GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Magnetospirillum magneticum AMB-1

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_043743213.1 AMB_RS02225 methionine synthase

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



>NCBI__GCF_000009985.1:WP_043743213.1
          Length = 1157

 Score =  989 bits (2556), Expect = 0.0
 Identities = 573/1213 (47%), Positives = 757/1213 (62%), Gaps = 64/1213 (5%)

Query: 16   SEFLDALANHVLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFE 75
            +  LD L+ HVL+ DG  G  +Q  +L VEKDF  LE C EIL  +RPDV+R IH  YFE
Sbjct: 2    TNILDHLSRHVLLCDGGTGALVQAMNLSVEKDFQGLENCTEILVKSRPDVIRGIHARYFE 61

Query: 76   AGADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEM-GPGRNGMRRFVVGS 134
            AGAD+VE +TFG +   LA++ IA+R  EL      +A E A++  G GR    RFV+G+
Sbjct: 62   AGADMVEADTFGASPITLAEFGIAERAHELNQAAIELAWEAAEQFKGDGRT---RFVLGA 118

Query: 135  LGPGTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMA 194
            +GPGTKLPSLGH  Y +L   Y   A G I GG  AFL+ET QD LQ+KAAV+G + A A
Sbjct: 119  IGPGTKLPSLGHIGYDELEAAYVIQAAGQIAGGVSAFLVETCQDPLQIKAAVNGCKIANA 178

Query: 195  ELDTFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLS 254
               T +P+   VTVETTGT+L+G++I AA T +Q LG+ ++GLNCA GP EM EH ++L 
Sbjct: 179  AAGTDVPVFVQVTVETTGTLLVGADIAAAATVVQSLGVPLMGLNCAAGPQEMGEHFKWLI 238

Query: 255  KHADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIR 314
             +    VS+ PNAGLP L      YPL   +LA     FVS  G +++GGCCGTTP HI 
Sbjct: 239  DNWTGFVSIQPNAGLPELVDGQTRYPLLPAELAVWHERFVSA-GANLLGGCCGTTPPHIS 297

Query: 315  AVRDAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERT 374
            A  + +  +         K          R V    SVASLYT VPL QE     IGER 
Sbjct: 298  ATNEMLKRIGNGYRPNPVK----------RSVHWVPSVASLYTQVPLRQENAFLSIGERC 347

Query: 375  NSNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATS 434
            N+NGSK FR+   + DW+    IA++Q ++G+H LD+C  +VGR+  ADM  + + L  +
Sbjct: 348  NANGSKKFRDLQDAEDWDGITAIAREQVKEGSHTLDVCTAFVGRNEVADMTEVVSRLRGA 407

Query: 435  STLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVAL 494
             T P++IDSTE  V+  GL+  GG++I+NS+NFE+G+  +    R++ L ++ GAAVVAL
Sbjct: 408  VTTPLVIDSTELPVLEAGLKLYGGKAILNSINFENGE--KDAADRLV-LARKFGAAVVAL 464

Query: 495  TIDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETI 554
            TIDE+G A+ A  K+RIAKRL D     +GL   D++ D LTF I TG E+ R+  +ET+
Sbjct: 465  TIDEDGMAKDAAAKLRIAKRLYDFAVTKHGLPASDLLFDPLTFTICTGNEDDRKLAVETL 524

Query: 555  EAIRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPM 614
            +AI  + +  PE    LGLSN+SFGL PAARQVLNSVF++  I+ G+  AI H SKI+P+
Sbjct: 525  DAIEMITREMPECGIVLGLSNVSFGLKPAARQVLNSVFIDHAIKRGMTGAIVHVSKIVPL 584

Query: 615  NRIDDRQREVALDMVYDRRTEDYDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQ 674
            + + + + + A D++YDR   D   L  ++ LF    AA+ K  R  +       +RL Q
Sbjct: 585  HTLPEEEVKAAEDLIYDR---DPQALSRYIALFGDRKAAEIKKERPAKAE-----DRLKQ 636

