Alignments for a candidate for metH in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Sphingomonas wittichii RW1

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_041379258.1 SWIT_RS12140 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000016765.1:WP_041379258.1
          Length = 869

 Score = 1020 bits (2637), Expect = 0.0
 Identities = 541/874 (61%), Positives = 647/874 (74%), Gaps = 21/874 (2%)

Query: 356  FVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVR 415
            FVN+GERTNVTGSA FK+LI    Y++A++VARQQVENGAQI+D+NMDEG+LDAE AM  
Sbjct: 9    FVNIGERTNVTGSAAFKKLIMGGDYAKAVEVARQQVENGAQIVDVNMDEGLLDAELAMTT 68

Query: 416  FLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRR 475
            FL LIA EPDIARVP+MIDSSKW VIE GLKC+ GK IVNSISMKEG +AF+  A+  R 
Sbjct: 69   FLKLIAAEPDIARVPVMIDSSKWSVIEAGLKCVSGKPIVNSISMKEGEEAFLAQARKCRA 128

Query: 476  YGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEH 535
            YGAAVVVMAFDE GQADT+ RK++IC RAYK+L  + GF PEDIIFDPNIFAVATGI+EH
Sbjct: 129  YGAAVVVMAFDEVGQADTKQRKVDICERAYKLLVGD-GFAPEDIIFDPNIFAVATGIDEH 187

Query: 536  NNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMG 595
              YA DFI A  +IK+  PH  ISGGVSN+SFSFRGN+PVR A+H+VFLY+AI+ GMDMG
Sbjct: 188  RRYAIDFIEATAEIKKRCPHCHISGGVSNLSFSFRGNEPVRRAMHSVFLYHAIQAGMDMG 247

Query: 596  IVNAGQLAIYDDLPAELRDAVEDVILNRR----DDGTERLLELAEKYRGSKTDDTANAQQ 651
            IVNAGQL +YD +   LR+A EDVI +RR     D TERL+ELAE ++G   D  A    
Sbjct: 248  IVNAGQLDVYDAIDPVLREACEDVIWDRRPKNGGDATERLIELAESFKGK--DAAAEKAA 305

Query: 652  AEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEG 711
             EWR W+V KRLE++LVKGI   +  DTEEARQ   RPIEVIEGPLMDGMNVVGDLFG G
Sbjct: 306  EEWRGWDVAKRLEHALVKGIDAHVVDDTEEARQHFARPIEVIEGPLMDGMNVVGDLFGSG 365

Query: 712  KMFLPQVVKSARVMKQAVAYLEPFIEASKEQG-KTNGKMVIATVKGDVHDIGKNIVGVVL 770
            KMFLPQVVKSARVMK+AVAYL P+IEA K QG ++ G++V+ATVKGDVHDIGKNIVGVVL
Sbjct: 366  KMFLPQVVKSARVMKKAVAYLLPYIEAGKVQGERSKGRIVMATVKGDVHDIGKNIVGVVL 425

Query: 771  QCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPL 830
            QCN YE++DLGVMVP   ILR A E +AD+IGLSGLITPSLDEMV VA EM+R    +PL
Sbjct: 426  QCNGYEVIDLGVMVPWTDILRAANENDADIIGLSGLITPSLDEMVTVATEMDRAKMQLPL 485

Query: 831  LIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETV 890
            +IGGATTSK HTA++I   Y+GP ++V +ASR VGV + LLSDTQRDDFVA+T  +YE V
Sbjct: 486  MIGGATTSKVHTALRIAPAYAGPVIHVLDASRAVGVASTLLSDTQRDDFVAKTAADYEAV 545

Query: 891  RIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQE-VEASIETLRNYIDWTP 949
            R +    K +    T+E AR N F  D+ A  P    + G     +  +E LR  IDWTP
Sbjct: 546  R-KAREGKGQNELATIEEARANAFVADF-ALKPDAPKQPGTHVFTDWPLEDLREIIDWTP 603

Query: 950  FFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGD 1009
            FF  W LAG YP IL+D VVG  A+ LF DA  MLD++ AEK L  +GV  L+PA+  GD
Sbjct: 604  FFRAWELAGNYPAILDDAVVGESARGLFADAQKMLDQIIAEKWLTAKGVAALWPAHADGD 663

Query: 1010 DIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLE 1068
            D+ +  D     +      LRQQ +K  G AN CLADFVAP      D++G FAV G   
Sbjct: 664  DVIVRADSGEVRL----PFLRQQIKKREGRANMCLADFVAP----ADDWLGGFAV-GIHG 714

