Alignments for a candidate for metH in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Burkholderia phytofirmans PsJN

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate BPHYT_RS02305 BPHYT_RS02305 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__BFirm:BPHYT_RS02305
          Length = 902

 Score = 1060 bits (2741), Expect = 0.0
 Identities = 559/904 (61%), Positives = 664/904 (73%), Gaps = 27/904 (2%)

Query: 341  RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400
            RLSGLEP N+   +LF+NVGERTNVTGS  F R+I  +++ EA+ VARQQVENGAQ+ID+
Sbjct: 4    RLSGLEPFNVTSGTLFINVGERTNVTGSKAFARMILNDQFDEAVAVARQQVENGAQVIDV 63

Query: 401  NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460
            NMDE MLD++AAMVRF+NLIA EPDIARVPIMIDSSKW+VIE GLKC+QGK IVNSIS+K
Sbjct: 64   NMDEAMLDSKAAMVRFMNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKAIVNSISLK 123

Query: 461  EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520
            EG +AF HHA L+RRYGAA VVMAFDEQGQADT  RK +IC+R+Y  L  EVGFPPEDII
Sbjct: 124  EGEEAFRHHANLIRRYGAAAVVMAFDEQGQADTFERKTQICKRSYDFLVNEVGFPPEDII 183

Query: 521  FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580
            FDPNIFA+ATGIEEHNNYA DFI A   IK  LP+A +SGGVSNVSFSFRGNDPVREAIH
Sbjct: 184  FDPNIFAIATGIEEHNNYAVDFINATRWIKENLPYAKVSGGVSNVSFSFRGNDPVREAIH 243

Query: 581  AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG 640
             VFLY+AI+ GMDMGIVNAGQL +Y DL  ELR+ VEDV+LNRR+DGT+RLLE+A+K+  
Sbjct: 244  TVFLYHAIQAGMDMGIVNAGQLGVYADLDPELRERVEDVVLNRREDGTDRLLEIADKF-- 301

Query: 641  SKTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEAR----QQATRPIEVIEGP 696
             KT      +  EWR+  V KRL ++LV GIT FI +DTEE R     +  RPI VIEGP
Sbjct: 302  -KTGAAKKEENLEWRNQPVEKRLSHALVHGITNFIVEDTEEVRAKIAAEGGRPINVIEGP 360

Query: 697  LMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASK----EQG---KTNGKM 749
            LMDGMN+VGDLFG+GKMFLPQVVKSARVMKQAVA+L P+IE  K    E G   +  GK+
Sbjct: 361  LMDGMNIVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPYIEEEKKLLAEAGADVRAKGKI 420

Query: 750  VIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITP 809
            VIATVKGDVHDIGKNIV VVLQCNN+E+V++GVMV    IL  AK   AD+IGLSGLITP
Sbjct: 421  VIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVSCNDILAKAKVEGADIIGLSGLITP 480

Query: 810  SLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVG 865
            SL+EM  VA EM+R  +     IPLLIGGATTS+ HTAVKI  +Y GP VYV +ASR+V 
Sbjct: 481  SLEEMAYVASEMQRDDYFRVKKIPLLIGGATTSRVHTAVKIAPHYEGPVVYVPDASRSVS 540

Query: 866  VVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPV 925
            V ++LLSD     ++   + +YE +R+QH  KK   P VTL  AR N    DW +Y P  
Sbjct: 541  VASSLLSDEGAAKYLDELKSDYERIRVQHANKK-ALPMVTLAEARANKTKVDWASYQPVK 599

Query: 926  AHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDML 984
               +G +  +   +  L NYIDW PFF TW LAG YP IL DE+VG  A+R+F D   ML
Sbjct: 600  PKFIGRRVFKNFDLSELANYIDWGPFFQTWDLAGPYPAILNDEIVGESARRVFSDGKSML 659

Query: 985  DKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDETRTHVINVSHHLRQQTEKTGF----- 1038
             +L   + L   GV+ L PAN V  DDIEIY DE+R+ V     +LRQQ+ +        
Sbjct: 660  ARLIQGRWLQANGVIALLPANTVNDDDIEIYTDESRSEVALTWRNLRQQSVRPVVDGVMR 719