Query: 675  RIIDGDKNGLEDDLEAGMKEK-SPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETM 733
            RIIDGD+ GLEDDL   M+E   P+ IIN  LL+GMK VGELFGSG+MQLPFVLQSAETM
Sbjct: 637  RIIDGDRTGLEDDLAQVMEEGWKPLDIINTLLLDGMKVVGELFGSGKMQLPFVLQSAETM 696

Query: 734  KTAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNL 793
            K +VA+LEP ME+       A  + K  +V+ATVKGDVHDIGKNLVDIIL+NNGY V+N+
Sbjct: 697  KASVAFLEPHMEK-------ADGQQKATMVLATVKGDVHDIGKNLVDIILTNNGYKVINI 749

Query: 794  GIKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTR 853
            GIKQP++ +++AA+EHKAD +GMSGLLVKSTV+M+ENLEEM NAG  + PV+LGGAALTR
Sbjct: 750  GIKQPVAEIIKAAKEHKADAVGMSGLLVKSTVIMRENLEEMTNAGL-DVPVLLGGAALTR 808

Query: 854  TYVENDLNEVY-TGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKA 912
             YVE D ++ Y +G V YARDAF+GL LM +V           +       A K A    
Sbjct: 809  KYVEEDCSKAYGSGRVAYARDAFDGLDLMAKV----------ADGSFDAHVAAKAASPHR 858

Query: 913  RNERSRKIAAERKANAAPV----IVPERSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNL 968
                SR +    +    PV    I   R+++  D P   PPFWG R+++  PL   +  L
Sbjct: 859  PGSPSRTLGEAAQPATRPVDWDEINLRRAELHKDVPAPVPPFWGARVIESAPLQNLIPFL 918

Query: 969  DERALFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILDHVALVYGYFPA 1028
            +E  L+   WG +  +G     ++     E RP     L R   E IL   A VYGY+ A
Sbjct: 919  NETMLYQFHWGYRK-QGKSIEEFKAWAHKEIRPVAMDMLKRCAKEEILRPQA-VYGYWKA 976

Query: 1029 VAEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLV 1088
             ++ D VV+    +    E  RF FPRQ +   LCIADF RP    V D   DV+  Q+V
Sbjct: 977  ASDNDSVVLF--AEDGTTEVARFPFPRQAKDGGLCIADFFRP----VSDPVRDVIGLQVV 1030

Query: 1089 TMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFD 1148
            TMG    + A + F A++Y++YL +HG+ V++ EA+AEY H R+RSEL     G  A+ D
Sbjct: 1031 TMGKRATEVAQDWFKADKYQDYLYLHGLSVEMAEAMAEYVHKRIRSEL-----GFAAE-D 1084

Query: 1149 PEDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDA 1208
              D  +    +YRG+RFSFGY +CP +ED+ +L+ LL   RIGV LSEE QL PEQST A
Sbjct: 1085 AADMDRLLKQNYRGSRFSFGYPACPRIEDQTQLLSLLGAERIGVTLSEEFQLEPEQSTSA 1144

Query: 1209 FVLYHPEAKYFNV 1221
             V  HP+AKYF+V
Sbjct: 1145 IVTVHPQAKYFSV 1157


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: 3167
Number of extensions: 142
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: 1157
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1110
Effective search space:  1303140
Effective search space used:  1303140
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: 59 (27.3 bits)

Align candidate WP_043743213.1 AMB_RS02225 (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.2888.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 1227.4   0.0          0 1227.3   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_043743213.1  AMB_RS02225 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043743213.1  AMB_RS02225 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1227.3   0.0         0         0       2    1182 .]       9    1157 .]       8    1157 .] 0.94

