Alignments for a candidate for metE in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for metE in Desulfovibrio vulgaris Miyazaki F

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate 8501302 DvMF_2035 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase (RefSeq)

Query= BRENDA::P25665
         (753 letters)



>FitnessBrowser__Miya:8501302
          Length = 780

 Score =  768 bits (1983), Expect = 0.0
 Identities = 412/779 (52%), Positives = 509/779 (65%), Gaps = 34/779 (4%)

Query: 6   HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
           HTLGFPR+G  RELKKA E YW G +TR++L    R +R R+W  Q++AGID++PVGDFA
Sbjct: 4   HTLGFPRIGGNRELKKAVEDYWKGAATRQQLEDAARAIRLRNWTLQREAGIDVVPVGDFA 63

Query: 66  WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHY 125
            YDH+L  +LLLG +P R +N D   DID +FR+ RG+     P A  EMTKWF+TNYHY
Sbjct: 64  LYDHILDAALLLGVIPPRFRNDDAPRDIDLMFRMARGQGGD-RPVAPLEMTKWFDTNYHY 122

Query: 126 MVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLN 185
           +VPE      F      LL  +DEALA G   K VL GP+T+LWL K + +   R SLL 
Sbjct: 123 LVPELDAATTFAPDAAPLLALIDEALAAGFTPKAVLPGPMTFLWLSK-RVDGGTRWSLLP 181

Query: 186 DILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQVK---LLLTT 242
            +L  Y  +L ++A R    +Q+DEP L L+L       + PAY  L+  V    LLL +
Sbjct: 182 ALLDAYGALLRDVAAR-CPLIQLDEPILSLDLADDIRSRFVPAYARLRVAVPDATLLLAS 240

Query: 243 YFEGVTPNLDTITALPVQGLHVDLVHGKDDVA-------ELHKRLPSDW----------- 284
           YF  V  NL    +LPV  +H+DLV G +D+            R P+D            
Sbjct: 241 YFAPVGDNLPVALSLPVDVVHLDLVRGPEDLTPALDILTRAAARQPADSGLPQSGSQSGI 300

Query: 285 LLSAGLINGRNVWRADLTEKYAQIKDIV---GKRDLWVASSCSLLHSPIDLSVETRLDAE 341
            LS G+INGRNVWR D  +  A ++  V   G   +WVA SCSLLH P+DL  ET LD E
Sbjct: 301 ALSLGVINGRNVWRVDADKAAAPVRAAVAALGPDRVWVAPSCSLLHCPVDLDAETGLDPE 360

Query: 342 VKSWFAFALQKCHELALLRDALNSGD-------TAALAEWSAPIQARRHSTRVHNPAVEK 394
           V  W AFA QKC E+ L+ D  +           AALA   A + AR  S  +H+PAV  
Sbjct: 361 VAQWLAFARQKCAEVRLVADMCDLNGRADAPETAAALARNRAALAARAASPVIHDPAVAV 420

Query: 395 RLAAITAQDSQRANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDA 454
           R   +T +   RA  Y  R  AQRA  +LP  P TTIGSFPQT +IR  R   + G +  
Sbjct: 421 RAGTVTPEMGWRATPYTARIAAQRAALRLPVLPATTIGSFPQTVDIRAQRRKLRTGQITE 480

Query: 455 NNYRTGIAEHIKQAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGS 514
             Y   + E I  AI EQE LGLDVLVHGE ERNDMVEYFGE L GF  T NGWVQSYG+
Sbjct: 481 AQYDAAMREAIATAIREQEALGLDVLVHGEPERNDMVEYFGEQLRGFCITANGWVQSYGT 540

Query: 515 RCVKPPIVIGDISRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIA 574
           RCVKPP++ GD++RP P+TV W  +AQSLT KPVKGMLTGPVTI CWSF R+DV R  + 
Sbjct: 541 RCVKPPLLYGDVARPGPMTVRWITHAQSLTQKPVKGMLTGPVTIACWSFVRDDVPRPVVF 600

Query: 575 KQIALALRDEVADLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKD 634
           +Q+ALA+RDEVADLEAAGIG+IQIDEPALREGLPLRR+   AYL   V AFR+ ++  +D
Sbjct: 601 RQLALAIRDEVADLEAAGIGVIQIDEPALREGLPLRRAAHAAYLDAAVGAFRLASSGVRD 660

Query: 635 DTQIHTHMCYCEFNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIH 694
            TQIHTHMCYC+F+DI+D +AALDADVI++E SRS MELL+ F    YPNE+GPGVYDIH
Sbjct: 661 ATQIHTHMCYCDFHDIIDHVAALDADVISLEASRSRMELLDVFATHAYPNEVGPGVYDIH 720

Query: 695 SPNVPSVEWIEALLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLRRG 753
           SP VPS++ +E LL+ A++ +P +RLW NPDCGLKTR WPETRA+LA++V AA  +R G
Sbjct: 721 SPRVPSIDEMETLLRAASRVLPLDRLWANPDCGLKTRDWPETRASLAHLVAAATRVREG 779


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: 1689
Number of extensions: 92
Number of successful extensions: 9
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: 780
Length adjustment: 41
Effective length of query: 712
Effective length of database: 739
Effective search space:   526168
Effective search space used:   526168
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 8501302 DvMF_2035 (5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase (RefSeq))
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.5324.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     7e-300  983.3   0.0   1.1e-299  982.6   0.0    1.3  1  lcl|FitnessBrowser__Miya:8501302  DvMF_2035 5-methyltetrahydropter


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501302  DvMF_2035 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  982.6   0.0  1.1e-299  1.1e-299       1     753 [.       6     778 ..       6     779 .. 0.95

