Alignments for a candidate for metH in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Denitrovibrio acetiphilus DSM 12809

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_013010175.1 DACET_RS04345 methionine synthase

Query= metacyc::G18NG-11090-MONOMER
         (1221 letters)



>NCBI__GCF_000025725.1:WP_013010175.1
          Length = 1116

 Score =  836 bits (2160), Expect = 0.0
 Identities = 489/1205 (40%), Positives = 713/1205 (59%), Gaps = 95/1205 (7%)

Query: 18   FLDALANHVLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFEAG 77
            F +   N +++ DGAMGT +Q +++  ++ +    GC+E LN   P++++QIH  YFEAG
Sbjct: 2    FNEFAKNRIILFDGAMGTSIQNYEI-TDEIWQGYNGCSEWLNVAAPEIIQQIHEQYFEAG 60

Query: 78   ADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGP 137
            AD+VETNTFG     +++YD+ DR  EL   G  +AR  AD+ G       ++  GS+GP
Sbjct: 61   ADVVETNTFGGTELVMSEYDLQDRTYELNLLGAQIARRAADKYG-------KYTAGSIGP 113

Query: 138  GTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELD 197
            GTKLPSLG   Y DL   Y   A  +++GG D F+IET QDLLQ+K+A++ V D  AE +
Sbjct: 114  GTKLPSLGQISYDDLYTMYHSQAEALLEGGVDLFIIETCQDLLQIKSALNAVIDVKAEKN 173

Query: 198  TFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHA 257
            +  P++  +TVE  GTMLMG++I AA+T L+   +  +GLNC+TGPD M   +  L+++ 
Sbjct: 174  SDAPVMVSITVEQNGTMLMGTDISAAVTLLREYPVFSLGLNCSTGPDLMHNPINDLAQNF 233

Query: 258  DIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVR 317
            +  +S +PNAGLP        Y +  + +A+ + G V E+ + ++GGCCGTTPEHI+A+R
Sbjct: 234  NGRISCIPNAGLPENRGGQMVYDMTPDKMAKIVEGMVQEFPIGVLGGCCGTTPEHIKALR 293

Query: 318  DAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNSN 377
                                P +  ++E   E S  SLY S  L Q    ++IGER N+N
Sbjct: 294  PIADKYK-------------PNKPQAKEYTGESS--SLYVSTTLMQTPPPALIGERANAN 338

Query: 378  GSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSSTL 437
            GSKAFRE +L+ D++  + +AK+Q   GAH +D CV Y GRD  ADMA    LL  + T 
Sbjct: 339  GSKAFRELLLAEDFDGMLAVAKEQEETGAHFIDACVAYAGRDEKADMAKFMHLLNKTLTA 398

Query: 438  PIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTID 497
            P++IDSTEP+V+ T L+   G+ ++NS+NFEDG     +   I++ VK+H A+V+ALTID
Sbjct: 399  PVVIDSTEPDVVETALKSCAGKPVINSINFEDGG---EKLHIILRAVKKHPASVIALTID 455

Query: 498  EEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEAI 557
            E+G A TAE K  IA+R+ +  T  YGL+  D++ D LTF I +G +      I+T +AI
Sbjct: 456  EDGMAMTAEKKFEIAERIYNIFTKEYGLNPNDLIFDPLTFSIGSGDKTLVDAAIQTNKAI 515

Query: 558  RELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNRI 617
            + +K+      T LGLSNISFGL+  +R +LNSVFL+E +E GLD AI H+SK++P   I
Sbjct: 516  KMIKEKLTGAKTALGLSNISFGLSKDSRPILNSVFLHEAVEHGLDMAIVHASKVMPQAAI 575

Query: 618  DDRQREVALDMVYDRRTEDYDPLQEFMQLF---EGVSAADAKDARAEQLAAMPLFERLAQ 674
             +   +V+ D++  +       L  F++ F   EG+        + E+   +P  E L  
Sbjct: 576  PEEDIKVSKDLLAGQE----GALSAFIEHFSKKEGI-------VQQEEKTDLPPDEMLKN 624

