GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metE in Pseudomonas fluorescens FW300-N2C3

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate AO356_17740 AO356_17740 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase

Query= BRENDA::P25665
         (753 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17740
          Length = 770

 Score =  932 bits (2409), Expect = 0.0
 Identities = 473/764 (61%), Positives = 563/764 (73%), Gaps = 16/764 (2%)

Query: 4   LNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGD 63
           L HTLGFPR+G  RELKKA E+YW G+     L AVGRELRARHW  QK AGIDLLPVGD
Sbjct: 3   LAHTLGFPRIGADRELKKALEAYWKGDLAPAALQAVGRELRARHWQLQKDAGIDLLPVGD 62

Query: 64  FAWYDHVLTTSLLLGNVPARHQ---NKDGSVDIDTLFRIGRGR------APTGEPAAAAE 114
           FAWYD VL+ +L LG VP R     N  G   +DTLF + RG       A  G+   A E
Sbjct: 63  FAWYDQVLSHTLTLGAVPQRFHGTLNAQGRPTLDTLFAMARGATASCCGAEHGQAQYAQE 122

Query: 115 MTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVK 174
           +TKWF+TNYHY+VPEF   Q F L+W QL DEVDEA ALGH+VKPV++GP+T+LWLGK K
Sbjct: 123 LTKWFDTNYHYLVPEFSADQTFALSWEQLFDEVDEAHALGHQVKPVIIGPLTYLWLGKAK 182

Query: 175 GEQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ- 233
           GE FD+L LL  +LPVY ++L  L  +G+EWVQIDEP L L+LP AW  A++ AY  LQ 
Sbjct: 183 GEAFDKLGLLERLLPVYGEILNRLKAQGVEWVQIDEPILTLDLPLAWRSAFERAYHILQY 242

Query: 234 GQVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLING 293
             +K L+ TYF G+  NL    +LPV GLH+D V   + + ++  RLP+  +LS GL+NG
Sbjct: 243 SPLKKLVATYFSGLQDNLGLAVSLPVDGLHIDAVRDPEQLGQVLDRLPTYKILSVGLVNG 302

Query: 294 RNVWRADLTEKYAQIKDIVGK--RDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQ 351
           RNVWR +L +  AQ++    +   +LWV++SCSLLHSP+DL  E RLD E+KSW AFA+Q
Sbjct: 303 RNVWRCELEQALAQLQAAQERFGDNLWVSTSCSLLHSPVDLEREDRLDPELKSWLAFAVQ 362

Query: 352 KCHELALLRDALNSGDTAALAEW---SAPIQARRH-STRVHNPAVEKRLAAITAQDSQRA 407
           KC E+A+LRDALN     A+ +    S  +QARR  S R+H   V+ RLAAI  QDSQR 
Sbjct: 363 KCGEVAVLRDALNDPQAPAVLQALSDSREVQARRAGSARIHKAEVQARLAAIGPQDSQRH 422

Query: 408 NVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQ 467
           + +  R E QRAR  LPA+PTTTIGSFPQT  IR  R  +K+G L AN+Y+  +   I+ 
Sbjct: 423 SPFAQRIERQRARLALPAFPTTTIGSFPQTPAIRLARQAYKQGKLSANDYQDAMHTEIRH 482

Query: 468 AIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDIS 527
           A+  QERLGLDVLVHGEAERNDMVEYF E LDG+ FT+ GWVQSYGSRCVKP I+ GDIS
Sbjct: 483 AVQIQERLGLDVLVHGEAERNDMVEYFAEQLDGYAFTRFGWVQSYGSRCVKPAIIYGDIS 542

Query: 528 RPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVAD 587
           RP  +TV+W +YAQSLTDK +KGMLTGPVT+L WSFPREDVSR+  A+Q+ALALRDEV D
Sbjct: 543 RPKAMTVDWIRYAQSLTDKVMKGMLTGPVTMLMWSFPREDVSRQVQARQLALALRDEVLD 602

Query: 588 LEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEF 647
           LE AGI I+QIDE A REGLPLRR  W  YL W VEAFR+ A+   DDTQIHTHMCY EF
Sbjct: 603 LEKAGIRIVQIDEAAFREGLPLRRGQWQHYLDWAVEAFRLCASGVGDDTQIHTHMCYSEF 662

Query: 648 NDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEAL 707
           ND++ +IA +DADVITIETSRSDMELLE+FE FDYPN+IGPGVYDIHSP VP    + AL
Sbjct: 663 NDVIKAIADMDADVITIETSRSDMELLEAFEAFDYPNDIGPGVYDIHSPRVPDTAEMVAL 722

Query: 708 LKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
           + KA KRI AERLW+NPDCGLKTRGWPET AAL NMV AA+ LR
Sbjct: 723 MSKAVKRIAAERLWINPDCGLKTRGWPETEAALVNMVAAARQLR 766


