Aligments for a candidate for metE in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Aligments for a candidate for metE in Shewanella sp. ANA-3

Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate 7026327 Shewana3_3469 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase (RefSeq)

Query= BRENDA::P25665
         (753 letters)



>lcl|FitnessBrowser__ANA3:7026327 Shewana3_3469
           5-methyltetrahydropteroyltriglutamate-- homocysteine
           S-methyltransferase (RefSeq)
          Length = 756

 Score =  848 bits (2191), Expect = 0.0
 Identities = 427/752 (56%), Positives = 545/752 (72%), Gaps = 7/752 (0%)

Query: 6   HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
           ++LGFPR+G RRELK A E YW G ST+ EL  V +ELR  HW  Q  AGI+ +PVGDFA
Sbjct: 4   NSLGFPRIGRRRELKFALEKYWRGESTQAELHEVAKELRRTHWQWQVAAGIEQVPVGDFA 63

Query: 66  WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHY 125
           +YD VLT S  L  +P RH+  +G++D+DTLFR+ RGRAPTG  A A+EMTK+FNTNYHY
Sbjct: 64  FYDQVLTLSATLNAIPDRHRG-EGAIDLDTLFRVARGRAPTGTDAPASEMTKYFNTNYHY 122

Query: 126 MVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLN 185
           +VPE  + Q F + + Q  DEV EA ALG++ KPVLLGPV++L+L K  G+ FD+LSLL 
Sbjct: 123 LVPELKQDQVFSIAYEQFFDEVAEAQALGYQAKPVLLGPVSYLYLAKTVGQDFDKLSLLP 182

Query: 186 DILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-GQVKLLLTTYF 244
           ++L  Y  +LA  A +G+ WVQ++EP L LEL   W  A   AY AL+  QVK+LLT+Y+
Sbjct: 183 NLLKAYADILARFAAQGVTWVQLEEPILALELTHDWQAAISEAYQALKTAQVKILLTSYY 242

Query: 245 EGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRAD---L 301
             ++ +   ++ALPV GLH+DLV   + +A     L SD +LSAG++NGRNVW A+   +
Sbjct: 243 GSISHHQALVSALPVAGLHLDLVTAPEQLALFANALRSDQILSAGVVNGRNVWAAEVDLI 302

Query: 302 TEKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLRD 361
            E+   +   +G R LW+ +SCSLLHSP+DL VET L   ++   AFA QK  ELA +R 
Sbjct: 303 VERIGSVARDLGAR-LWIGTSCSLLHSPVDLEVETTLTPALRQQLAFAKQKLLELANVRQ 361

Query: 362 ALNSGDTAALAEWSAPIQARRHS-TRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRAR 420
            L + ++ A  E      ARR +  +  +  V  R+AA+T  D +R + +  R   Q+ +
Sbjct: 362 LLQAPESIAAKEIVNTCLARREAKAQAADAKVIARVAALTQADYERVSEFTERQAVQQRK 421

Query: 421 FKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVL 480
           ++LP  PTTTIGSFPQT  IR LR  ++KG L    Y   + +  +  I  Q +LG+DVL
Sbjct: 422 YRLPLLPTTTIGSFPQTPAIRGLRSRWRKGELSDAQYTEQLQQVTRDTIDRQLKLGIDVL 481

Query: 481 VHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYA 540
           VHGEAERNDMVEYFGE L+G  FT+NGWVQSYGSRCVKPP++ GD+SRP  +TV+WA++A
Sbjct: 482 VHGEAERNDMVEYFGEQLEGVGFTKNGWVQSYGSRCVKPPLIYGDVSRPKAMTVDWAEFA 541

Query: 541 QSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDE 600
           QSLTDKPVKGMLTGPVTIL WSF RED+SR+TIA Q+ALA+RDEV DL+ AGIGIIQIDE
Sbjct: 542 QSLTDKPVKGMLTGPVTILHWSFAREDISRDTIATQLALAIRDEVVDLQNAGIGIIQIDE 601

Query: 601 PALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDAD 660
           PA REGLPL++S+W AYL W V AF+++AA   D+TQIHTHMCY EFND + +IAA+DAD
Sbjct: 602 PAFREGLPLKQSEWQAYLDWAVNAFKLSAAGVVDETQIHTHMCYSEFNDTIAAIAAMDAD 661

Query: 661 VITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERL 720
           VITIETSRS MELL +FE+F+YPNEIGPGVYDIHSPN PSVE +  L++KAA+++P  +L
Sbjct: 662 VITIETSRSRMELLNAFEDFEYPNEIGPGVYDIHSPNTPSVEAMVHLIEKAAQKVPVRQL 721

Query: 721 WVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
           WVNPDCGLKTR W E   AL NMV A + LRR
Sbjct: 722 WVNPDCGLKTRTWDEVEPALKNMVDATRELRR 753


