GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metE in Burkholderia phytofirmans PsJN

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate BPHYT_RS26655 BPHYT_RS26655 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase

Query= BRENDA::P25665
         (753 letters)



>FitnessBrowser__BFirm:BPHYT_RS26655
          Length = 764

 Score =  820 bits (2119), Expect = 0.0
 Identities = 428/752 (56%), Positives = 525/752 (69%), Gaps = 11/752 (1%)

Query: 6   HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
           H  GFPR+G +RELK AQES+W G S  + LL V RELRARHW  Q+ A +D + VGDFA
Sbjct: 5   HIPGFPRIGAQRELKFAQESFWRGESDEQYLLGVARELRARHWQLQQDAKLDFVTVGDFA 64

Query: 66  WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHY 125
           +YD +L  S LLG +P R      ++ +   + + RG A   +PA   EMTKWF+TNYHY
Sbjct: 65  YYDQMLNLSALLGALPQRFGFDAKTLSLARYYELARGNA--AQPAM--EMTKWFDTNYHY 120

Query: 126 MVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLN 185
           +VPE      F      L DE+DEALAL   VKPVL+GP+T+LWL K     FDRLSLL 
Sbjct: 121 LVPELGPQTTFDGGVEWLFDEIDEALALNLPVKPVLIGPITYLWLSKSHVAGFDRLSLLP 180

Query: 186 DILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDAL-QGQVKLLLTTYF 244
            ++  Y ++L +L +RGIEWVQ+DEPAL ++LP  WLDA+  AYD L    VK+LL TYF
Sbjct: 181 KLVIRYSRLLEKLKQRGIEWVQLDEPALCVDLPVEWLDAFSAAYDVLGTSGVKVLLATYF 240

Query: 245 EGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTEK 304
           E    +   +  LPV G+H+DLV     +      LP   +LSAG+I+GRN+WRADL E 
Sbjct: 241 ESAAEHAPRVAVLPVAGVHLDLVRAPQQLDAWRAALPKHAVLSAGVIDGRNIWRADLGEI 300

Query: 305 YAQIKDI---VGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLRD 361
           +  ++ +    G+R LWV+SSCSLLH P+ L  E +LDA++KSW AFA +K  E+A L  
Sbjct: 301 FESLQALHAEFGER-LWVSSSCSLLHVPVSLDAEQKLDADLKSWLAFATEKLGEVATLAL 359

Query: 362 ALN--SGDTAALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRA 419
           AL   +   A LA     + ARRHS+ V N  V+KR+AA+++  + R + +  R   QR 
Sbjct: 360 ALRDPAAAEATLAAADRALDARRHSSTVVNALVQKRVAAVSSAMADRQSPFAERNRLQRE 419

Query: 420 RFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDV 479
              LP  PTTTIGSFPQT  IR  R  +K+G L A +Y   +   I+ A+ +QE LGLDV
Sbjct: 420 ALGLPLLPTTTIGSFPQTPAIRQARAAYKRGELRALDYLQRMRAEIEIAVRKQEELGLDV 479

Query: 480 LVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKY 539
           LVHGEAERNDMVEYFGE L G+ FT+NGWVQSYGSRCVKPPI+ GD+ RP P+TVE  +Y
Sbjct: 480 LVHGEAERNDMVEYFGEQLWGYAFTENGWVQSYGSRCVKPPIIYGDVYRPEPMTVETTRY 539

Query: 540 AQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQID 599
           AQSLT + +KGMLTGPVT+L WSF R+D  R T A Q+ALA+RDEV DLE AGI IIQID
Sbjct: 540 AQSLTQRLMKGMLTGPVTMLQWSFVRDDQPRSTTALQLALAIRDEVVDLEKAGIRIIQID 599

Query: 600 EPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDA 659
           EPA REGLPLRR DW AYL+W    FRI+AA   D TQIHTHMCY EFNDI+ SIAA+DA
Sbjct: 600 EPAFREGLPLRRGDWAAYLEWATRVFRISAAGVADQTQIHTHMCYSEFNDILPSIAAMDA 659

Query: 660 DVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAER 719
           DVITIETSRS MELL+ F  F YPNEIGPGVYDIHSP VP  + ++ LL++A + IPAER
Sbjct: 660 DVITIETSRSAMELLDGFGAFAYPNEIGPGVYDIHSPRVPDAQAMQRLLERACEVIPAER 719

Query: 720 LWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
           LWVNPDCGLKTRGWPET AAL NMV+AA+ LR
Sbjct: 720 LWVNPDCGLKTRGWPETEAALTNMVRAAKALR 751


