKLTDADFI 404

Query: 417 RKSPFETRYAKQQASLKLPLFPTTTIGSFPQTKEIRVTRNRFAKGLISQEEYDAFIRKEI 476
           R      R A Q+  LKLPL PTTTIGSFPQTKE++  R +F +G IS+ EY  F + +I
Sbjct: 405 RLPVLTQRTAIQKEKLKLPLLPTTTIGSFPQTKEVKQNRAKFKRGEISEAEYTVFNQAKI 464

Query: 477 SDVVKFQEEVGLDVLVHGEPERNDMVQYFGERMEGFVFTVNGWVQSYGSRCVRPPIIVGD 536
           ++ V FQEE+GLDVLVHGE ERNDMV+YFGE ++G++FT   WVQSYG+RCV+PPII GD
Sbjct: 465 AECVAFQEEIGLDVLVHGEFERNDMVEYFGESLDGYLFTEKAWVQSYGTRCVKPPIIWGD 524

Query: 537 VYRPAPMTVKESQYAQSITSKPMKGMLTAPITILRWSFPRDDVHDSVQAQQIALGLRDEV 596
           V R  P+TV  S YAQS+T KPMKGMLT P+TIL WSFPR+D+       Q+AL +++EV
Sbjct: 525 VSRSKPITVAYSTYAQSLTDKPMKGMLTGPVTILNWSFPREDISLRESTLQLALAIQEEV 584

Query: 597 LDLEKAGIKVIQCDEPALREGLPLRRAEW-DEYLKWAIDAFRLATAAVQDDTQIHSHFCY 655
           LDLE  GI++IQ DE ALRE LPLR+++W  EYL WAI AFRL  + VQ  TQIH+H CY
Sbjct: 585 LDLEANGIEIIQIDEAALREKLPLRQSDWHSEYLDWAIPAFRLVHSKVQPTTQIHTHMCY 644

Query: 656 SDFNDIFDAIQRLDADVVSIENSKSDMKLLNVLSR--YTSCIGPGLFDIHSPRVPPVSEF 713
           S+F DI   I  +DADV+S E S+S + +L+ L+R  + + +GPG++DIHSPRVP V E 
Sbjct: 645 SEFADIIRDIDNMDADVISFEASRSSLTILDALNRIDFQTQVGPGVYDIHSPRVPLVGEI 704

Query: 714 KERIDAIVKHVPKDHLWLNPDCGLKTRGWPETTADLKNMIAAAREAR 760
           +  I  I+  +  + +W+NPDCGLKTRG PET A LKN++ AA++ R
Sbjct: 705 ETTIHNILNKLSIEKVWINPDCGLKTRGVPETEASLKNLVLAAKKVR 751


Lambda     K      H
   0.318    0.134    0.389 

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: 1260
Number of extensions: 64
Number of successful extensions: 10
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: 764
Length of database: 754
Length adjustment: 40
Effective length of query: 724
Effective length of database: 714
Effective search space:   516936
Effective search space used:   516936
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: 55 (25.8 bits)

Align candidate WP_069664705.1 BCR25_RS16550 (5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase)
to HMM TIGR01371 (metE: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase (EC 2.1.1.14))

# 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/TIGR01371.hmm
# target sequence database:        /tmp/gapView.2187022.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01371  [M=754]
Accession:   TIGR01371
Description: met_syn_B12ind: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
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 1052.5   0.1          0 1052.4   0.1    1.0  1  NCBI__GCF_001730305.1:WP_069664705.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069664705.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1052.4   0.1         0         0       1     752 [.       6     751 ..       6     753 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1052.4 bits;  conditional E-value: 0
                             TIGR01371   1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgai 73 
                                           +gfPr+ge Relk+a+eky++++i+++el+++   lrkk+++ + ++++d+ip++dfs++D+ Ldtav l+ +
  NCBI__GCF_001730305.1:WP_069664705.1   6 IGFPRVGELRELKFATEKYFRKEITADELEATGYALRKKHWQLLVNQELDFIPSGDFSFFDTTLDTAVSLNLV 78 
                                           69*********************************************************************** PP

                             TIGR01371  74 perfkeladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeake 144
                                           p+++++l  + s l+tyFa+aRG++    dv+al+m+kwfntnYhY+vPe+++e++++l  + l+e +kea +
  NCBI__GCF_001730305.1:WP_069664705.1  79 PKKYQDL--HLSPLETYFALARGYQGeaGDVTALAMKKWFNTNYHYMVPEIDDETNLELVGHTLVETFKEAAA 149
                                           ******9..5557***********987789******************************************* PP