  Alignments for each domain:
  == domain 1  score: 1227.3 bits;  conditional E-value: 0
                                 TIGR02082    2 nkrilvlDGamGtqlqsanLt.eadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67  
                                                ++++l+ DG+ G  +q++nL  e+dF+g        l+ + ++L++++P+vi+ ih +yfeaGaD+v
  lcl|NCBI__GCF_000009985.1:WP_043743213.1    9 SRHVLLCDGGTGALVQAMNLSvEKDFQG--------LENCTEILVKSRPDVIRGIHARYFEAGADMV 67  
                                                789*****************8478****........8****************************** PP

                                 TIGR02082   68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134 
                                                e +tF++++i+la+++++++a+eln++a +la e+a++f+    + Rfv+G++GP++kl++l+    
  lcl|NCBI__GCF_000009985.1:WP_043743213.1   68 EADTFGASPITLAEFGIAERAHELNQAAIELAWEAAEQFK-GDGRTRFVLGAIGPGTKLPSLG---- 129 
                                                ****************************************.77889*****************.... PP

                                 TIGR02082  135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201 
                                                     ++ ydel +aY+ q+ g + GGv ++L+et++D l++kaa+++ + + +++g+++P++++ v
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  130 -----HIGYDELEAAYVIQAAGQIAGGVSAFLVETCQDPLQIKAAVNGCKIANAAAGTDVPVFVQ-V 190 
                                                .....************************************************************.* PP

                                 TIGR02082  202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268 
                                                +v+++G++L+G +++a+++ ++  ++ ++GLnCa G++e+ e+ k l  + + +vs+ PnaGLP+ +
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  191 TVETTGTLLVGADIAAAATVVQSLGVPLMGLNCAAGPQEMGEHFKWLIDNWTGFVSIQPNAGLPELV 257 
                                                ******************************************************************9 PP

                                 TIGR02082  269 g...eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdi......kprkrqeleek 326 
                                                     Y+l+p ela   + f+++g  n++GGCCGttP hi a  e+ k i      +p kr  +  +
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  258 DgqtRYPLLPAELAVWHERFVSAG-ANLLGGCCGTTPPHISATNEMLKRIgngyrpNPVKRSVHWVP 323 
                                                77889***************9876.6********************999844443335566669999 PP

                                 TIGR02082  327 svlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevl 393 
                                                sv+s+++++++ qe+ f+ iGeR+n++Gskkfr+l  aed++    ia++qv+eG++ lD++   v+
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  324 SVASLYTQVPLRQENAFLSIGERCNANGSKKFRDLQDAEDWDGITAIAREQVKEGSHTLDVCTAFVG 390 
                                                ******************************************************************* PP

                                 TIGR02082  394 lDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekakli 460 
                                                ++ +adm++++s+l +   + + Pl++Ds+e  vleaGLk  +Gkai+nsi++++Ge++ ++++ l+
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  391 RNEVADMTEVVSRLRGA--V-TTPLVIDSTELPVLEAGLKLYGGKAILNSINFENGEKDAADRLVLA 454 
                                                ****************9..6.99******************************************** PP

                                 TIGR02082  461 keyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryai 527 
                                                +++Gaavv++++De+G+a++a+ k++iakR+y+ ++ k g+p++d++fDp+++ti tG e++++ a+
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  455 RKFGAAVVALTIDEDGMAKDAAAKLRIAKRLYDFAVTKHGLPASDLLFDPLTFTICTGNEDDRKLAV 521 
                                                ******************************************************************* PP

                                 TIGR02082  528 dfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavydd 594 
                                                ++++ai+ i +e+P++ i +G+snvsF+l+  +a+R++l+svF+ +aik G+  +iv+ +k+ +++ 
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  522 ETLDAIEMITREMPECGIVLGLSNVSFGLK--PAARQVLNSVFIDHAIKRGMTGAIVHVSKIVPLHT 586 
                                                ******************************..*********************************** PP