Query: 1069 EDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRE 1128
             D     F+A HDDY  I++KALADRLAEAFAE LH  VR   WGYA  E L+NE LI+E
Sbjct: 715  IDPHIARFKADHDDYRDILLKALADRLAEAFAERLHLHVRTTLWGYAEGEQLTNEALIKE 774

Query: 1129 NYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSK 1188
             Y+GIRPAPGYPACP+H++K  +++LL+    TG+ LTESFAM P A+VSG+YF HP++ 
Sbjct: 775  QYRGIRPAPGYPACPDHSQKPILFDLLKAGDATGITLTESFAMLPTAAVSGFYFGHPEAS 834

Query: 1189 YYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222
            Y+ VA+I RDQ+EDYA R+ + +   ERWL PNL
Sbjct: 835  YFGVARIGRDQLEDYAARRAIDLATAERWLRPNL 868


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: 2592
Number of extensions: 110
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 1
Length of query: 1227
Length of database: 869
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 824
Effective search space:   973968
Effective search space used:   973968
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: 57 (26.6 bits)

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012048616.1 SWIT_RS12145 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000016765.1:WP_012048616.1
          Length = 353

 Score =  366 bits (939), Expect = e-105
 Identities = 188/340 (55%), Positives = 238/340 (70%), Gaps = 3/340 (0%)

Query: 9   RAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIH 68
           R Q  +RIL+ DG  GTMIQSY+L EAD+RG    + P D KGNNDLLVL++P+VI AI 
Sbjct: 13  RDQAKQRILLTDGAFGTMIQSYKLQEADYRGSY--ELPSDQKGNNDLLVLTRPDVIDAIT 70

Query: 69  NAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRY 128
             Y +AG+DI+ TNTFN+  I+  DY    L  EIN AAA++AR  AD++ AR   +PR+
Sbjct: 71  RQYLDAGSDIVSTNTFNANIISQEDYDAVHLVREINLAAARIARTAADDYAARDG-RPRF 129

Query: 129 VAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLN 188
           VAG +GPTN+T S+SPDVNDP +R + FD +   Y++ T AL++GG D ILIET+FDTLN
Sbjct: 130 VAGAIGPTNKTLSLSPDVNDPGYRAVDFDTMRDVYQDQTAALLDGGCDFILIETIFDTLN 189

Query: 189 AKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCA 248
           AKAA+ AV  E    GVE+P+MIS TITD SGR LSG + EAF++++RHA  LT GLNCA
Sbjct: 190 AKAAIMAVLDEQAKRGVEIPMMISMTITDMSGRNLSGHSVEAFWHAVRHAHPLTIGLNCA 249

Query: 249 LGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVG 308
            G D LR +VQ LS +A+  V  +PNAGLPN  G+YD    T    IR+WA  G +NIVG
Sbjct: 250 FGADLLRPHVQVLSGLADALVMIYPNAGLPNDLGQYDEQPATTGGFIRDWADQGLVNIVG 309

Query: 309 GCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPL 348
           GCCG+TP HIAAM+ AV G   R L       RL+GL+P+
Sbjct: 310 GCCGSTPAHIAAMADAVAGKPARALHAHDHRTRLAGLDPM 349


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: 1016
Number of extensions: 33
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: 353
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 315
Effective search space:   374535
Effective search space used:   374535
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_041379258.1 SWIT_RS12140 (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.25822.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 1159.2   0.0          0 1159.0   0.0    1.0  1  lcl|NCBI__GCF_000016765.1:WP_041379258.1  SWIT_RS12140 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_041379258.1  SWIT_RS12140 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1159.0   0.0         0         0     336    1182 .]       2     838 ..       1     838 [. 0.97

  Alignments for each domain:
  == domain 1  score: 1159.0 bits;  conditional E-value: 0
                                 TIGR02082  336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402 
                                                + a  ++fvniGeRtnv+Gs+ f+kli+ +dy +a+++a+qqve+Gaqi+D+n+De+llD+e +m++
  lcl|NCBI__GCF_000016765.1:WP_041379258.1    2 TTASTTQFVNIGERTNVTGSAAFKKLIMGGDYAKAVEVARQQVENGAQIVDVNMDEGLLDAELAMTT 68  
                                                567889************************************************************* PP

                                 TIGR02082  403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469 
                                                +l+l+a+epdia+vP+m+Dss++ v+eaGLk++ Gk ivnsis+k+Gee+Fl +a++ + yGaavvv
  lcl|NCBI__GCF_000016765.1:WP_041379258.1   69 FLKLIAAEPDIARVPVMIDSSKWSVIEAGLKCVSGKPIVNSISMKEGEEAFLAQARKCRAYGAAVVV 135 
                                                ******************************************************************* PP