                             TIGR01371 145 lgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaa 217
                                           +gv+t+P +lGp+t+lkLa  +   ek++++  ++ +++Y++++++l+eag+ew+qideP+lvldls++e+++
  NCBI__GCF_001730305.1:WP_069664705.1 150 AGVKTRPTILGPFTLLKLATYHG--EKQAEDFYQAAISAYSQLFTELSEAGCEWLQIDEPALVLDLSQKEIQQ 220
                                           *******************6664..57899******************************************* PP

                             TIGR01371 218 vkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakee.lelakakfeedkvLvaGvidG 289
                                           ++++y++l +++ +lk+l+qtYf++v++ +++l++lp++++glD+ve++++   +++++f++dk+L+aG+++G
  NCBI__GCF_001730305.1:WP_069664705.1 221 FEALYQSLLSEKGTLKILVQTYFGDVRDVYQELIRLPFDGIGLDFVEGRKTrDLIEQYGFPKDKILFAGIVNG 293
                                           ************************************************9995667899*************** PP

                             TIGR01371 290 rniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkeale 362
                                           +niw +d+++sl+ll++l + a  ++v++tscsllhvp++l++e++l +e+k+++afa+ekl+el+ lk++ e
  NCBI__GCF_001730305.1:WP_069664705.1 294 KNIWINDYQQSLNLLENLGSVA--EVVLNTSCSLLHVPFTLTNETSLTSEVKDYFAFAVEKLAELNDLKKISE 364
                                           *******************887..8*********************************************999 PP

                             TIGR01371 363 geaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfP 435
                                           ++ a + a+ ++++a+  +kk++++++e+ k++le+l+++++ r   +++R+++q++kl+lPllPtttiGsfP
  NCBI__GCF_001730305.1:WP_069664705.1 365 DKVASQ-AIVEKNRAL--FKKERFTKNERLKQQLEKLTDADFIRLPVLTQRTAIQKEKLKLPLLPTTTIGSFP 434
                                           855554.454544555..8999999************************************************ PP

                             TIGR01371 436 qtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngW 508
                                           qtkev+++Rakf++geise+eY+ f +++i++++++qee+glDvLvhGefeRnDmveyFge l+G++ft+++W
  NCBI__GCF_001730305.1:WP_069664705.1 435 QTKEVKQNRAKFKRGEISEAEYTVFNQAKIAECVAFQEEIGLDVLVHGEFERNDMVEYFGESLDGYLFTEKAW 507
                                           ************************************************************************* PP

                             TIGR01371 509 vqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialal 581
                                           vqsYG+RcvkPpii+gdvsr kp+tv+ s+yaqslt+kp+kGmLtGPvtilnWsf+ReD++++e++ q+ala+
  NCBI__GCF_001730305.1:WP_069664705.1 508 VQSYGTRCVKPPIIWGDVSRSKPITVAYSTYAQSLTDKPMKGMLTGPVTILNWSFPREDISLRESTLQLALAI 580
                                           ************************************************************************* PP

                             TIGR01371 582 rdevkdLeeagikiiqiDepalReglPlrksdk.eeYldwaveaFrlaasgvkdetqihthmCYsefneiiea 653
                                           ++ev dLe++gi+iiqiDe+alRe+lPlr+sd+ +eYldwa+ aFrl++s+v+++tqihthmCYsef +ii+ 
  NCBI__GCF_001730305.1:WP_069664705.1 581 QEEVLDLEANGIEIIQIDEAALREKLPLRQSDWhSEYLDWAIPAFRLVHSKVQPTTQIHTHMCYSEFADIIRD 653
                                           ********************************9789************************************* PP

                             TIGR01371 654 iaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPD 726
                                           i+++daDvis+easrs   +ldal+  +++++++G+GvyDihsprvP + e++++++++l+kl  e++W+nPD
  NCBI__GCF_001730305.1:WP_069664705.1 654 IDNMDADVISFEASRSSLTILDALNR-IDFQTQVGPGVYDIHSPRVPLVGEIETTIHNILNKLSIEKVWINPD 725
                                           **************************.66******************************************** PP

                             TIGR01371 727 CGLktRkweevkaalknlveaakelR 752
                                           CGLktR ++e++a+lknlv aak++R
  NCBI__GCF_001730305.1:WP_069664705.1 726 CGLKTRGVPETEASLKNLVLAAKKVR 751
                                           ************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (754 nodes)
Target sequences:                          1  (754 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 31.00
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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