Alignments for a candidate for metH in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Sphingomonas koreensis DSMZ 15582

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate Ga0059261_0990 Ga0059261_0990 methionine synthase (B12-dependent) (EC 2.1.1.13)

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Korea:Ga0059261_0990
          Length = 865

 Score = 1043 bits (2696), Expect = 0.0
 Identities = 545/870 (62%), Positives = 653/870 (75%), Gaps = 16/870 (1%)

Query: 356  FVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVR 415
            FVN+GERTNVTGSA+FK+LI    Y+ A++VA QQVE+GAQ++D+NMDEG+LDA  AM  
Sbjct: 8    FVNIGERTNVTGSARFKKLIMAGDYTAAIEVALQQVESGAQVLDVNMDEGLLDAHEAMTT 67

Query: 416  FLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRR 475
            FL LI  EPDIAR+P+M+DSSKWDVIE GLKC+ GK IVNSISMKEGVD F+ HA+    
Sbjct: 68   FLKLIQAEPDIARIPVMVDSSKWDVIEAGLKCVSGKPIVNSISMKEGVDQFLEHARKCMA 127

Query: 476  YGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEH 535
            YGAAVVVMAFDE GQADT+ RK+EIC RAYK+L   +GFPPEDIIFDPN+FAVATGIEEH
Sbjct: 128  YGAAVVVMAFDEVGQADTKDRKVEICERAYKLLV-GIGFPPEDIIFDPNVFAVATGIEEH 186

Query: 536  NNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMG 595
            NNY  DFI AC +IK   PH  ISGG+SN+SFSFRGN+PVR+A+H+VFLY+AI  GMDM 
Sbjct: 187  NNYGVDFIEACREIKARCPHVHISGGLSNLSFSFRGNEPVRKAMHSVFLYHAIPAGMDMA 246

Query: 596  IVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWR 655
            IVNAGQL +YD +  ELR A EDVILNR  +  ERL+ LAEK+RG  TD  A  Q AEWR
Sbjct: 247  IVNAGQLDVYDQIEPELRTACEDVILNRDPEAGERLVALAEKFRG--TDAVAEKQAAEWR 304

Query: 656  SWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFL 715
             W V KRLE++LVKGI +++ +DTEE RQ+A RPIEVIEGPLMDGMNVVGDLFG GKMFL
Sbjct: 305  GWAVEKRLEHALVKGIDQYVVEDTEECRQKADRPIEVIEGPLMDGMNVVGDLFGSGKMFL 364

Query: 716  PQVVKSARVMKQAVAYLEPFIEASKEQG-KTNGKMVIATVKGDVHDIGKNIVGVVLQCNN 774
            PQVVKSARVMK+AVA+L P+IEA+KE G K  GK+V+ATVKGDVHDIGKNIVGVVLQCN 
Sbjct: 365  PQVVKSARVMKKAVAHLLPYIEAAKEPGAKGKGKVVMATVKGDVHDIGKNIVGVVLQCNG 424

Query: 775  YEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGG 834
            +E+VDLGVMVP  KIL  A E +AD+IGLSGLITPSLDEMV VA+EM+R   T+PLLIGG
Sbjct: 425  FEVVDLGVMVPWSKILEAANENDADMIGLSGLITPSLDEMVTVAEEMKRARMTMPLLIGG 484

Query: 835  ATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQH 894
            ATTSK HTA+KI   Y GP V+V +ASR VGV   L+SDT RDD+VA+   EYE VRI  
Sbjct: 485  ATTSKVHTALKIAPAYDGPVVHVLDASRAVGVATTLVSDTIRDDYVAKVAGEYEAVRIAR 544

Query: 895  GRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMT 953
               K ++  V +  ARDN F  D  +  P      GV    +  +  LR YIDWTPFF  
Sbjct: 545  A-NKGQSELVPIAVARDNAFEAD-MSLKPGKPRMPGVHSFPDWDLADLRQYIDWTPFFRA 602

Query: 954  WSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEI 1013
            W LAG YP IL D+VVG  A  LF DA  MLDK+  EK L  RGV GL+P  R GDDI +
Sbjct: 603  WELAGNYPAILTDKVVGESATSLFADAQKMLDKIVEEKWLTARGVAGLWPCRREGDDIIV 662

Query: 1014 YRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDAL 1072
            + ++ +   + +   LRQQ +K  G AN CLADF+      + D+IG FAV     E  L
Sbjct: 663  HVEDEKHVTLPM---LRQQIQKREGRANMCLADFI----DRQGDWIGGFAVGIHGIEPHL 715

Query: 1073 ADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQG 1132
            A  F+   DDY+ I++KALADRLAEAFAE LH  VR   WGYA  E L+NE LI+E Y+G
Sbjct: 716  A-RFKNAIDDYSDILLKALADRLAEAFAERLHHYVRTALWGYAEGEQLTNEALIKEEYRG 774

