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

GapMind for Amino acid biosynthesis

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

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate Echvi_2559 Echvi_2559 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase

Query= BRENDA::P25665
         (753 letters)



>FitnessBrowser__Cola:Echvi_2559
          Length = 775

 Score =  773 bits (1997), Expect = 0.0
 Identities = 406/765 (53%), Positives = 513/765 (67%), Gaps = 16/765 (2%)

Query: 3   ILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVG 62
           +L   LG+PR+G +R+LKKA E+YWAG     +L     E+R  +W  Q+QAG+DL+P  
Sbjct: 1   MLTQNLGYPRIGSKRQLKKACEAYWAGKIPLNDLQKAAAEIRETNWKLQQQAGLDLIPSN 60

Query: 63  DFAWYDHVLTTSLLLGNVPARHQN---KDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWF 119
           DF++YD VL  +  +G +P R+     +    ++D  F + RG    G    A EMTKWF
Sbjct: 61  DFSFYDQVLDMAFTVGAIPGRYHEILTELKKPELDLYFAMARGYQKDGLDIIAMEMTKWF 120

Query: 120 NTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFD 179
           +TNYHY+VPEF K QQFKL  T++LDE  EA  LG   KPVLLGPV++L LGK K   F 
Sbjct: 121 DTNYHYIVPEFTKDQQFKLFSTKVLDEFKEAKRLGIHTKPVLLGPVSFLLLGKEKEAGFH 180

Query: 180 RLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQV--- 236
           R+ LL  +LPVY  +L +L     +WVQ+DEP LV++L      A + AY  ++  V   
Sbjct: 181 RIDLLKALLPVYIDLLKKLESLHADWVQLDEPFLVMDLKDEEKAAVRWAYQEIKKAVPGI 240

Query: 237 KLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNV 296
           K LLTTYF  +  NL     LP+ GLHVDLV   + +  + +++P++  LS GL++GRN+
Sbjct: 241 KTLLTTYFGALDDNLTLAAGLPICGLHVDLVRNPEQLEAVLEKVPANMSLSLGLVDGRNI 300

Query: 297 WRADLTEKYAQI-KDIVGKRD--LWVASSCSLLHSPIDLSVETR---LDAEVKSWFAFAL 350
           W+ D       I K    K+D  L +  SCSLLHSP DL  E+    L AE+K W AFA 
Sbjct: 301 WKNDYQASLELINKARAAKQDERLLIGPSCSLLHSPCDLEEESNEHTLSAELKDWLAFAR 360

Query: 351 QKCHELALLR----DALNSGDTAALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQR 406
           QK  E+  L+    DA ++   A L E  A I  +R S R+H PAV K +  +T   SQR
Sbjct: 361 QKTTEITALKVIVEDAGSAKSKALLEENQASIAKKRTSERIHKPAVRKAVEGLTPNHSQR 420

Query: 407 ANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIK 466
            + +  R   Q  +  LP +PTTTIGSFPQT E+R  R   KK  L  N Y   I    +
Sbjct: 421 KSAFASRKTIQAEKLYLPDFPTTTIGSFPQTKEVRQWRSQLKKEVLTENQYVDNIKAATQ 480

Query: 467 QAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDI 526
           +AI  QE +GLDVLVHGE ERNDMVEYFGE L+GF FTQ GWVQSYGSRCVKPPI+ GD+
Sbjct: 481 EAIRWQEEVGLDVLVHGEFERNDMVEYFGEKLEGFAFTQYGWVQSYGSRCVKPPIIYGDV 540

Query: 527 SRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVA 586
           SRP P+T+ W  +AQSLTDKPVKGMLTGPVTIL WSF R D SR+   +QIALA+R+EV 
Sbjct: 541 SRPKPMTLFWTTFAQSLTDKPVKGMLTGPVTILQWSFVRNDQSRKATCQQIALAIREEVK 600

Query: 587 DLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCE 646
           DLE +GI IIQIDEPALREGLPLR ++W+ YLQW VE FRI+A+  +D TQIHTHMCY E
Sbjct: 601 DLEKSGIQIIQIDEPALREGLPLRHAEWNDYLQWAVECFRISASAVEDSTQIHTHMCYSE 660

Query: 647 FNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEA 706
           FNDI++ IAA+DADVITIE SRS MELL++F +F+YPN+IGPGVYDIHSP VP+ E +  
Sbjct: 661 FNDIIEHIAAMDADVITIECSRSQMELLDAFAQFNYPNDIGPGVYDIHSPRVPASEEMVT 720

Query: 707 LLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
           L++KA   +P  +LWVNPDCGLKTRGW ET+ AL  MV+AA+ LR
Sbjct: 721 LMQKAQAVVPYRQLWVNPDCGLKTRGWEETKEALGRMVEAARKLR 765


Lambda     K      H
   0.319    0.135    0.416 

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: 1587
Number of extensions: 63
Number of successful extensions: 8
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: 753
Length of database: 775
Length adjustment: 40
Effective length of query: 713
Effective length of database: 735
Effective search space:   524055
Effective search space used:   524055
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

Align candidate Echvi_2559 Echvi_2559 (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.20829.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 1118.3   0.0          0 1118.1   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2559  Echvi_2559 5-methyltetrahydropte