Query: 675  RIIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMK 734
             I  G K GLE+ L A M+   PI IIN  +L+ MK +GELFG+G+M LPFVLQSAETMK
Sbjct: 625  LIKKGRKAGLEETLTALMQTMKPIEIINNIMLDTMKEIGELFGAGKMLLPFVLQSAETMK 684

Query: 735  TAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLG 794
            TAV  LEPFME+       +  E +G+IV+ATVKGDVHDIGKNLVDIILSNNGY+V NLG
Sbjct: 685  TAVTVLEPFMEK-------SDTETRGRIVLATVKGDVHDIGKNLVDIILSNNGYEVYNLG 737

Query: 795  IKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTRT 854
            IK  +  M+  A E  AD IGMSGLLVKST +M+EN+ E+N  G S   V+LGGAALT  
Sbjct: 738  IKVSVEEMIAKAVEMDADAIGMSGLLVKSTNIMRENIAEINRQGLSK-KVLLGGAALTEK 796

Query: 855  YVENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKARN 914
            +V+ND   +  G V Y RDAF+ L+++        GE     +PE     K  A+     
Sbjct: 797  FVKNDCMPIMPGMVSYCRDAFDALKVLS-------GESEGSIAPE-----KTYAD----- 839

Query: 915  ERSRKIAAERKANAAPVIVPERSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERALF 974
                 I+A+ K   +P +         +TP  APPF+G +  +     + L  +++ ALF
Sbjct: 840  -----ISAKPKKVQSPKL---------ETP-PAPPFFGVKTAENYTADDILEYMNKLALF 884

Query: 975  MGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILDHVALVYGYFPAVAEGDD 1034
              +WG  S +      YE+L+     P     +  +K + +L+ + + Y YFP  ++G++
Sbjct: 885  SHRWGY-SKKNMPDYEYEELLTKTVIPEFNETVQEIKDKELLE-MGIRYAYFPCNSDGEE 942

Query: 1035 VVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLVTMGNPI 1094
            +++    +   +E  RF FPRQ     +C+AD+  P    V  G  DV+ F +VT G+  
Sbjct: 943  LIVY---NEDGSELTRFVFPRQNLENGVCLADYFHP----VSSGVKDVVAFHIVTAGSKP 995

Query: 1095 ADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFDPEDKTK 1154
            A++  +LF  NEY++Y + HG   +  EA+AEY H  +R++LK++        D +    
Sbjct: 996  AEYCQQLFKNNEYKKYYQFHGFFTEFAEAMAEYAHKMIRTDLKIDHA------DAKTAHG 1049

Query: 1155 FFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDAFVLYHP 1214
               L Y G R+SFGY SCPDL    +L  +L+  +IGV ++E  ++  E +T A ++++ 
Sbjct: 1050 IISLGYSGRRYSFGYPSCPDLAQNNQLDSILDFSQIGVSITENHEMVSEYTTCAIIIHNS 1109

Query: 1215 EAKYF 1219
             A+YF
Sbjct: 1110 SAEYF 1114


Lambda     K      H
   0.316    0.135    0.386 

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: 3033
Number of extensions: 128
Number of successful extensions: 13
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: 1221
Length of database: 1116
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1069
Effective search space:  1255006
Effective search space used:  1255006
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)

Align candidate WP_013010175.1 DACET_RS04345 (methionine synthase)
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))

# 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/TIGR02082.hmm
# target sequence database:        /tmp/gapView.1210627.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02082  [M=1182]
Accession:   TIGR02082
Description: metH: methionine synthase
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 1097.4  10.1          0 1090.1  10.1    2.0  1  NCBI__GCF_000025725.1:WP_013010175.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025725.1:WP_013010175.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1090.1  10.1         0         0       2    1181 ..       7    1115 ..       6    1116 .] 0.96

