Alignments for a candidate for metH in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Burkholderia vietnamiensis G4

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_011886165.1 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000016205.1:WP_011886165.1
          Length = 905

 Score = 1061 bits (2745), Expect = 0.0
 Identities = 563/904 (62%), Positives = 664/904 (73%), Gaps = 27/904 (2%)

Query: 341  RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400
            RL+GLEP N+   +LF+NVGERTNVTGS  F R+I   ++ EAL VARQQVENGAQ+ID+
Sbjct: 7    RLAGLEPFNVTSGTLFINVGERTNVTGSKAFARMILNGQFDEALAVARQQVENGAQVIDV 66

Query: 401  NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460
            NMDE MLD++AAMVRFLNLIA EPDIARVPIMIDSSKWDVIE GLKC+QGK IVNSIS+K
Sbjct: 67   NMDEAMLDSKAAMVRFLNLIASEPDIARVPIMIDSSKWDVIEAGLKCVQGKAIVNSISLK 126

Query: 461  EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520
            EG DAF HHAKL+RRYGAA VVMAFDE GQADT  RK EIC+R+Y  L  EVGFPPEDII
Sbjct: 127  EGEDAFRHHAKLIRRYGAAAVVMAFDETGQADTYQRKTEICKRSYDFLVNEVGFPPEDII 186

Query: 521  FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580
            FDPNIFAVATGIEEHNNYA DFI A   IK+ LP+A +SGGVSNVSFSFRGNDPVREAIH
Sbjct: 187  FDPNIFAVATGIEEHNNYAVDFIEATRWIKQNLPYAKVSGGVSNVSFSFRGNDPVREAIH 246

Query: 581  AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG 640
             VFLY+AI+ GMDMGIVNAGQL +Y DL  ELR+ VEDVILNRR D T+RLLE+A+K+  
Sbjct: 247  TVFLYHAIQAGMDMGIVNAGQLGVYADLDPELRERVEDVILNRRADSTDRLLEIADKF-- 304

Query: 641  SKTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQAT----RPIEVIEGP 696
             KT      +  EWR+  V KRL ++LV GIT FI +DTEEAR        RPI VIEGP
Sbjct: 305  -KTGAAKKEENLEWRNQPVEKRLAHALVHGITNFIVEDTEEARAAIAAAGGRPINVIEGP 363

Query: 697  LMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASK----EQG---KTNGKM 749
            LMDGMN+VGDLFG+GKMFLPQVVKSARVMKQAVA+L PFIE  K    E G   +  GK+
Sbjct: 364  LMDGMNIVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPFIEEEKRLLAEAGGDVRAKGKI 423

Query: 750  VIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITP 809
            VIATVKGDVHDIGKNIV VVLQCNN+E+V++GVMVP  +IL  AK   AD+IGLSGLITP
Sbjct: 424  VIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVPCNEILAKAKVEGADIIGLSGLITP 483

Query: 810  SLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVG 865
            SL+EM  VA EM+R  +     IPLLIGGATTS+ HTAVKI  +Y GP VYV +ASR+V 
Sbjct: 484  SLEEMAYVASEMQRDDYFRVKKIPLLIGGATTSRVHTAVKIAPHYEGPVVYVPDASRSVS 543

Query: 866  VVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPV 925
            V + LLSD     ++   + +YE +R QH  +K + P VTL  AR N    DW +Y P  
Sbjct: 544  VASNLLSDEGAAKYLDDLKADYERIRDQHANRKAQ-PMVTLAEARANKTRIDWSSYRPVK 602

Query: 926  AHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDML 984
               +G +  +   +  L NYIDW PFF TW LAG YP IL DE+VG  A+R+F DA  ML
Sbjct: 603  PKFIGRRVFKNYDLNELANYIDWGPFFQTWDLAGPYPAILNDEIVGESARRVFSDAKSML 662

Query: 985  DKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDETRTHVINVSHHLRQQTEKTGF----- 1038
             +L   + L   GV+ L PAN V  DDIEIY D+TR+ V+    +LRQQ+ +        
Sbjct: 663  ARLIQGRWLTANGVISLLPANTVNDDDIEIYTDDTRSEVLLTWRNLRQQSVRPVVDGVMR 722

Query: 1039 ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEA 1098
             N  LADF+APK SG ADYIG FAVT GL  D     FEA HDDY+ IM+KALADR AEA
Sbjct: 723  PNRSLADFIAPKDSGVADYIGMFAVTAGLGVDVKEKQFEADHDDYSAIMLKALADRFAEA 782

