GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metE in Pseudomonas fluorescens GW456-L13

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate PfGW456L13_3767 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (EC 2.1.1.14)

Query= BRENDA::P25665
         (753 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767
           5-methyltetrahydropteroyltriglutamate-- homocysteine
           methyltransferase (EC 2.1.1.14)
          Length = 762

 Score =  917 bits (2371), Expect = 0.0
 Identities = 457/756 (60%), Positives = 562/756 (74%), Gaps = 10/756 (1%)

Query: 6   HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
           H+LGFPR+G  RELKKAQE++W G      L  VGR+LR  HWD QK+AGI+LLPVGDFA
Sbjct: 5   HSLGFPRIGRDRELKKAQEAFWKGELDEAGLRTVGRDLRKTHWDLQKKAGIELLPVGDFA 64

Query: 66  WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAA-AAEMTKWFNTNYH 124
           WYD VLT SL+ G +P R +  DG   + TLF + RG + +    A A EMTKWF+TNYH
Sbjct: 65  WYDQVLTHSLMFGVIPERFRPHDGKASLQTLFGMARGVSDSCCGGAHAQEMTKWFDTNYH 124

Query: 125 YMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLL 184
           Y+VPEF   QQF+L W QL +EV+EA ALGH VKPV++GP+T+LWLGK KG +FD+L LL
Sbjct: 125 YLVPEFSADQQFQLGWDQLFEEVEEARALGHNVKPVIIGPLTYLWLGKAKGVEFDKLELL 184

Query: 185 NDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQ-VKLLLTTY 243
           + +LP+Y Q+   LA +G+EWVQIDEP LVL+LPQ W +A++ AY+ +Q   +K L+ TY
Sbjct: 185 DRLLPLYGQIFQRLAAQGVEWVQIDEPILVLDLPQDWKNAFERAYNLIQRDPLKKLVATY 244

Query: 244 FEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTE 303
           F G+  NL     LPV GLH+DLV   +    +  RLP+  +LS GL+NGRNVWR DL  
Sbjct: 245 FGGLEENLGLAANLPVDGLHIDLVRAPEQYPTILDRLPAYKVLSLGLVNGRNVWRCDLEN 304

Query: 304 KYAQIK---DIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLR 360
             A ++   + +G R LWVA SCSLLHSP+DL  E +LDAE+KSW AFA+QKC E+A+L 
Sbjct: 305 ALATLQHAHERLGDR-LWVAPSCSLLHSPVDLGREDKLDAELKSWLAFAVQKCEEVAVLA 363

Query: 361 DALNSGDTAALAE---WSAPIQARRH-STRVHNPAVEKRLAAITAQDSQRANVYEVRAEA 416
            A+N  +   + E    S  +QA R  S R+H PAV+ R+AAIT +DSQR +++  R E 
Sbjct: 364 QAVNEPEAPKVLEALTQSRAVQASRAASPRIHKPAVQARVAAITVKDSQRHSLFARRIEK 423

Query: 417 QRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLG 476
           QRA   LP +PTTTIGSFPQT  IR  R  +K+G L    Y   +   I+ A+  QE LG
Sbjct: 424 QRAGLNLPLFPTTTIGSFPQTASIRLARQSYKQGKLTEAEYTEAMHSEIRHAVQVQENLG 483

Query: 477 LDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEW 536
           LDVLVHGEAERNDMVEYF E LDG+VFT+ GWVQSYGSRCVKP ++ GD+SRP  +TVEW
Sbjct: 484 LDVLVHGEAERNDMVEYFAEQLDGYVFTRFGWVQSYGSRCVKPAVIFGDLSRPKAMTVEW 543

Query: 537 AKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGII 596
            +YAQ LTDK +KGMLTGPVT+L WSFPREDV+RE  A+Q+ALA+RDEV DLEAAGI I+
Sbjct: 544 IRYAQGLTDKVMKGMLTGPVTMLMWSFPREDVTREVQARQLALAIRDEVVDLEAAGIKIV 603

Query: 597 QIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAA 656
           QIDE A REGLPLR++ W  YL W  E FR+ A+  +D+TQIHTHMCY EFND+++SIAA
Sbjct: 604 QIDEAAFREGLPLRQAQWQHYLDWATEVFRLCASGVRDETQIHTHMCYSEFNDVIESIAA 663

Query: 657 LDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIP 716
           +DADVITIETSRSDMELL++FE F YPNEIGPGVYDIHSP VP    +  LL+KAAKRIP
Sbjct: 664 MDADVITIETSRSDMELLDAFEAFAYPNEIGPGVYDIHSPRVPDSSEMANLLRKAAKRIP 723

Query: 717 AERLWVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
           A+RLWVNPDCGLKTRGWPET AAL +MV AA+ LR+
Sbjct: 724 ADRLWVNPDCGLKTRGWPETEAALVHMVNAARQLRK 759


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: 1720
Number of extensions: 70
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: 762
Length adjustment: 40
Effective length of query: 713
Effective length of database: 722
Effective search space:   514786
Effective search space used:   514786
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 PfGW456L13_3767 (5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (EC 2.1.1.14))
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.16664.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 1107.1   0.0          0 1107.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767  5-methyltetrahydropteroyltriglut