Query: 1133 IRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAV 1192
            IRPAPGYPACPEH+ K  ++++L+  K TG+ LTESFAM P A+VSG+YF HP ++Y+ V
Sbjct: 775  IRPAPGYPACPEHSLKPILFDMLDAHKRTGISLTESFAMLPTAAVSGFYFGHPQAEYFGV 834

Query: 1193 AQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222
            A++ RDQ+E+YA R+G+S+ + ERWL PNL
Sbjct: 835  ARVGRDQLEEYATRRGVSIEQAERWLRPNL 864


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: 2622
Number of extensions: 115
Number of successful extensions: 7
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: 865
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 820
Effective search space:   969240
Effective search space used:   969240
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 Ga0059261_0991 Ga0059261_0991 Methionine synthase I (cobalamin-dependent), methyltransferase domain

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Korea:Ga0059261_0991
          Length = 348

 Score =  362 bits (928), Expect = e-104
 Identities = 185/345 (53%), Positives = 243/345 (70%), Gaps = 3/345 (0%)

Query: 6   EQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIA 65
           E+L A+  +RIL+ DG  GT IQ+++L+EA + G+       D KGNND+L L+KPEV A
Sbjct: 5   EKLMAEAAKRILITDGAFGTEIQNWKLDEAAYAGDLGLSH--DQKGNNDILALTKPEVPA 62

Query: 66  AIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEK 125
           +IH AYFEAGADI ETNTF++  I+ ADY  E L   IN  +AK+ARA ADE+ A+   +
Sbjct: 63  SIHRAYFEAGADIAETNTFSANRISQADYGAEHLVHAINCESAKMARAIADEFEAKDG-R 121

Query: 126 PRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFD 185
           PR+VAG LGPTN+T S+SPDVNDP +R I FD L   YRE   ALVEGG D +LIETVFD
Sbjct: 122 PRFVAGALGPTNKTLSLSPDVNDPGYREIDFDHLKDVYREQIDALVEGGIDFVLIETVFD 181

Query: 186 TLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGL 245
           TLNAKA + A     +ALG +LPIM+S T+TD SGR LSG T EAF++++RHA+ +T GL
Sbjct: 182 TLNAKAGIMAAIEAGQALGRDLPIMLSMTLTDLSGRNLSGHTVEAFWHAVRHAKPVTIGL 241

Query: 246 NCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLN 305
           NC+ G ++LR +V+ LS + +  +  +PNAGLPN  G YD   +T A  + EWA+   +N
Sbjct: 242 NCSFGAEQLRPHVKTLSGLCDTLIMVYPNAGLPNELGAYDEAPETTAGLVGEWAEQAQVN 301

Query: 306 IVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNI 350
           ++GGCCG+TP HI A++ AV GL PR +P   V  RL+GLEP  +
Sbjct: 302 VLGGCCGSTPAHIKAIADAVAGLPPRAIPVPEVRTRLAGLEPFTM 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: 1042
Number of extensions: 45
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 Ga0059261_0990 Ga0059261_0990 (methionine synthase (B12-dependent) (EC 2.1.1.13))
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.928.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 1163.3   0.0          0 1163.1   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0990  Ga0059261_0990 methionine syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0990  Ga0059261_0990 methionine synthase (B12-dependent) (EC 2.1.1.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1163.1   0.0         0         0     339    1182 .]       4     834 ..       1     834 [. 0.97

  Alignments for each domain:
  == domain 1  score: 1163.1 bits;  conditional E-value: 0
                                 TIGR02082  339 qessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkklls 405 
                                                  + fvniGeRtnv+Gs++f+kli+a+dy +a+++a qqve+Gaq+lD+n+De+llD++++m+++l+
  lcl|FitnessBrowser__Korea:Ga0059261_0990    4 SSTAFVNIGERTNVTGSARFKKLIMAGDYTAAIEVALQQVESGAQVLDVNMDEGLLDAHEAMTTFLK 70  
                                                6789*************************************************************** PP

                                 TIGR02082  406 llasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmaf 472 
                                                l+ +epdia++P+m+Dss+++v+eaGLk++ Gk ivnsis+k+G+++Fle+a++   yGaavvvmaf
  lcl|FitnessBrowser__Korea:Ga0059261_0990   71 LIQAEPDIARIPVMVDSSKWDVIEAGLKCVSGKPIVNSISMKEGVDQFLEHARKCMAYGAAVVVMAF 137 
                                                ******************************************************************* PP

                                 TIGR02082  473 DeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireikee 539 
                                                De Gqa+t+d+k+ei++Raykll+  +gfppediifDpn++++atGieeh++y++dfiea+reik +
  lcl|FitnessBrowser__Korea:Ga0059261_0990  138 DEVGQADTKDRKVEICERAYKLLVG-IGFPPEDIIFDPNVFAVATGIEEHNNYGVDFIEACREIKAR 203 
                                                *************************.***************************************** PP