Query: 1099 FAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVE 1158
            FAE +H RVR+  WGYA +E L N+ LI E Y GIRPAPGYPACP+H  K  ++  L  +
Sbjct: 783  FAEAMHARVRRELWGYASDETLDNDALIAEKYAGIRPAPGYPACPDHLVKRDMFAALHAD 842

Query: 1159 KHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWL 1218
            +  GM +T+S AM P ASVSG+Y +HPDS+Y++V +I +DQ++DYARR  +S+ +  R L
Sbjct: 843  E-IGMSVTDSLAMLPAASVSGFYLAHPDSRYFSVGKIGQDQLDDYARRMSLSLDDARRAL 901

Query: 1219 APNL 1222
            AP L
Sbjct: 902  APQL 905


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: 113
Number of successful extensions: 10
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: 905
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 860
Effective search space:  1016520
Effective search space used:  1016520
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_011886164.1 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000016205.1:WP_011886164.1
          Length = 355

 Score =  395 bits (1016), Expect = e-114
 Identities = 194/330 (58%), Positives = 252/330 (76%), Gaps = 4/330 (1%)

Query: 7   QLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAA 66
           +L A L  RIL+LDG MGTMIQ Y+L+EA +RGERF D+P D+KGNN+LL L++P++I+ 
Sbjct: 21  ELPALLKSRILILDGAMGTMIQRYKLDEAAYRGERFKDFPRDVKGNNELLSLTQPQIISE 80

Query: 67  IHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKP 126
           IH+ YF AGADI+ETNTF +TT+A ADY ME L  E+N  +A+LAR  A      TP KP
Sbjct: 81  IHDQYFAAGADIVETNTFGATTVAQADYGMEDLVVEMNVESARLARESAARHA--TPGKP 138

Query: 127 RYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDT 186
           R+VAG +GPT +TASISPDVNDP  RNITFD L AAY +  KAL++GG DL L+ET+FDT
Sbjct: 139 RFVAGAIGPTPKTASISPDVNDPGARNITFDELHAAYYQQAKALLDGGVDLFLVETIFDT 198

Query: 187 LNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLN 246
           LNAKAA+FA+   FE  G  LPIM+SGT+TDASGR LSGQT EAF+NSLRHA+ LTFGLN
Sbjct: 199 LNAKAALFALDELFEDTGERLPIMVSGTVTDASGRILSGQTVEAFWNSLRHAKPLTFGLN 258

Query: 247 CALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGE--YDLDADTMAKQIREWAQAGFL 304
           CALG   +R Y+ E++++ + YV+ +PNAGLPN   +  +D   D  +  ++E+AQAG +
Sbjct: 259 CALGAALMRPYIAEIAKLCDTYVSCYPNAGLPNPMSDTGFDETPDVTSGLLKEFAQAGLV 318

Query: 305 NIVGGCCGTTPQHIAAMSRAVEGLAPRKLP 334
           N+ GGCCGTTP+HIA +++A+  + PR+ P
Sbjct: 319 NLAGGCCGTTPEHIAEIAKALADVKPRRWP 348


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: 1021
Number of extensions: 35
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: 355
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 317
Effective search space:   376913
Effective search space used:   376913
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_011886165.1 (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.26897.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 1212.9   0.2          0 1212.8   0.2    1.0  1  lcl|NCBI__GCF_000016205.1:WP_011886165.1  methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011886165.1  methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1212.8   0.2         0         0     325    1182 .]       4     875 ..       1     875 [. 0.96

  Alignments for each domain:
  == domain 1  score: 1212.8 bits;  conditional E-value: 0
                                 TIGR02082  325 eksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDe 391 
                                                + ++l+gle+++++  + f+n+GeRtnv+Gsk f+++i +++++eal +a+qqve+Gaq++D+n+De
  lcl|NCBI__GCF_000016205.1:WP_011886165.1    4 HMMRLAGLEPFNVTSGTLFINVGERTNVTGSKAFARMILNGQFDEALAVARQQVENGAQVIDVNMDE 70  
                                                56899************************************************************** PP

                                 TIGR02082  392 vllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekak 458 
                                                ++lD++a+m+++l+l+asepdia+vP+m+Dss+++v+eaGLk++qGkaivnsislk+Ge++F ++ak
  lcl|NCBI__GCF_000016205.1:WP_011886165.1   71 AMLDSKAAMVRFLNLIASEPDIARVPIMIDSSKWDVIEAGLKCVQGKAIVNSISLKEGEDAFRHHAK 137 
                                                ******************************************************************* PP