  Alignments for each domain:
  == domain 1  score: 1090.1 bits;  conditional E-value: 0
                             TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntF 72  
                                            ++ri+++DGamGt +q++++t++ ++g        ++G+ + Ln + Pe+i++ih++yfeaGaD+vetntF
  NCBI__GCF_000025725.1:WP_013010175.1    7 KNRIILFDGAMGTSIQNYEITDEIWQG--------YNGCSEWLNVAAPEIIQQIHEQYFEAGADVVETNTF 69  
                                            78**********************999........9*********************************** PP

                             TIGR02082   73 nsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvty 143 
                                            ++te+++++Ydl+d++yeln  +a++ar++ad+++      ++ aGs+GP++kl++l+         ++ y
  NCBI__GCF_000025725.1:WP_013010175.1   70 GGTELVMSEYDLQDRTYELNLLGAQIARRAADKYG------KYTAGSIGPGTKLPSLG---------QISY 125 
                                            ***********************************......7****************.........9*** PP

                             TIGR02082  144 delvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqt 214 
                                            d+l   Y+ q+++ll+GGvDl++iet++D+l++k+al+av +v +ek+++ P+++s ++v++ G++L+G++
  NCBI__GCF_000025725.1:WP_013010175.1  126 DDLYTMYHSQAEALLEGGVDLFIIETCQDLLQIKSALNAVIDVKAEKNSDAPVMVS-ITVEQNGTMLMGTD 195 
                                            ********************************************************.************** PP

                             TIGR02082  215 leaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg...eYdltpeelakal 282 
                                            + a+++ l+++++++lGLnC++G+d++++ ++ l+++ +  +s+iPnaGLP++ g    Yd tp+++ak++
  NCBI__GCF_000025725.1:WP_013010175.1  196 ISAAVTLLREYPVFSLGLNCSTGPDLMHNPINDLAQNFNGRISCIPNAGLPENRGgqmVYDMTPDKMAKIV 266 
                                            *****************************************************999999************ PP

                             TIGR02082  283 kefaeegllnivGGCCGttPehiraiaeavkdikprkrqe.leeksvlsglealkiaqessfvniGeRtnv 352 
                                            + +++e+ + ++GGCCGttPehi+a+  ++++ kp+k q+  ++   +s++ + ++ q      iGeR n+
  NCBI__GCF_000025725.1:WP_013010175.1  267 EGMVQEFPIGVLGGCCGTTPEHIKALRPIADKYKPNKPQAkEYTGESSSLYVSTTLMQTPPPALIGERANA 337 
                                            *************************************99845667788999******************** PP

                             TIGR02082  353 aGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDss 423 
                                            +Gsk fr+l+ aed++ +l +ak+q e Ga+ +D +v ++++D +adm k+++ll +   + + P+++Ds+
  NCBI__GCF_000025725.1:WP_013010175.1  338 NGSKAFRELLLAEDFDGMLAVAKEQEETGAHFIDACVAYAGRDEKADMAKFMHLLNKT--L-TAPVVIDST 405 
                                            *******************************************************998..5.99******* PP

                             TIGR02082  424 efevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykl 494 
                                            e +v+e+ Lk++ Gk ++nsi+++dG e+    ++ +k++ a+v+++++De+G+a ta+kk+eia+R+y++
  NCBI__GCF_000025725.1:WP_013010175.1  406 EPDVVETALKSCAGKPVINSINFEDGGEKLHIILRAVKKHPASVIALTIDEDGMAMTAEKKFEIAERIYNI 476 
                                            *********************************************************************** PP

                             TIGR02082  495 ltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRea 565 
                                             t+++g++p+d+ifDp++++i+ G       ai++ +ai+ ike+l  ak+++G+sn+sF+l   +  R +
  NCBI__GCF_000025725.1:WP_013010175.1  477 FTKEYGLNPNDLIFDPLTFSIGSGDKTLVDAAIQTNKAIKMIKEKLTGAKTALGLSNISFGLS--KDSRPI 545 
                                            ***************************************************************..999*** PP

                             TIGR02082  566 lhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskea 636 
                                            l+svFL+ea++ GlDm+iv+a+k+ + + i++e  +v +dl+  ++      L  ++e++ +++       
  NCBI__GCF_000025725.1:WP_013010175.1  546 LNSVFLHEAVEHGLDMAIVHASKVMPQAAIPEEDIKVSKDLLAGQE----GALSAFIEHFSKKEGI----V 608 
                                            *****************************************97765....5688888888777666....6 PP