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: 1572
Number of extensions: 68
Number of successful extensions: 6
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: 756
Length adjustment: 40
Effective length of query: 713
Effective length of database: 716
Effective search space:   510508
Effective search space used:   510508
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 7026327 Shewana3_3469 (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.20812.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 1075.0   0.0          0 1074.8   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7026327  Shewana3_3469 5-methyltetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026327  Shewana3_3469 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1074.8   0.0         0         0       1     753 [.       6     753 ..       6     754 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1074.8 bits;  conditional E-value: 0
                         TIGR01371   1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaiperf 77 
                                       lgfPrig++Relk+alekyw+g+++++el++vak+lr+++++ q +ag++ +pv+df++YD+vL++++ l+aip+r+
  lcl|FitnessBrowser__ANA3:7026327   6 LGFPRIGRRRELKFALEKYWRGESTQAELHEVAKELRRTHWQWQVAAGIEQVPVGDFAFYDQVLTLSATLNAIPDRH 82 
                                       79*************************************************************************** PP

                         TIGR01371  78 keladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkPv 152
                                       +    +++dldt+F++aRG +   +d++a+emtk+fntnYhYlvPel++++ f+++ ++ ++e+ ea++lg ++kPv
  lcl|FitnessBrowser__ANA3:7026327  83 RGE--GAIDLDTLFRVARGRAPtgTDAPASEMTKYFNTNYHYLVPELKQDQVFSIAYEQFFDEVAEAQALGYQAKPV 157
                                       997..7889**********98777899************************************************** PP

                         TIGR01371 153 llGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeas 229
                                       llGp+++l+Lak++ ++++++l+ll++ll++Y ++l ++a++gv+wvq++eP+l+l+l+++++aa+ eay++l+   
  lcl|FitnessBrowser__ANA3:7026327 158 LLGPVSYLYLAKTV-GQDFDKLSLLPNLLKAYADILARFAAQGVTWVQLEEPILALELTHDWQAAISEAYQALKT-- 231
                                       **************.599*******************************************************97.. PP

                         TIGR01371 230 kelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkk 306
                                       +++k+ll++Y++s++++ + ++ lpv++l+lDlv+a+e+l+l ++++++d++L+aGv++Grn+w+a++  +++++ +
  lcl|FitnessBrowser__ANA3:7026327 232 AQVKILLTSYYGSISHHQALVSALPVAGLHLDLVTAPEQLALFANALRSDQILSAGVVNGRNVWAAEVDLIVERIGS 308
                                       69************99999999******************************************************* PP

                         TIGR01371 307 leakagdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg.eaavaealeaeaaaiaark 382
                                       +++  g++l++ tscsllh+pvdle e++l ++l++ lafak+kl el+ ++++l+  e+ +a+++ +  + +a+r+
  lcl|FitnessBrowser__ANA3:7026327 309 VARDLGARLWIGTSCSLLHSPVDLEVETTLTPALRQQLAFAKQKLLELANVRQLLQApESIAAKEIVN--TCLARRE 383
                                       ********************************************************955555555544..6899999 PP

                         TIGR01371 383 kskrvadekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYek 459
                                        ++++ad+kv +r++al++++ +r s+f+eR++ q++k++lPllPtttiGsfPqt  +R  R+++rkge+s+++Y++
  lcl|FitnessBrowser__ANA3:7026327 384 AKAQAADAKVIARVAALTQADYERVSEFTERQAVQQRKYRLPLLPTTTIGSFPQTPAIRGLRSRWRKGELSDAQYTE 460
                                       999************************************************************************** PP

                         TIGR01371 460 fikeeikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvke 536
                                        +++ ++++i+ q +lg+DvLvhGe+eRnDmveyFge+l+G  ft+ngWvqsYGsRcvkPp+iygdvsrpk+mtv++
  lcl|FitnessBrowser__ANA3:7026327 461 QLQQVTRDTIDRQLKLGIDVLVHGEAERNDMVEYFGEQLEGVGFTKNGWVQSYGSRCVKPPLIYGDVSRPKAMTVDW 537
                                       ***************************************************************************** PP

                         TIGR01371 537 skyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksd 613
                                        ++aqslt+kpvkGmLtGPvtil+Wsf ReD++r +ia+q+ala+rdev+dL++agi iiqiDepa+ReglPl++s+
  lcl|FitnessBrowser__ANA3:7026327 538 AEFAQSLTDKPVKGMLTGPVTILHWSFAREDISRDTIATQLALAIRDEVVDLQNAGIGIIQIDEPAFREGLPLKQSE 614
                                       ***************************************************************************** PP

                         TIGR01371 614 keeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlG 690
                                       +++Yldwav+aF+l+a+gv detqihthmCYsefn+ i+aiaa+daDvi+ie+srs mell+a+++ ++y++eiG+G
  lcl|FitnessBrowser__ANA3:7026327 615 WQAYLDWAVNAFKLSAAGVVDETQIHTHMCYSEFNDTIAAIAAMDADVITIETSRSRMELLNAFED-FEYPNEIGPG 690
                                       ******************************************************************.67******** PP

                         TIGR01371 691 vyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
                                       vyDihsp+ Ps+e + +l+eka +k+p ++lWvnPDCGLktR w+ev++alkn+v+a++elR 
  lcl|FitnessBrowser__ANA3:7026327 691 VYDIHSPNTPSVEAMVHLIEKAAQKVPVRQLWVNPDCGLKTRTWDEVEPALKNMVDATRELRR 753
                                       ************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (754 nodes)
Target sequences:                          1  (756 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 13.29
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, 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

GapMind for Amino acid biosynthesis