GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Sphingomonas indica Dd16

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_085217824.1 B9N75_RS05095 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_900177405.1:WP_085217824.1
          Length = 892

 Score =  996 bits (2576), Expect = 0.0
 Identities = 541/883 (61%), Positives = 646/883 (73%), Gaps = 30/883 (3%)

Query: 354  SLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAM 413
            S FVN+GERTNVTGSA FK+LI    Y++A++VARQQVENGAQ+IDINMDEG+LDAEAAM
Sbjct: 25   SSFVNIGERTNVTGSAAFKKLIMAGDYAKAVEVARQQVENGAQVIDINMDEGLLDAEAAM 84

Query: 414  VRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLL 473
              FL LIA EPDIARVP MIDSSKW VIE GLKC+ GK IVNSIS+KEG   F+ HA+  
Sbjct: 85   TTFLKLIAAEPDIARVPFMIDSSKWSVIEAGLKCVSGKPIVNSISLKEGEAEFLAHARKC 144

Query: 474  RRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIE 533
            R YGAAVVVMAFDE GQADT+ RK+EIC RAY +L  + GF PEDIIFDPNIFAVATGI+
Sbjct: 145  RNYGAAVVVMAFDETGQADTKERKVEICARAYDMLVAD-GFAPEDIIFDPNIFAVATGID 203

Query: 534  EHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMD 593
            EH  YA DFI AC  I+   PHA ISGG+SN+SFSFRGN+PVR A+H+VFLY+AI  G+D
Sbjct: 204  EHRRYALDFIEACRAIRIRCPHAHISGGLSNLSFSFRGNEPVRRAMHSVFLYHAIPAGLD 263

Query: 594  MGIVNAGQLAIYDDLPAELRDAVEDVILNRR----DDGTERLLELAEKYRGSKTDDTANA 649
            M IVNAGQL +YD + AELR+A EDVIL+R      D TERL+ LAEKY GS  D     
Sbjct: 264  MAIVNAGQLDVYDTIDAELREACEDVILDREPKDGGDATERLVALAEKYLGS--DPVREK 321

Query: 650  QQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFG 709
            + AEWR W V  RL ++LVKGI   + +DTEEARQ A RPI VIEGPLMDGMNVVGDLFG
Sbjct: 322  EAAEWRGWPVAARLSHALVKGIDAHVVEDTEEARQSAERPIHVIEGPLMDGMNVVGDLFG 381

Query: 710  EGKMFLPQVVKSARVMKQAVAYLEPFIEASKE-QGKTNGK--MVIATVKGDVHDIGKNIV 766
             GKMFLPQVVKSARVMK+AVA+L PFIEA KE  G T GK  +V+ATVKGDVHDIGKNIV
Sbjct: 382  SGKMFLPQVVKSARVMKKAVAHLIPFIEAEKEATGATAGKGRIVMATVKGDVHDIGKNIV 441

Query: 767  GVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGF 826
            GVVLQCN +EI+DLGVMV  + IL+ A +  AD+IGLSGLITPSLDEMV VA EM+R G 
Sbjct: 442  GVVLQCNGFEIIDLGVMVAWQDILQAANDNRADMIGLSGLITPSLDEMVTVADEMQRAGM 501

Query: 827  TIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKE 886
            T+PLLIGGATTS+ HTA+KI+  Y GP ++V +ASR VGV +AL+S+TQRD  V++T  +
Sbjct: 502  TMPLLIGGATTSRVHTALKIDPAYEGPVIHVLDASRAVGVASALVSETQRDPLVSKTAGD 561

Query: 887  YETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYI 945
            Y+ VR+     K +    TL  AR N   FD +   PP A   G+   +   ++ LR  I
Sbjct: 562  YDAVRVTRA-NKGQNELATLAEARANAQPFDPEGVAPPPAEP-GIHRFDDWPLDDLRQTI 619

Query: 946  DWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPAN 1005
            DWTPFF  W LAG YP IL+D VVG  A+ LF DA  MLD++ AEK +  RGV GL+   
Sbjct: 620  DWTPFFRAWELAGTYPAILDDAVVGESARNLFADAEAMLDRIVAEKWVTARGVAGLWRCR 679

Query: 1006 RVGDDIEIY--RDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFA 1062
            R GDDI +    DETR  +      LRQQ +K  G  N+ LADF+A       D++G FA
Sbjct: 680  RDGDDIMVLAGNDETRLPM------LRQQVKKREGRWNHSLADFIA----ADEDWMGGFA 729

Query: 1063 VTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSN 1122
            V     E  LA  F+A+ DDY+ I++KALADRLAEAFAE LH  VR   W YAP+E LSN
Sbjct: 730  VAIHGLEPHLA-RFKAETDDYSDILLKALADRLAEAFAERLHRHVRTTLWAYAPDEALSN 788

