Alignments for a candidate for metE in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for metE in Desulfovibrio vulgaris Hildenborough

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate 208898 DVU3371 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase

Query= BRENDA::P25665
         (753 letters)



>MicrobesOnline__882:208898
          Length = 785

 Score =  746 bits (1926), Expect = 0.0
 Identities = 399/780 (51%), Positives = 506/780 (64%), Gaps = 37/780 (4%)

Query: 6   HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
           H LGFPR+G  RELKKA E YW G  +R  L      LRA HW  Q+ AGID++PVGDFA
Sbjct: 4   HNLGFPRIGAGRELKKAVEGYWKGRVSRHALEGEAARLRACHWAMQRDAGIDVVPVGDFA 63

Query: 66  WYDHVLTTSLLLGNVPARHQNKDGSV-------DIDTLFRIGRGRAPTGEPAAAAEMTKW 118
            YDH+L  +L+LG +P R      +        DID +FR+ RG A    P A  EMTKW
Sbjct: 64  LYDHMLDLTLMLGAIPPRFSPSGAAASPAGTGQDIDLMFRMARGEAGLS-PVAPLEMTKW 122

Query: 119 FNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGK-VKGEQ 177
           F+TNYHY+VPE      F    + L+ ++ EA   G   K VL GP+TWLWL + V G  
Sbjct: 123 FDTNYHYLVPELDADTAFAPDASPLVAQLREAQDAGFTPKAVLPGPLTWLWLARSVDGS- 181

Query: 178 FDRLSLLNDILPVYQQVLAELAK-------RGIE----WVQIDEPALVLELPQAWLDAYK 226
            DR +LL  +   Y  +L EL         RG       VQ+DEP L L+LPQ   D + 
Sbjct: 182 -DRFALLPALCDAYATLLRELTSACPPACPRGYSSGGLMVQLDEPVLALDLPQTVRDLFP 240

Query: 227 PAYDALQGQVK---LLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSD 283
             Y  L+  V    L++ +YF     NL     LPV  LH+DLV G+DD+    + L + 
Sbjct: 241 AVYTRLRAAVPDATLMVASYFAPCADNLPVALNLPVDVLHLDLVRGRDDLDAALQVLGAG 300

Query: 284 -----WLLSAGLINGRNVWRADLTEKYAQIK---DIVGKRDLWVASSCSLLHSPIDLSVE 335
                  LS G+++GRNVW AD+      ++   D +G+  +WVA SCSLLH P+DL  E
Sbjct: 301 EGTPGLALSLGVVDGRNVWCADIDAAVNLVRRAADSLGEDRVWVAPSCSLLHCPVDLGSE 360

Query: 336 TRLDAEVKSWFAFALQKCHELALLRDALNS---GDTAALAEWSAPIQARRH-STRVHNPA 391
             LD EV  W AFA QKC E+ L+ + +       TAA  E +  ++ +R  S R+H+PA
Sbjct: 361 RELDPEVARWLAFARQKCAEVRLVAEVVRGVYGPSTAASLEANREVRRQRAVSPRIHDPA 420

Query: 392 VEKRLAAITAQDSQRANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGN 451
           V  RLAA+T+    R + Y  R  AQRA   LP  PTTTIGSFPQT +IR  R   + G+
Sbjct: 421 VASRLAAVTSDMEHRTSPYAERIVAQRAALHLPTLPTTTIGSFPQTPDIRAARRALRDGS 480

Query: 452 LDANNYRTGIAEHIKQAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQS 511
           L  + Y   + + +   + EQE LGLDVLVHGE ERNDMVEYFG  L GF  T +GWVQS
Sbjct: 481 LTQDAYEAAMRDALAMMVREQEALGLDVLVHGEPERNDMVEYFGGLLQGFCITSDGWVQS 540

Query: 512 YGSRCVKPPIVIGDISRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRE 571
           YG+RCVKPP++ GD+SRP P+TV W+ YA+SLT +P+K MLTGPVTI CWSF R+D+SRE
Sbjct: 541 YGTRCVKPPLLYGDVSRPEPMTVAWSAYARSLTARPMKAMLTGPVTIACWSFVRDDISRE 600

Query: 572 TIAKQIALALRDEVADLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAV 631
           T+ +Q+ALALRDEVADLE+AG+ ++Q+DEPALREGLPLRR+  +AYL   V AFR+  + 
Sbjct: 601 TVLRQLALALRDEVADLESAGLAVVQVDEPALREGLPLRRAAQEAYLDAAVRAFRLATSG 660

Query: 632 AKDDTQIHTHMCYCEFNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVY 691
             D TQ+HTHMCYC+F+DI+D IA +DADVI++E SRS MELL+ F    YPNE+GPGVY
Sbjct: 661 VADATQLHTHMCYCDFHDIIDRIAGMDADVISLEASRSRMELLDVFATHGYPNEVGPGVY 720

Query: 692 DIHSPNVPSVEWIEALLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
           DIHSP VPSV+ +EALL +AA  +P +RLWVNPDCGLKTR WPETRAALANMV+AA+ +R
Sbjct: 721 DIHSPRVPSVDEMEALLLRAAAVLPVDRLWVNPDCGLKTREWPETRAALANMVEAARRVR 780


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: 1641
Number of extensions: 91
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: 753
Length of database: 785
Length adjustment: 41
Effective length of query: 712
Effective length of database: 744
Effective search space:   529728
Effective search space used:   529728
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 208898 DVU3371 (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.9711.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.3e-297  975.0   0.0   2.6e-297  974.8   0.0    1.0  1  lcl|MicrobesOnline__882:208898  DVU3371 5-methyltetrahydropteroy