                                 TIGR02082  459 likeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdry 525 
                                                li++yGaa+vvmafDe Gqa+t+++k ei+kR y+ l+++vgfppediifDpni+++atGieeh++y
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  138 LIRRYGAAAVVMAFDETGQADTYQRKTEICKRSYDFLVNEVGFPPEDIIFDPNIFAVATGIEEHNNY 204 
                                                ******************************************************************* PP

                                 TIGR02082  526 aidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavy 592 
                                                a+dfiea+r+ik++lP+ak+sgGvsnvsFs+rgnd+vRea+h+vFLy+ai+aG+Dmgivnag+l vy
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  205 AVDFIEATRWIKQNLPYAKVSGGVSNVSFSFRGNDPVREAIHTVFLYHAIQAGMDMGIVNAGQLGVY 271 
                                                ******************************************************************* PP

                                 TIGR02082  593 ddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGer 659 
                                                +d+d+elre ved+il+rr ++t++Lle+a+++k   +k   ++++ ewrn+pve+RL++alv+G++
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  272 ADLDPELRERVEDVILNRRADSTDRLLEIADKFKTGAAK---KEENLEWRNQPVEKRLAHALVHGIT 335 
                                                *********************************987777...56789******************** PP

                                 TIGR02082  660 egieedleear....kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePy 722 
                                                ++i ed+eear        +p+++iegpL+dGm++vGdLFG+GkmfLPqvvksarvmk+ava+L+P+
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  336 NFIVEDTEEARaaiaAAGGRPINVIEGPLMDGMNIVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPF 402 
                                                ***********555445679*********************************************** PP

                                 TIGR02082  723 lekekeed.......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakk 782 
                                                +e+ek          ++kGkiv+atvkGDvhDiGkniv+vvL+cn++evv++Gv+vP+++il +ak 
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  403 IEEEKRLLaeaggdvRAKGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVPCNEILAKAKV 469 
                                                ****964466789999*************************************************** PP

                                 TIGR02082  783 kkaDviglsGLivksldemvevaeemerrgvk....iPlllGGaalskahvavkiaekYkgevvyvk 845 
                                                + aD+iglsGLi++sl+em++va em+r        iPll+GGa++s+ h+avkia++Y+g+vvyv 
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  470 EGADIIGLSGLITPSLEEMAYVASEMQRDDYFrvkkIPLLIGGATTSRVHTAVKIAPHYEGPVVYVP 536 
                                                ****************************87422446******************************* PP

                                 TIGR02082  846 daseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevp 912 
                                                das++v+v+++lls++  a++l+ +k++ye ir ++ + ++ +  +++++ar ++  +d+s  ++++
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  537 DASRSVSVASNLLSDEGAAKYLDDLKADYERIRDQHAN-RKAQPMVTLAEARANKTRIDWS-SYRPV 601 
                                                ************************************99.6677899***************.9**** PP

                                 TIGR02082  913 apkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsae 978 
                                                +pkf+G++v++++ ++el +yiDw ++F +W+l+g yp il+de++g+ ar++f+dak++l +l++ 
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  602 KPKFIGRRVFKNYdLNELANYIDWGPFFQTWDLAGPYPAILNDEIVGESARRVFSDAKSMLARLIQG 668 
                                                ******************************************************************* PP

                                 TIGR02082  979 kllrargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrek.leqlrqqsdr....ylclaDfia 1039
                                                + l+a+gv+ l Pa++v+ ddieiytd+t+s   +++ t r+  ++ +r   d     + +laDfia
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  669 RWLTANGVISLLPANTVNdDDIEIYTDDTRS---EVLLTWRNLrQQSVRPVVDGvmrpNRSLADFIA 732 
                                                ***************876268*******994...4444444330333333333266799******** PP

                                 TIGR02082 1040 skesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgya 1106
                                                +k+sG +Dy+g+++vtaglg++   k++ea++ddy++i++kaladr+aea+ae +h rvR+elwgya
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  733 PKDSGVADYIGMFAVTAGLGVDVKEKQFEADHDDYSAIMLKALADRFAEAFAEAMHARVRRELWGYA 799 
                                                ******************************************************************* PP

                                 TIGR02082 1107 eeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfa 1173
                                                ++e ld++ l+ e+Y Girpa+GYpacPdh  k+ +++ l+a++iG+ +t+sla+ P+asvsg+y+a
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  800 SDETLDNDALIAEKYAGIRPAPGYPACPDHLVKRDMFAALHADEIGMSVTDSLAMLPAASVSGFYLA 866 
                                                ******************************************************************* PP

                                 TIGR02082 1174 hpeakYfav 1182
                                                hp+++Yf+v
  lcl|NCBI__GCF_000016205.1:WP_011886165.1  867 HPDSRYFSV 875 
                                                *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (905 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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 12.44
//
[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