Query: 1123 EELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKH---TGMKLTESFAMWPGASVSG 1179
            +ELIRE Y+GIRPAPGYPACPEH+ K  ++++L  +      G+ LT SFAM P A+VSG
Sbjct: 789  DELIREKYRGIRPAPGYPACPEHSLKPILFDMLGGDGDAGPAGISLTSSFAMLPTAAVSG 848

Query: 1180 WYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222
            +YF+H D+ Y+ VA+I RDQ+EDYA R+G+   + ERWL PNL
Sbjct: 849  FYFAHRDASYFGVARIGRDQLEDYASRRGVDADQAERWLRPNL 891


Lambda     K      H
   0.318    0.134    0.391 

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: 2655
Number of extensions: 106
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1227
Length of database: 892
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 847
Effective search space:  1001154
Effective search space used:  1001154
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 (21.7 bits)
S2: 58 (26.9 bits)

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_085217823.1 B9N75_RS05090 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_900177405.1:WP_085217823.1
          Length = 348

 Score =  356 bits (914), Expect = e-102
 Identities = 181/345 (52%), Positives = 239/345 (69%), Gaps = 3/345 (0%)

Query: 6   EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65
           E L A   +RIL+ DG  GT IQ  +L EAD+ G        D KGNNDLL L++P+++ 
Sbjct: 5   ETLIAAAKDRILIKDGPFGTEIQKRKLKEADYAGS--LGLARDQKGNNDLLALTRPDIVQ 62

Query: 66  AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125
           AI + Y  AGADII TNTF++ +I+ ADY  E L  EIN A+A++AR  AD W A+   +
Sbjct: 63  AITDDYLAAGADIIATNTFSANSISQADYAAEHLVREINTASARIARTAADTWAAKDG-R 121

Query: 126 PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185
           PR+VAG +GPTN+T S+SPDVNDP +R I FD L A YRE T AL+ GGAD ILIET+FD
Sbjct: 122 PRFVAGAIGPTNKTLSLSPDVNDPGYREIDFDQLKAVYREQTDALLAGGADFILIETIFD 181

Query: 186 TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGL 245
           TLNAKA + A +   + LG ++P+MIS TITD +GR LSG T EAF+N++RHA  +T GL
Sbjct: 182 TLNAKAGIMAAREAADDLGRDVPLMISMTITDLAGRNLSGHTVEAFWNAVRHARPVTIGL 241

Query: 246 NCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLN 305
           NC+ G ++LR +VQ L++IA+  +  +PNAGLPN  GEYD      A  I  WA+ G +N
Sbjct: 242 NCSFGAEQLRPHVQALAQIADALLMVYPNAGLPNEIGEYDELPVETAALIGAWAEKGLVN 301

Query: 306 IVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNI 350
            VGGCCG++P HIAA+++AV  L  R +P+  V  RL+GLEP+ +
Sbjct: 302 AVGGCCGSSPAHIAAIAKAVAALPARAVPKPAVRTRLAGLEPMTL 346


Lambda     K      H
   0.318    0.134    0.391 

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: 944
Number of extensions: 34
Number of successful extensions: 3
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: 1227
Length of database: 348
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 310
Effective search space:   368590
Effective search space used:   368590
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_085217824.1 B9N75_RS05095 (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.147033.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 1115.0   0.0          0 1114.7   0.0    1.0  1  NCBI__GCF_900177405.1:WP_085217824.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217824.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1114.7   0.0         0         0     341    1182 .]      25     861 ..      17     861 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1114.7 bits;  conditional E-value: 0
                             TIGR02082  341 ssfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasep 411 
                                            ssfvniGeRtnv+Gs+ f+kli+a+dy +a+++a+qqve+Gaq++Din+De+llD+ea+m+++l+l+a+ep
  NCBI__GCF_900177405.1:WP_085217824.1   25 SSFVNIGERTNVTGSAAFKKLIMAGDYAKAVEVARQQVENGAQVIDINMDEGLLDAEAAMTTFLKLIAAEP 95  
                                            79********************************************************************* PP

                             TIGR02082  412 diakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartad 482 
                                            dia+vP m+Dss++ v+eaGLk++ Gk ivnsislk+Ge++Fl +a++ ++yGaavvvmafDe Gqa+t++
  NCBI__GCF_900177405.1:WP_085217824.1   96 DIARVPFMIDSSKWSVIEAGLKCVSGKPIVNSISLKEGEAEFLAHARKCRNYGAAVVVMAFDETGQADTKE 166 
                                            *********************************************************************** PP

                             TIGR02082  483 kkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvs 553 
                                            +k+ei+ Ray++l++  gf pediifDpni+++atGi+eh+rya+dfiea+r i+ + P+a+isgG+sn+s
  NCBI__GCF_900177405.1:WP_085217824.1  167 RKVEICARAYDMLVA-DGFAPEDIIFDPNIFAVATGIDEHRRYALDFIEACRAIRIRCPHAHISGGLSNLS 236 
                                            **************9.7****************************************************** PP