                                 TIGR02082  540 lPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedl 606 
                                                 P+++isgG+sn+sFs+rgn++vR+a+hsvFLy+ai aG+Dm+ivnag+l+vyd+i++elr ++ed+
  lcl|FitnessBrowser__Korea:Ga0059261_0990  204 CPHVHISGGLSNLSFSFRGNEPVRKAMHSVFLYHAIPAGMDMAIVNAGQLDVYDQIEPELRTACEDV 270 
                                                ******************************************************************* PP

                                 TIGR02082  607 ildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkkl 673 
                                                il+r++ea e+L+ lae+++gt +   +e+q aewr++ ve+RLe+alvkG+ +++ ed+ee r+k+
  lcl|FitnessBrowser__Korea:Ga0059261_0990  271 ILNRDPEAGERLVALAEKFRGTDAV--AEKQAAEWRGWAVEKRLEHALVKGIDQYVVEDTEECRQKA 335 
                                                **********************999..778************************************* PP

                                 TIGR02082  674 kapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGkivla 739 
                                                 +p+e+iegpL+dGm+vvGdLFGsGkmfLPqvvksarvmkkava+L Py+e+ ke   k kGk+v+a
  lcl|FitnessBrowser__Korea:Ga0059261_0990  336 DRPIEVIEGPLMDGMNVVGDLFGSGKMFLPQVVKSARVMKKAVAHLLPYIEAAKEPGaKGKGKVVMA 402 
                                                ****************************************************99876699******* PP

                                 TIGR02082  740 tvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevae 806 
                                                tvkGDvhDiGkniv+vvL+cng+evvdlGv+vP  kileaa++++aD+iglsGLi++sldemv+vae
  lcl|FitnessBrowser__Korea:Ga0059261_0990  403 TVKGDVHDIGKNIVGVVLQCNGFEVVDLGVMVPWSKILEAANENDADMIGLSGLITPSLDEMVTVAE 469 
                                                ******************************************************************* PP

                                 TIGR02082  807 emerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikee 873 
                                                em+r  +++Pll+GGa++sk h+a kia++Y+g+vv+v das+av v+ +l+s++ ++++++k+  e
  lcl|FitnessBrowser__Korea:Ga0059261_0990  470 EMKRARMTMPLLIGGATTSKVHTALKIAPAYDGPVVHVLDASRAVGVATTLVSDTIRDDYVAKVAGE 536 
                                                ******************************************************************* PP

                                 TIGR02082  874 yeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalF 939 
                                                ye +r    + k + + ++++ ar++ f+ d+s  l++ +p++ G++ + +  +++l++yiDw+++F
  lcl|FitnessBrowser__Korea:Ga0059261_0990  537 YEAVRIARAN-KGQSELVPIAVARDNAFEADMS--LKPGKPRMPGVHSFPDWdLADLRQYIDWTPFF 600 
                                                *****98766.788999***************9..******************************** PP

                                 TIGR02082  940 vqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiytdet 1006
                                                 +Wel+g+yp il+d+++g+ a+ lf+da+++ldk+++ek l+argv Gl+P++++gddi +  ++ 
  lcl|FitnessBrowser__Korea:Ga0059261_0990  601 RAWELAGNYPAILTDKVVGESATSLFADAQKMLDKIVEEKWLTARGVAGLWPCRREGDDIIVHVEDE 667 
                                                ************************************************************9998554 PP

                                 TIGR02082 1007 vsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleaked 1072
                                                     ++  ++   ++q+++ ++r ++claDfi      + D++g ++v  + g+e    ++++  d
  lcl|FitnessBrowser__Korea:Ga0059261_0990  668 K----HVTLPM--LRQQIQKREGRaNMCLADFIDR----QGDWIGGFAVG-IHGIEPHLARFKNAID 723 
                                                4....433333..4677777777779*******99....88****99998.7788888889****** PP

                                 TIGR02082 1073 dydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtek 1139
                                                dy+ il+kaladrlaea+ae lh+ vR  lwgyae e+l +e l+ke+YrGirpa+GYpacP+h+ k
  lcl|FitnessBrowser__Korea:Ga0059261_0990  724 DYSDILLKALADRLAEAFAERLHHYVRTALWGYAEGEQLTNEALIKEEYRGIRPAPGYPACPEHSLK 790 
                                                ******************************************************************* PP

                                 TIGR02082 1140 atlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                                  l+++l+a++ +G+ ltes+a+ P+a+vsg+yf hp+a Yf v
  lcl|FitnessBrowser__Korea:Ga0059261_0990  791 PILFDMLDAHKrTGISLTESFAMLPTAAVSGFYFGHPQAEYFGV 834 
                                                ********9988******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (865 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 0.02s 00:00:00.10 Elapsed: 00:00:00.10
# Mc/sec: 10.18
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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
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