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767  5-methyltetrahydropteroyltriglutamate-- homocysteine methyltr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1107.0   0.0         0         0       1     754 []       7     760 ..       7     760 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1107.0 bits;  conditional E-value: 0
                                               TIGR01371   1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvn 55 
                                                             lgfPrig+ Relkka+e++wkg+++++ l +v +dlrk++++ qk+ag++++pv+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767   7 LGFPRIGRDRELKKAQEAFWKGELDEAGLRTVGRDLRKTHWDLQKKAGIELLPVG 61 
                                                             79***************************************************** PP

                                               TIGR01371  56 dfslYDhvLdtavllgaiperfkeladdesdldtyFaiaRGtek...kdvaalem 107
                                                             df++YD+vL+ ++++g+iperf+   d++++l+t+F +aRG ++    +++a+em
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767  62 DFAWYDQVLTHSLMFGVIPERFRPH-DGKASLQTLFGMARGVSDsccGGAHAQEM 115
                                                             ************************8.66679**********988888899***** PP

                                               TIGR01371 108 tkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkPvllGpitflkL 162
                                                             tkwf+tnYhYlvPe+s++++f+l +++l+ee++ea++lg+++kPv++Gp+t+l+L
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 116 TKWFDTNYHYLVPEFSADQQFQLGWDQLFEEVEEARALGHNVKPVIIGPLTYLWL 170
                                                             ******************************************************* PP

                                               TIGR01371 163 akakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaa 217
                                                             +kak + e+++lell++llp+Y +++++la++gvewvqideP+lvldl++++++a
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 171 GKAK-GVEFDKLELLDRLLPLYGQIFQRLAAQGVEWVQIDEPILVLDLPQDWKNA 224
                                                             **99.589*********************************************** PP

                                               TIGR01371 218 vkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelela 272
                                                             +++ay+ +++    lk l++tYf+ +ee+l  +++lpv++l++Dlv+a+e+  + 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 225 FERAYNLIQR--DPLKKLVATYFGGLEENLGLAANLPVDGLHIDLVRAPEQYPTI 277
                                                             *******997..5778899************************************ PP

                                               TIGR01371 273 kakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvp 327
                                                               ++++ kvL++G+++Grn+w+ dle++l++l++ +++ gd+l+v++scsllh+p
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 278 LDRLPAYKVLSLGLVNGRNVWRCDLENALATLQHAHERLGDRLWVAPSCSLLHSP 332
                                                             ******************************************************* PP

                                               TIGR01371 328 vdleleekldkelkellafakekleelkvlkealeg..eaavaealeaeaaaiaa 380
                                                             vdl +e+kld+elk++lafa++k+ee++vl++a+++    +v eal++++a  a+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 333 VDLGREDKLDAELKSWLAFAVQKCEEVAVLAQAVNEpeAPKVLEALTQSRAVQAS 387
                                                             ***********************************98444667788888888889 PP

                                               TIGR01371 381 rkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfP 435
                                                             r+ s+r+++ +v++r++a++ k+++r+s f++R e+q++ lnlPl+PtttiGsfP
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 388 RAASPRIHKPAVQARVAAITVKDSQRHSLFARRIEKQRAGLNLPLFPTTTIGSFP 442
                                                             99***************************************************** PP

                                               TIGR01371 436 qtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDm 490
                                                             qt+++R aR+++++g+++e+eY++++++ei++++++qe+lglDvLvhGe+eRnDm
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 443 QTASIRLARQSYKQGKLTEAEYTEAMHSEIRHAVQVQENLGLDVLVHGEAERNDM 497
                                                             ******************************************************* PP

                                               TIGR01371 491 veyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqslts 545
                                                             veyF+e+l+G++ft++gWvqsYGsRcvkP++i+gd+srpk+mtv++++yaq+lt+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 498 VEYFAEQLDGYVFTRFGWVQSYGSRCVKPAVIFGDLSRPKAMTVEWIRYAQGLTD 552
                                                             ******************************************************* PP

                                               TIGR01371 546 kpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDe 600
                                                             k +kGmLtGPvt+l Wsf+ReD+ r+ +a+q+ala+rdev+dLe+agiki+qiDe
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 553 KVMKGMLTGPVTMLMWSFPREDVTREVQARQLALAIRDEVVDLEAAGIKIVQIDE 607
                                                             ******************************************************* PP

                                               TIGR01371 601 palReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaia 655
                                                             +a+ReglPlr++++++Yldwa e+Frl asgv+detqihthmCYsefn++ie+ia
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 608 AAFREGLPLRQAQWQHYLDWATEVFRLCASGVRDETQIHTHMCYSEFNDVIESIA 662
                                                             ******************************************************* PP

                                               TIGR01371 656 aldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaelle 710
                                                             a+daDvi+ie+srsdmellda+++ ++y++eiG+GvyDihsprvP + e+a+ll+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 663 AMDADVITIETSRSDMELLDAFEA-FAYPNEIGPGVYDIHSPRVPDSSEMANLLR 716
                                                             ************************.67**************************** PP

                                               TIGR01371 711 kalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
                                                             ka k++p++rlWvnPDCGLktR w+e++aal ++v+aa++lR++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3767 717 KAAKRIPADRLWVNPDCGLKTRGWPETEAALVHMVNAARQLRKE 760
                                                             *****************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (754 nodes)
Target sequences:                          1  (762 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: 00:00:00.05
# Mc/sec: 9.61
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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