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: 1695
Number of extensions: 74
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: 764
Length adjustment: 40
Effective length of query: 713
Effective length of database: 724
Effective search space:   516212
Effective search space used:   516212
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 BPHYT_RS26655 BPHYT_RS26655 (5-methyltetrahydropteroyltriglutamate-- homocysteine 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.27340.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 1075.1   0.0          0 1074.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS26655  BPHYT_RS26655 5-methyltetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS26655  BPHYT_RS26655 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltra
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1074.9   0.0         0         0       2     754 .]       8     753 ..       7     753 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1074.9 bits;  conditional E-value: 0
                                TIGR01371   2 gfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllg 71 
                                              gfPrig++Relk+a+e++w+g+++++ ll va++lr+++++ q++a++d+++v+df++YD++L++++llg
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655   8 GFPRIGAQRELKFAQESFWRGESDEQYLLGVARELRARHWQLQQDAKLDFVTVGDFAYYDQMLNLSALLG 77 
                                              9********************************************************************* PP

                                TIGR01371  72 aiperfkeladdesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeefklsknklleeyke 141
                                              a+p+rf     ++ +l++y+++aRG++    +a+emtkwf+tnYhYlvPel ++++f    + l++e++e
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655  78 ALPQRFGFD-AKTLSLARYYELARGNAA--QPAMEMTKWFDTNYHYLVPELGPQTTFDGGVEWLFDEIDE 144
                                              *******98.55569**********966..89************************************** PP

                                TIGR01371 142 akelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldls 211
                                              a +l++ +kPvl+Gpit+l+L+k++    +++l+ll+kl+  Y+++l+kl+++g+ewvq+deP+l +dl+
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655 145 ALALNLPVKPVLIGPITYLWLSKSHV-AGFDRLSLLPKLVIRYSRLLEKLKQRGIEWVQLDEPALCVDLP 213
                                              ***********************996.88***************************************** PP

                                TIGR01371 212 keelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkv 281
                                               e+l+a+ +ay+ l    + +k+ll+tYf+s  e+   ++ lpv++++lDlv+a+++l++  a+++++ v
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655 214 VEWLDAFSAAYDVLGT--SGVKVLLATYFESAAEHAPRVAVLPVAGVHLDLVRAPQQLDAWRAALPKHAV 281
                                              **************97..79************************************************** PP

                                TIGR01371 282 LvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakekl 351
                                              L+aGvidGrniw+adl +++++l++l+a+ g++l+vs+scsllhvpv+l++e+kld++lk++lafa+ekl
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655 282 LSAGVIDGRNIWRADLGEIFESLQALHAEFGERLWVSSSCSLLHVPVSLDAEQKLDADLKSWLAFATEKL 351
                                              ********************************************************************** PP

                                TIGR01371 352 eelkvlkealegeaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekkl 421
                                               e+++l+ al++ aa++++l+a+++a+ ar++s++v ++ v++r++a+++++a r+s+f+eR++ q++ l
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655 352 GEVATLALALRDPAAAEATLAAADRALDARRHSSTVVNALVQKRVAAVSSAMADRQSPFAERNRLQREAL 421
                                              ************999999999999********************************************** PP

                                TIGR01371 422 nlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmv 491
                                               lPllPtttiGsfPqt  +R+aRa++++ge+ + +Y + +++ei+ +++ qeelglDvLvhGe+eRnDmv
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655 422 GLPLLPTTTIGSFPQTPAIRQARAAYKRGELRALDYLQRMRAEIEIAVRKQEELGLDVLVHGEAERNDMV 491
                                              ********************************************************************** PP

                                TIGR01371 492 eyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGPvtilnW 561
                                              eyFge+l G+aft+ngWvqsYGsRcvkPpiiygdv rp+pmtv+ ++yaqslt++ +kGmLtGPvt+l+W
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655 492 EYFGEQLWGYAFTENGWVQSYGSRCVKPPIIYGDVYRPEPMTVETTRYAQSLTQRLMKGMLTGPVTMLQW 561
                                              ********************************************************************** PP

                                TIGR01371 562 sfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwaveaFrlaasg 631
                                              sfvR+D+pr+++a q+ala+rdev+dLe+agi+iiqiDepa+ReglPlr+ d+++Yl+wa ++Fr++a+g
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655 562 SFVRDDQPRSTTALQLALAIRDEVVDLEKAGIRIIQIDEPAFREGLPLRRGDWAAYLEWATRVFRISAAG 631
                                              ********************************************************************** PP

                                TIGR01371 632 vkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprvPs 701
                                              v+d+tqihthmCYsefn+i+ +iaa+daDvi+ie+srs melld + + ++y++eiG+GvyDihsprvP 
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655 632 VADQTQIHTHMCYSEFNDILPSIAAMDADVITIETSRSAMELLDGFGA-FAYPNEIGPGVYDIHSPRVPD 700
                                              ************************************************.67******************* PP

                                TIGR01371 702 keelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
                                              ++ +++lle+a +++p+erlWvnPDCGLktR w+e++aal+n+v aak+lR+k
  lcl|FitnessBrowser__BFirm:BPHYT_RS26655 701 AQAMQRLLERACEVIPAERLWVNPDCGLKTRGWPETEAALTNMVRAAKALRAK 753
                                              ***************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (754 nodes)
Target sequences:                          1  (764 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 12.66
//
[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:

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