                                 TIGR02082  595 idkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGereg 661 
                                                +++e  +++edli+dr+++a   L +++ l+ + k+++      ++ r  + e+RL++++++G r g
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  587 LPEEEVKAAEDLIYDRDPQA---LSRYIALFGDRKAAEI-----KKERPAKAEDRLKQRIIDGDRTG 645 
                                                ****************9986...7889999999888843.....466788899************** PP

                                 TIGR02082  662 ieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekeke 728 
                                                +e+dl + +++  +pl+ii++ LldGmkvvG+LFGsGkm+LP+v++sa++mk++va+LeP++ek + 
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  646 LEDDLAQVMEEGWKPLDIINTLLLDGMKVVGELFGSGKMQLPFVLQSAETMKASVAFLEPHMEKAD- 711 
                                                **************************************************************9988. PP

                                 TIGR02082  729 edkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLiv 795 
                                                  ++k ++vlatvkGDvhDiGkn+vd++L++ngy+v+++G+k+Pv++i++aak++kaD +g+sGL+v
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  712 -GQQKATMVLATVKGDVHDIGKNLVDIILTNNGYKVINIGIKQPVAEIIKAAKEHKADAVGMSGLLV 777 
                                                .78899************************************************************* PP

                                 TIGR02082  796 ksldemvevaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvkdaseavkvvdkllsek 861 
                                                ks++ m e++eem++ g+++P+llGGaal++++v+ ++ ++Y +g+v y++da++++ +++k+ +  
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  778 KSTVIMRENLEEMTNAGLDVPVLLGGAALTRKYVEEDCSKAYgSGRVAYARDAFDGLDLMAKVADGS 844 
                                                ******************************************7799****************99888 PP

                                 TIGR02082  862 kkaeelekikeeye...eirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas 925 
                                                  a+ ++k  + +      r+  +  +  ++ +     + +    ++++d+  p+p+f+G +v+e+ 
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  845 FDAHVAAKAASPHRpgsPSRTLGEAAQPATRPVD--WDEINLRRAELHKDVPAPVPPFWGARVIESA 909 
                                                6544444333322200022222222222233332..2333344455555999**************9 PP

                                 TIGR02082  926 .ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlf 990 
                                                 +++l++++++++l+  +W+ r++ +  + +e +    +++++ a ++l++  +e+ lr+++v+G++
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  910 pLQNLIPFLNETMLYQfHWGYRKQGK--SIEEFKAWAHKEIRPVAMDMLKRCAKEEILRPQAVYGYW 974 
                                                9**************99*****9987..66788899999**************************** PP

                                 TIGR02082  991 PaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtag 1057
                                                 a s +d +++++++++        t  +++ ++rq +d  lc+aDf+++ +   +D++g+++vt+g
  lcl|NCBI__GCF_000009985.1:WP_043743213.1  975 KAASDNDSVVLFAEDGT--------TEVARFPFPRQAKDGGLCIADFFRPVSDPVRDVIGLQVVTMG 1033
                                                *************8887........4455789*********************************** PP

                                 TIGR02082 1058 lgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGi 1124
                                                + a+e a+++++ ++++d++++++l++ +aea+ae++h+r+R el +  +e++ d++ llk++YrG+
  lcl|NCBI__GCF_000009985.1:WP_043743213.1 1034 KRATEVAQDWFKADKYQDYLYLHGLSVEMAEAMAEYVHKRIRSELGFA-AEDAADMDRLLKQNYRGS 1099
                                                *********************************************998.88999************* PP

                                 TIGR02082 1125 rpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                                r++fGYpacP  +++++ll+Ll aeriG++l+e+++l+Pe+s+s+++  hp+akYf+v
  lcl|NCBI__GCF_000009985.1:WP_043743213.1 1100 RFSFGYPACPRIEDQTQLLSLLGAERIGVTLSEEFQLEPEQSTSAIVTVHPQAKYFSV 1157
                                                ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1157 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.20
# Mc/sec: 6.57
//
[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