                             TIGR02082  637 qeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvk 707 
                                            q++e  +lp +e L++ + kG + g+ee l + + ++ +p+eii++ +ld mk +G+LFG+Gkm LP+v++
  NCBI__GCF_000025725.1:WP_013010175.1  609 QQEEKTDLPPDEMLKNLIKKGRKAGLEETLTALM-QTMKPIEIINNIMLDTMKEIGELFGAGKMLLPFVLQ 678 
                                            78999************************99888.8899******************************** PP

                             TIGR02082  708 sarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekile 778 
                                            sa++mk av +LeP++ek++  ++++G+ivlatvkGDvhDiGkn+vd++Ls+ngyev +lG+kv ve+++ 
  NCBI__GCF_000025725.1:WP_013010175.1  679 SAETMKTAVTVLEPFMEKSD--TETRGRIVLATVKGDVHDIGKNLVDIILSNNGYEVYNLGIKVSVEEMIA 747 
                                            *****************998..8899********************************************* PP

                             TIGR02082  779 aakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdase 849 
                                            +a + +aD ig+sGL+vks++ m e++ e++r+g++  +llGGaal++++v++++ ++  g v y +da++
  NCBI__GCF_000025725.1:WP_013010175.1  748 KAVEMDADAIGMSGLLVKSTNIMRENIAEINRQGLSKKVLLGGAALTEKFVKNDCMPIMPGMVSYCRDAFD 818 
                                            *********************************************************************** PP

                             TIGR02082  850 avkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtk 920 
                                            a+kv++     +++ +   + +++y                  ++a+ k+v +++++   ++pap+f+G+k
  NCBI__GCF_000025725.1:WP_013010175.1  819 ALKVLS----GESEGSI--APEKTYA----------------DISAKPKKVQSPKLE---TPPAPPFFGVK 864 
                                            **9854....4431111..2222222................333333344455555...89********* PP

                             TIGR02082  921 vleas.ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGl 989 
                                            + e++  +++l+y+++ alF   W+  +k     + e+e+l+ + + ++ +e +++++ ++ll+    + +
  NCBI__GCF_000025725.1:WP_013010175.1  865 TAENYtADDILEYMNKLALFShRWGYSKKNM--PDYEYEELLTKTVIPEFNETVQEIKDKELLEMGIRYAY 933 
                                            *****99*************999**987765..68899********************************* PP

                             TIGR02082  990 fPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglga 1060
                                            fP++s g+++ +y++++            +++ ++rq+ ++ +claD++ + +sG kD++++ +vtag + 
  NCBI__GCF_000025725.1:WP_013010175.1  934 FPCNSDGEELIVYNEDGS---------ELTRFVFPRQNLENGVCLADYFHPVSSGVKDVVAFHIVTAGSKP 995 
                                            **************7766.........345689************************************** PP

                             TIGR02082 1061 eelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYp 1131
                                            +e+ ++l+++++++++ ++++    +aea+ae+ h+ +R +l+   + +++  + ++ + Y G r++fGYp
  NCBI__GCF_000025725.1:WP_013010175.1  996 AEYCQQLFKNNEYKKYYQFHGFFTEFAEAMAEYAHKMIRTDLKID-HADAKTAHGIISLGYSGRRYSFGYP 1065
                                            ********************************************9.99*********************** PP

                             TIGR02082 1132 acPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfa 1181
                                            +cPd+ ++ +l ++l+  +iG+ +te+ ++  e +++++++++ +a Yf+
  NCBI__GCF_000025725.1:WP_013010175.1 1066 SCPDLAQNNQLDSILDFSQIGVSITENHEMVSEYTTCAIIIHNSSAEYFT 1115
                                            *************************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1116 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: 0.09u 0.02s 00:00:00.11 Elapsed: 00:00:00.09
# Mc/sec: 14.07
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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