  Alignments for each domain:
  == domain 1  score: 982.6 bits;  conditional E-value: 1.1e-299
                         TIGR01371   1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaiperf 77 
                                       lgfPrig +Relkka+e+ywkg  ++++l++ a+ +r ++++ q+eag+dv+pv+df+lYDh+Ld+a+llg+ip rf
  lcl|FitnessBrowser__Miya:8501302   6 LGFPRIGGNRELKKAVEDYWKGAATRQQLEDAARAIRLRNWTLQREAGIDVVPVGDFALYDHILDAALLLGVIPPRF 82 
                                       79*************************************************************************** PP

                         TIGR01371  78 keladdesdldtyFaiaRGtek.kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkPvl 153
                                       ++  d+  d+d +F++aRG+   + va lemtkwf+tnYhYlvPel+++++f+ ++  ll  ++ea ++g   k vl
  lcl|FitnessBrowser__Miya:8501302  83 RND-DAPRDIDLMFRMARGQGGdRPVAPLEMTKWFDTNYHYLVPELDAATTFAPDAAPLLALIDEALAAGFTPKAVL 158
                                       **8.7778***********977345889************************************************* PP

                         TIGR01371 154 lGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeask 230
                                        Gp+tfl+L+k++++   ++ +ll++ll++Y  +l+++a+  +  +q+deP+l ldl+++ ++ +  ay+ l+ a  
  lcl|FitnessBrowser__Miya:8501302 159 PGPMTFLWLSKRVDG--GTRWSLLPALLDAYGALLRDVAA-RCPLIQLDEPILSLDLADDIRSRFVPAYARLRVAVP 232
                                       *************85..5799****************987.89********************************** PP

                         TIGR01371 231 elklllqtYfdsveealeklvslpvealglDlveakee..................lelakakfeedkvLvaGvidG 289
                                       +++lll++Yf  v ++l  ++slpv+ ++lDlv+++e+                    l +++ ++   L++Gvi+G
  lcl|FitnessBrowser__Miya:8501302 233 DATLLLASYFAPVGDNLPVALSLPVDVVHLDLVRGPEDltpaldiltraaarqpadSGLPQSGSQSGIALSLGVING 309
                                       ***********************************9877777666544333222212233455667789******** PP

                         TIGR01371 290 rniwkadlekslkllkkleakag.dklvvstscsllhvpvdleleekldkelkellafakekleelkvlkea..leg 363
                                       rn+w+ d  k+++ +++  a+ g d+++v++scsllh pvdl++e+ ld+e+ ++lafa++k++e+++++++  l+g
  lcl|FitnessBrowser__Miya:8501302 310 RNVWRVDADKAAAPVRAAVAALGpDRVWVAPSCSLLHCPVDLDAETGLDPEVAQWLAFARQKCAEVRLVADMcdLNG 386
                                       *****************9999999**********************************************9744677 PP

                         TIGR01371 364 .ea..avaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqt 437
                                         +  ++a+al+ ++aa+aar+ s++++d +v+ r  +++ ++  r++++++R +aq++ l+lP+lP ttiGsfPqt
  lcl|FitnessBrowser__Miya:8501302 387 rADapETAAALARNRAALAARAASPVIHDPAVAVRAGTVTPEMGWRATPYTARIAAQRAALRLPVLPATTIGSFPQT 463
                                       422114566788899************************************************************** PP

                         TIGR01371 438 kevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGs 514
                                        ++R +R+k+r g+i+e++Y+++++e i+ +i+ qe+lglDvLvhGe+eRnDmveyFge+l Gf +t+ngWvqsYG+
  lcl|FitnessBrowser__Miya:8501302 464 VDIRAQRRKLRTGQITEAQYDAAMREAIATAIREQEALGLDVLVHGEPERNDMVEYFGEQLRGFCITANGWVQSYGT 540
                                       ***************************************************************************** PP

                         TIGR01371 515 RcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeea 591
                                       RcvkPp++ygdv rp pmtv+++++aqslt+kpvkGmLtGPvti +WsfvR+D+pr  + +q+ala+rdev+dLe+a
  lcl|FitnessBrowser__Miya:8501302 541 RCVKPPLLYGDVARPGPMTVRWITHAQSLTQKPVKGMLTGPVTIACWSFVRDDVPRPVVFRQLALAIRDEVADLEAA 617
                                       ***************************************************************************** PP

                         TIGR01371 592 gikiiqiDepalReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasr 668
                                       gi +iqiDepalReglPlr++ +++Yld av aFrla+sgv+d+tqihthmCY++f++ii+++aaldaDvis+easr
  lcl|FitnessBrowser__Miya:8501302 618 GIGVIQIDEPALREGLPLRRAAHAAYLDAAVGAFRLASSGVRDATQIHTHMCYCDFHDIIDHVAALDADVISLEASR 694
                                       ***************************************************************************** PP

                         TIGR01371 669 sdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlv 745
                                       s melld +   ++y++e+G+GvyDihsprvPs +e+++ll++a ++lp +rlW nPDCGLktR+w+e++a+l +lv
  lcl|FitnessBrowser__Miya:8501302 695 SRMELLDVFAT-HAYPNEVGPGVYDIHSPRVPSIDEMETLLRAASRVLPLDRLWANPDCGLKTRDWPETRASLAHLV 770
                                       **********9.66*************************************************************** PP

                         TIGR01371 746 eaakelRe 753
                                       +aa ++Re
  lcl|FitnessBrowser__Miya:8501302 771 AAATRVRE 778
                                       ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (754 nodes)
Target sequences:                          1  (780 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: 0.11u 0.02s 00:00:00.13 Elapsed: 00:00:00.12
# Mc/sec: 4.89
//
[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