                                 TIGR02082  470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536 
                                                mafDe Gqa+t+++k++i++Raykll+   gf pediifDpni+++atGi+eh+ryaidfiea+ ei
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  136 MAFDEVGQADTKQRKVDICERAYKLLVG-DGFAPEDIIFDPNIFAVATGIDEHRRYAIDFIEATAEI 201 
                                                ****************************.7************************************* PP

                                 TIGR02082  537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603 
                                                k++ P+++isgGvsn+sFs+rgn++vR+a+hsvFLy+ai+aG+Dmgivnag+l+vyd id+ lre++
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  202 KKRCPHCHISGGVSNLSFSFRGNEPVRRAMHSVFLYHAIQAGMDMGIVNAGQLDVYDAIDPVLREAC 268 
                                                ******************************************************************* PP

                                 TIGR02082  604 edlildrr....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedl 666 
                                                ed+i+drr     +ate+L elae +kg+ ++  +e++ +ewr+++v +RLe+alvkG+  ++ +d+
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  269 EDVIWDRRpkngGDATERLIELAESFKGKDAA--AEKAAEEWRGWDVAKRLEHALVKGIDAHVVDDT 333 
                                                ********7777789**************999..77799**************************** PP

                                 TIGR02082  667 eearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.ks 732 
                                                eear++  +p+e+iegpL+dGm+vvGdLFGsGkmfLPqvvksarvmkkavayL Py+e+ k +  +s
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  334 EEARQHFARPIEVIEGPLMDGMNVVGDLFGSGKMFLPQVVKSARVMKKAVAYLLPYIEAGKVQGeRS 400 
                                                ************************************************************9886589 PP

                                 TIGR02082  733 kGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksld 799 
                                                kG+iv+atvkGDvhDiGkniv+vvL+cngyev+dlGv+vP   il+aa++++aD+iglsGLi++sld
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  401 KGRIVMATVKGDVHDIGKNIVGVVLQCNGYEVIDLGVMVPWTDILRAANENDADIIGLSGLITPSLD 467 
                                                ******************************************************************* PP

                                 TIGR02082  800 emvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaee 866 
                                                emv+va em+r  +++Pl++GGa++sk h+a  ia++Y g+v++v das+av v+++lls+++++++
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  468 EMVTVATEMDRAKMQLPLMIGGATTSKVHTALRIAPAYAGPVIHVLDASRAVGVASTLLSDTQRDDF 534 
                                                ******************************************************************* PP

                                 TIGR02082  867 lekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellky 932 
                                                ++k+ ++ye +r+   e k + + +++++ar + f+ d    l++ apk+ Gt+v+ +  +e+l++ 
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  535 VAKTAADYEAVRKAR-EGKGQNELATIEEARANAFVADFA--LKPDAPKQPGTHVFTDWpLEDLREI 598 
                                                **********99765.5578889999999**9******99..9***************99******* PP

                                 TIGR02082  933 iDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddi 999 
                                                iDw+++F +Wel+g+yp il+d ++g+ ar lf+da+++ld+++aek l+a+gv  l+Pa+  gdd+
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  599 IDWTPFFRAWELAGNYPAILDDAVVGESARGLFADAQKMLDQIIAEKWLTAKGVAALWPAHADGDDV 665 
                                                ******************************************************************* PP

                                 TIGR02082 1000 eiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelak 1065
                                                 + +d +       + ++   ++q+++ ++r ++claDf+a+      D+lg ++v  + g++    
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  666 IVRADSGE----VRL-PF--LRQQIKKREGRaNMCLADFVAP----ADDWLGGFAVG-IHGIDPHIA 720 
                                                **997766....333.33..357777777777**********....89****99998.899999999 PP

                                 TIGR02082 1066 kleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpa 1132
                                                +++a++ddy  il+kaladrlaea+ae lh +vR  lwgyae e+l +e l+ke+YrGirpa+GYpa
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  721 RFKADHDDYRDILLKALADRLAEAFAERLHLHVRTTLWGYAEGEQLTNEALIKEQYRGIRPAPGYPA 787 
                                                ******************************************************************* PP

                                 TIGR02082 1133 cPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                                cPdh++k  l++Ll+a   +G++ltes+a+ P+a+vsg+yf hpea Yf v
  lcl|NCBI__GCF_000016765.1:WP_041379258.1  788 CPDHSQKPILFDLLKAGDaTGITLTESFAMLPTAAVSGFYFGHPEASYFGV 838 
                                                ***************9888******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (869 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: 12.99
//
[ok]

This GapMind analysis is from Apr 10 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:

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