                             TIGR02082  554 FslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrr....reatekLle 620 
                                            Fs+rgn++vR+a+hsvFLy+ai aGlDm+ivnag+l+vyd id+elre++ed+ildr+     +ate+L+ 
  NCBI__GCF_900177405.1:WP_085217824.1  237 FSFRGNEPVRRAMHSVFLYHAIPAGLDMAIVNAGQLDVYDTIDAELREACEDVILDREpkdgGDATERLVA 307 
                                            **********************************************************7766689****** PP

                             TIGR02082  621 laelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvv 691 
                                            lae+y g      +e++ aewr++pv  RL++alvkG+  ++ ed+eear+ +++p+++iegpL+dGm+vv
  NCBI__GCF_900177405.1:WP_085217824.1  308 LAEKYLGSDPV--REKEAAEWRGWPVAARLSHALVKGIDAHVVEDTEEARQSAERPIHVIEGPLMDGMNVV 376 
                                            ******99998..66699***************************************************** PP

                             TIGR02082  692 GdLFGsGkmfLPqvvksarvmkkavayLePylekekeed...kskGkivlatvkGDvhDiGknivdvvLsc 759 
                                            GdLFGsGkmfLPqvvksarvmkkava+L+P++e+eke++     kG+iv+atvkGDvhDiGkniv+vvL+c
  NCBI__GCF_900177405.1:WP_085217824.1  377 GDLFGSGKMFLPQVVKSARVMKKAVAHLIPFIEAEKEATgatAGKGRIVMATVKGDVHDIGKNIVGVVLQC 447 
                                            ************************************99888799*************************** PP

                             TIGR02082  760 ngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahva 830 
                                            ng+e++dlGv+v  + il+aa++++aD+iglsGLi++sldemv+va em+r g+++Pll+GGa++s+ h+a
  NCBI__GCF_900177405.1:WP_085217824.1  448 NGFEIIDLGVMVAWQDILQAANDNRADMIGLSGLITPSLDEMVTVADEMQRAGMTMPLLIGGATTSRVHTA 518 
                                            *********************************************************************** PP

                             TIGR02082  831 vkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgek.keklialsekaarkev 900 
                                             ki+++Y+g+v++v das+av v+++l+se+++++ ++k+  +y+ +r +  +k +++l +l+e++a+ + 
  NCBI__GCF_900177405.1:WP_085217824.1  519 LKIDPAYEGPVIHVLDASRAVGVASALVSETQRDPLVSKTAGDYDAVRVTRANKgQNELATLAEARANAQP 589 
                                            ************************************************87655314555555555555555 PP

                             TIGR02082  901 faldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdake 970 
                                            f+++       p p   G++ +++  +++l++ iDw+++F +Wel+g+yp il+d ++g+ ar+lf+da++
  NCBI__GCF_900177405.1:WP_085217824.1  590 FDPE----GVAPPPAEPGIHRFDDWpLDDLRQTIDWTPFFRAWELAGTYPAILDDAVVGESARNLFADAEA 656 
                                            5444....457889999*******9********************************************** PP

                             TIGR02082  971 lldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfias 1040
                                            +ld+++aek ++argv Gl+ +++ gddi++++++      + +  +   ++q+++ ++r + +laDfia 
  NCBI__GCF_900177405.1:WP_085217824.1  657 MLDRIVAEKWVTARGVAGLWRCRRDGDDIMVLAGNDE----TRLPML---RQQVKKREGRwNHSLADFIAA 720 
                                            ********************************95544....333333...588888888889********9 PP

                             TIGR02082 1041 kesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenl 1111
                                                 +D++g ++v+ + g e    +++a++ddy+ il+kaladrlaea+ae lh++vR  lw+ya +e+l
  NCBI__GCF_900177405.1:WP_085217824.1  721 ----DEDWMGGFAVA-IHGLEPHLARFKAETDDYSDILLKALADRLAEAFAERLHRHVRTTLWAYAPDEAL 786 
                                            ....99*****9998.7778888889********************************************* PP

                             TIGR02082 1112 dkedllkerYrGirpafGYpacPdhtekatlleLleaer....iGlklteslalaPeasvsglyfahpeak 1178
                                            ++++l++e+YrGirpa+GYpacP+h+ k  l+++l  +      G+ lt s+a+ P+a+vsg+yfah +a 
  NCBI__GCF_900177405.1:WP_085217824.1  787 SNDELIREKYRGIRPAPGYPACPEHSLKPILFDMLGGDGdagpAGISLTSSFAMLPTAAVSGFYFAHRDAS 857 
                                            ***********************************6543224589************************** PP

                             TIGR02082 1179 Yfav 1182
                                            Yf v
  NCBI__GCF_900177405.1:WP_085217824.1  858 YFGV 861 
                                            **86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (892 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 41.01
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

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:

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