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208898  DVU3371 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  974.8   0.0  2.6e-297  2.6e-297       1     753 [.       6     781 ..       6     782 .. 0.95

  Alignments for each domain:
  == domain 1  score: 974.8 bits;  conditional E-value: 2.6e-297
                       TIGR01371   1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaiperfke 79 
                                     lgfPrig+ Relkka+e+ywkg++s+++l+ +a+ lr+ +++ q++ag+dv+pv+df+lYDh+Ld++++lgaip rf+ 
  lcl|MicrobesOnline__882:208898   6 LGFPRIGAGRELKKAVEGYWKGRVSRHALEGEAARLRACHWAMQRDAGIDVVPVGDFALYDHMLDLTLMLGAIPPRFSP 84 
                                     79***************************************************************************98 PP

                       TIGR01371  80 laddesd......ldtyFaiaRGtek.kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkP 151
                                     +  ++s       +d +F++aRG++  + va lemtkwf+tnYhYlvPel+++++f+ +++ l+ +++ea+ +g   k 
  lcl|MicrobesOnline__882:208898  85 SGAAASPagtgqdIDLMFRMARGEAGlSPVAPLEMTKWFDTNYHYLVPELDADTAFAPDASPLVAQLREAQDAGFTPKA 163
                                     8655433444455**********988677999*********************************************** PP

                       TIGR01371 152 vllGpitflkLakakeeeekellellekllpvYkevlkklaea...........gvewvqidePvlvldlskeelaavk 219
                                     vl Gp+t+l+La++++   +++ +ll++l ++Y  +l++l++a           g  +vq+dePvl+ldl+++ ++++ 
  lcl|MicrobesOnline__882:208898 164 VLPGPLTWLWLARSVD--GSDRFALLPALCDAYATLLRELTSAcppacprgyssGGLMVQLDEPVLALDLPQTVRDLFP 240
                                     ***************8..56899*****************975333333322225679********************* PP

                       TIGR01371 220 eayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakee..lelakakfee...dkvLvaGvidGrniw 293
                                     ++y+ l+ a  +++l++++Yf  + ++l  +++lpv+ l+lDlv+++++  ++l++ +  e      L++Gv+dGrn+w
  lcl|MicrobesOnline__882:208898 241 AVYTRLRAAVPDATLMVASYFAPCADNLPVALNLPVDVLHLDLVRGRDDldAALQVLGAGEgtpGLALSLGVVDGRNVW 319
                                     **********************************************999553444444433111679************ PP

                       TIGR01371 294 kadlekslkllkkleakag.dklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg..eaavae 369
                                      ad+ ++++l+++ +++ g d+++v++scsllh pvdl  e++ld+e+ ++lafa++k++e+++++e+++g    ++a+
  lcl|MicrobesOnline__882:208898 320 CADIDAAVNLVRRAADSLGeDRVWVAPSCSLLHCPVDLGSERELDPEVARWLAFARQKCAEVRLVAEVVRGvyGPSTAA 398
                                     ****************9999***************************************************86678889 PP

                       TIGR01371 370 aleaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfr 448
                                     +lea+++  ++r+ s+r++d +v++rl+a+++++ +r+s+++eR  aq++ l+lP+lPtttiGsfPqt ++R aR+++r
  lcl|MicrobesOnline__882:208898 399 SLEANREVRRQRAVSPRIHDPAVASRLAAVTSDMEHRTSPYAERIVAQRAALHLPTLPTTTIGSFPQTPDIRAARRALR 477
                                     99999999999******************************************************************** PP

                       TIGR01371 449 kgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvs 527
                                      g++++++Ye+++++ ++ +++ qe+lglDvLvhGe+eRnDmveyFg  l+Gf +t+ gWvqsYG+RcvkPp++ygdvs
  lcl|MicrobesOnline__882:208898 478 DGSLTQDAYEAAMRDALAMMVREQEALGLDVLVHGEPERNDMVEYFGGLLQGFCITSDGWVQSYGTRCVKPPLLYGDVS 556
                                     ******************************************************************************* PP

                       TIGR01371 528 rpkpmtvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReg 606
                                     rp+pmtv++s+ya slt +p+k mLtGPvti +WsfvR+D++r+++ +q+alalrdev+dLe+ag++++q+DepalReg
  lcl|MicrobesOnline__882:208898 557 RPEPMTVAWSAYARSLTARPMKAMLTGPVTIACWSFVRDDISRETVLRQLALALRDEVADLESAGLAVVQVDEPALREG 635
                                     ******************************************************************************* PP

                       TIGR01371 607 lPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyek 685
                                     lPlr++ +e+Yld av+aFrla+sgv+d+tq+hthmCY++f++ii+ ia +daDvis+easrs melld +   ++y++
  lcl|MicrobesOnline__882:208898 636 LPLRRAAQEAYLDAAVRAFRLATSGVADATQLHTHMCYCDFHDIIDRIAGMDADVISLEASRSRMELLDVFAT-HGYPN 713
                                     ************************************************************************9.78*** PP

                       TIGR01371 686 eiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
                                     e+G+GvyDihsprvPs++e+++ll +a ++lp +rlWvnPDCGLktR+w+e++aal n+veaa+++R+
  lcl|MicrobesOnline__882:208898 714 EVGPGVYDIHSPRVPSVDEMEALLLRAAAVLPVDRLWVNPDCGLKTREWPETRAALANMVEAARRVRA 781
                                     ******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (754 nodes)
Target sequences:                          1  (785 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 0.02s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 7.71
//
[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