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: 1709
Number of extensions: 75
Number of successful extensions: 7
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: 770
Length adjustment: 40
Effective length of query: 713
Effective length of database: 730
Effective search space:   520490
Effective search space used:   520490
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 AO356_17740 AO356_17740 (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.13850.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 1090.3   0.0          0 1090.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740  AO356_17740 5-methyltetrahydropt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740  AO356_17740 5-methyltetrahydropteroyltriglutamate-- homocysteine meth
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1090.1   0.0         0         0       1     753 [.       7     767 ..       7     768 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1090.1 bits;  conditional E-value: 0
                                       TIGR01371   1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhv 63 
                                                     lgfPrig+ Relkkale+ywkg++  ++l++v ++lr+++++ qk+ag+d++pv+df++YD+v
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740   7 LGFPRIGADRELKKALEAYWKGDLAPAALQAVGRELRARHWQLQKDAGIDLLPVGDFAWYDQV 69 
                                                     79************************************************************* PP

                                       TIGR01371  64 Ldtavllgaiperfkel..addesdldtyFaiaRGtek........kdvaalemtkwfntnYh 116
                                                     L  ++ lga+p+rf+ +  a+++ +ldt+Fa+aRG +         +   a+e+tkwf+tnYh
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740  70 LSHTLTLGAVPQRFHGTlnAQGRPTLDTLFAMARGATAsccgaehgQAQYAQELTKWFDTNYH 132
                                                     **************98722345567**********9889****9988889************* PP

                                       TIGR01371 117 YlvPelskeeefklsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellek 179
                                                     YlvPe+s++++f+ls+++l++e++ea++lg+++kPv++Gp+t+l+L+kak +e +++l lle+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 133 YLVPEFSADQTFALSWEQLFDEVDEAHALGHQVKPVIIGPLTYLWLGKAK-GEAFDKLGLLER 194
                                                     *************************************************9.588********* PP

                                       TIGR01371 180 llpvYkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfds 242
                                                     llpvY e+l++l+++gvewvqideP+l ldl+ ++++a+++ay+ l+   + lk l++tYf  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 195 LLPVYGEILNRLKAQGVEWVQIDEPILTLDLPLAWRSAFERAYHILQY--SPLKKLVATYFSG 255
                                                     **********************************************96..6778899****** PP

                                       TIGR01371 243 veealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllk 305
                                                     ++++l  +vslpv++l++D v+++e+l ++  ++++ k+L++G+++Grn+w+ +le++l++l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 256 LQDNLGLAVSLPVDGLHIDAVRDPEQLGQVLDRLPTYKILSVGLVNGRNVWRCELEQALAQLQ 318
                                                     *************************************************************** PP

                                       TIGR01371 306 kleakagdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg.ea.a 366
                                                     + +++ gd+l+vstscsllh+pvdle+e++ld+elk++lafa++k+ e++vl++al++ +a a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 319 AAQERFGDNLWVSTSCSLLHSPVDLEREDRLDPELKSWLAFAVQKCGEVAVLRDALNDpQApA 381
                                                     **********************************************************85514 PP

                                       TIGR01371 367 vaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtt 429
                                                     v +al+++++  a+r+ s+r+++++v++rl+a+  ++++r+s+f++R e q+++l lP++Ptt
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 382 VLQALSDSREVQARRAGSARIHKAEVQARLAAIGPQDSQRHSPFAQRIERQRARLALPAFPTT 444
                                                     5566666655666677899******************************************** PP

                                       TIGR01371 430 tiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvhGefeRnDmve 492
                                                     tiGsfPqt  +R aR+++++g++s+++Y++++++ei++++++qe+lglDvLvhGe+eRnDmve
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 445 TIGSFPQTPAIRLARQAYKQGKLSANDYQDAMHTEIRHAVQIQERLGLDVLVHGEAERNDMVE 507
                                                     *************************************************************** PP

                                       TIGR01371 493 yFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGmLtGP 555
                                                     yF+e+l+G+aft++gWvqsYGsRcvkP+iiygd+srpk+mtv++++yaqslt+k +kGmLtGP
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 508 YFAEQLDGYAFTRFGWVQSYGSRCVKPAIIYGDISRPKAMTVDWIRYAQSLTDKVMKGMLTGP 570
                                                     *************************************************************** PP

                                       TIGR01371 556 vtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYl 618
                                                     vt+l Wsf+ReD++r+ +a+q+alalrdev dLe+agi+i+qiDe+a+ReglPlr+ ++++Yl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 571 VTMLMWSFPREDVSRQVQARQLALALRDEVLDLEKAGIRIVQIDEAAFREGLPLRRGQWQHYL 633
                                                     *************************************************************** PP

                                       TIGR01371 619 dwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeik 681
                                                     dwaveaFrl asgv d+tqihthmCYsefn++i+aia++daDvi+ie+srsdmell+a+++ +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 634 DWAVEAFRLCASGVGDDTQIHTHMCYSEFNDVIKAIADMDADVITIETSRSDMELLEAFEA-F 695
                                                     *************************************************************.7 PP

                                       TIGR01371 682 kyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknl 744
                                                     +y+++iG+GvyDihsprvP + e+ +l++ka+k++++erlW+nPDCGLktR w+e++aal n+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 696 DYPNDIGPGVYDIHSPRVPDTAEMVALMSKAVKRIAAERLWINPDCGLKTRGWPETEAALVNM 758
                                                     7************************************************************** PP

                                       TIGR01371 745 veaakelRe 753
                                                     v+aa++lR+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17740 759 VAAARQLRS 767
                                                     *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (754 nodes)
Target sequences:                          1  (770 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 8.21
//
[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