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2559  Echvi_2559 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransfera
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1118.1   0.0         0         0       1     753 [.       6     766 ..       6     767 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1118.1 bits;  conditional E-value: 0
                            TIGR01371   1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaip 74 
                                          lg+Prig+kR lkka e+yw+gki  ++l+k a+++r++++k q++ag+d+ip+ndfs+YD+vLd+a  +gaip
  lcl|FitnessBrowser__Cola:Echvi_2559   6 LGYPRIGSKRQLKKACEAYWAGKIPLNDLQKAAAEIRETNWKLQQQAGLDLIPSNDFSFYDQVLDMAFTVGAIP 79 
                                          79************************************************************************ PP

                            TIGR01371  75 erfkelad..desdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeake 144
                                           r++e+ +  ++ +ld yFa+aRG++k   d+ a+emtkwf+tnYhY+vPe++k+++fkl ++k+l+e+keak+
  lcl|FitnessBrowser__Cola:Echvi_2559  80 GRYHEILTelKKPELDLYFAMARGYQKdgLDIIAMEMTKWFDTNYHYIVPEFTKDQQFKLFSTKVLDEFKEAKR 153
                                          ****9754115567***********99656899***************************************** PP

                            TIGR01371 145 lgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaav 218
                                          lg++tkPvllGp++fl+L+k+ke   +++ +ll++llpvY ++lkkl++  ++wvq+deP lv+dl++ee+aav
  lcl|FitnessBrowser__Cola:Echvi_2559 154 LGIHTKPVLLGPVSFLLLGKEKE-AGFHRIDLLKALLPVYIDLLKKLESLHADWVQLDEPFLVMDLKDEEKAAV 226
                                          *********************96.88************************************************ PP

                            TIGR01371 219 keayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrni 292
                                          + ay+e+++a    k ll+tYf++++++l+ ++ lp+ +l++Dlv+++e+le++  k++++  L++G++dGrni
  lcl|FitnessBrowser__Cola:Echvi_2559 227 RWAYQEIKKAVPGIKTLLTTYFGALDDNLTLAAGLPICGLHVDLVRNPEQLEAVLEKVPANMSLSLGLVDGRNI 300
                                          ************************************************************************** PP

                            TIGR01371 293 wkadlekslkllkkleakag.dklvvstscsllhvpvdlele...ekldkelkellafakekleelkvlkeale 362
                                          wk+d+++sl+l++k  a+++ ++l++ +scsllh+p dle+e   ++l++elk++lafa++k +e+++lk ++e
  lcl|FitnessBrowser__Cola:Echvi_2559 301 WKNDYQASLELINKARAAKQdERLLIGPSCSLLHSPCDLEEEsneHTLSAELKDWLAFARQKTTEITALKVIVE 374
                                          ***************9999989****************986511167**************************9 PP

                            TIGR01371 363 g..eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsf 434
                                          +  +a+ ++ le+++a+ia++++s+r+++ +v++++e l+ ++++r+s f+ R+++q++kl lP +PtttiGsf
  lcl|FitnessBrowser__Cola:Echvi_2559 375 DagSAKSKALLEENQASIAKKRTSERIHKPAVRKAVEGLTPNHSQRKSAFASRKTIQAEKLYLPDFPTTTIGSF 448
                                          986777788899999*********************************************************** PP

                            TIGR01371 435 PqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngW 508
                                          PqtkevR+ R++++k+ ++e++Y++ ik+ ++++i++qee+glDvLvhGefeRnDmveyFgekl+Gfaftq+gW
  lcl|FitnessBrowser__Cola:Echvi_2559 449 PQTKEVRQWRSQLKKEVLTENQYVDNIKAATQEAIRWQEEVGLDVLVHGEFERNDMVEYFGEKLEGFAFTQYGW 522
                                          ************************************************************************** PP

                            TIGR01371 509 vqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalr 582
                                          vqsYGsRcvkPpiiygdvsrpkpmt+ ++++aqslt+kpvkGmLtGPvtil+WsfvR+D++rk +++qiala+r
  lcl|FitnessBrowser__Cola:Echvi_2559 523 VQSYGSRCVKPPIIYGDVSRPKPMTLFWTTFAQSLTDKPVKGMLTGPVTILQWSFVRNDQSRKATCQQIALAIR 596
                                          ************************************************************************** PP

                            TIGR01371 583 devkdLeeagikiiqiDepalReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaa 656
                                          +evkdLe++gi+iiqiDepalReglPlr++++++Yl+wave Fr++as+v+d+tqihthmCYsefn+iie+iaa
  lcl|FitnessBrowser__Cola:Echvi_2559 597 EEVKDLEKSGIQIIQIDEPALREGLPLRHAEWNDYLQWAVECFRISASAVEDSTQIHTHMCYSEFNDIIEHIAA 670
                                          ************************************************************************** PP

                            TIGR01371 657 ldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLk 730
                                          +daDvi+ie srs+mellda+ + ++y+++iG+GvyDihsprvP++ee+ +l++ka +++p ++lWvnPDCGLk
  lcl|FitnessBrowser__Cola:Echvi_2559 671 MDADVITIECSRSQMELLDAFAQ-FNYPNDIGPGVYDIHSPRVPASEEMVTLMQKAQAVVPYRQLWVNPDCGLK 743
                                          ***********************.67************************************************ PP

                            TIGR01371 731 tRkweevkaalknlveaakelRe 753
                                          tR wee+k+al  +veaa++lR+
  lcl|FitnessBrowser__Cola:Echvi_2559 744 TRGWEETKEALGRMVEAARKLRA 766
                                          *********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (754 nodes)
Target sequences:                          1  (775 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 10.58
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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