Query: 1039 ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEA 1098
             N  LADF+APK SG ADYIG FAVT GL  D     FE  HDDY+ IM+KALADR AEA
Sbjct: 720  PNRSLADFIAPKDSGVADYIGMFAVTAGLGVDVKEKQFEKDHDDYSAIMLKALADRFAEA 779

Query: 1099 FAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVE 1158
            FAE LH RVR+  WGYA  E LSN++LI E Y GIRPAPGYPACP+H  K  ++++L   
Sbjct: 780  FAEALHARVRRDLWGYANAETLSNDDLIAEKYHGIRPAPGYPACPDHLVKRDMFDVLHAT 839

Query: 1159 KHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWL 1218
            +  GM +TES AM P ASVSG+Y +HPDS Y++V +I +DQ+EDYA+R  +S T+ ER L
Sbjct: 840  E-IGMSVTESLAMLPAASVSGFYLAHPDSTYFSVGKIGQDQLEDYAKRMSLSKTDAERAL 898

Query: 1219 APNL 1222
            AP L
Sbjct: 899  APLL 902


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: 2609
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: 902
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 857
Effective search space:  1012974
Effective search space used:  1012974
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 BPHYT_RS02310 BPHYT_RS02310 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__BFirm:BPHYT_RS02310
          Length = 356

 Score =  402 bits (1032), Expect = e-116
 Identities = 202/330 (61%), Positives = 257/330 (77%), Gaps = 6/330 (1%)

Query: 8   LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67
           L A L  RIL+LDG MGTMIQ Y+L+EA +RGERF D+  D+KGNN+LL +++P++I  I
Sbjct: 23  LPALLKSRILILDGAMGTMIQRYKLDEARYRGERFKDYGRDIKGNNELLSITQPQIIREI 82

Query: 68  HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127
           H  Y  AGADIIETNTF +TT+A ADY ME L+ E+N  +AKLARA  D+++  TP+KPR
Sbjct: 83  HEQYLAAGADIIETNTFGATTVAQADYGMEGLAIEMNLESAKLARAACDKYS--TPDKPR 140

Query: 128 YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187
           +VAG +GPT +TASISPDVNDP  RN+TFD L AAY E  KAL++GGADL L+ET+FDTL
Sbjct: 141 FVAGAIGPTPKTASISPDVNDPGARNVTFDELRAAYYEQAKALLDGGADLFLVETIFDTL 200

Query: 188 NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247
           NAKAA+FA+   FE  G  LPIMISGT+TDASGR LSGQT EAF+NSLRHA+ LTFGLNC
Sbjct: 201 NAKAALFALDELFEDTGERLPIMISGTVTDASGRILSGQTVEAFWNSLRHAKPLTFGLNC 260

Query: 248 ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAF---GEYDLDADTMAKQIREWAQAGFL 304
           ALG   +R Y+ EL+++ + YV+ +PNAGLPN     G  +L ADT +  ++E+AQAG +
Sbjct: 261 ALGAALMRPYIAELAKLCDTYVSCYPNAGLPNPMSDTGFDELPADT-SGLLKEFAQAGLV 319

Query: 305 NIVGGCCGTTPQHIAAMSRAVEGLAPRKLP 334
           NI GGCCGTTP+HIAA+++A+  + PR+ P
Sbjct: 320 NIAGGCCGTTPEHIAAIAQALAEVKPRQWP 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: 1028
Number of extensions: 29
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: 356
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 318
Effective search space:   378102
Effective search space used:   378102
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 BPHYT_RS02305 BPHYT_RS02305 (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.1096.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 1203.3   0.5          0 1203.1   0.5    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  BPHYT_RS02305 methionine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS02305  BPHYT_RS02305 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1203.1   0.5         0         0     326    1182 .]       2     872 ..       1     872 [. 0.96

  Alignments for each domain:
  == domain 1  score: 1203.1 bits;  conditional E-value: 0
                                TIGR02082  326 ksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevl 393 
                                               +++lsgle+++++  + f+n+GeRtnv+Gsk f+++i +++++ea+ +a+qqve+Gaq++D+n+De++
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305    2 TMRLSGLEPFNVTSGTLFINVGERTNVTGSKAFARMILNDQFDEAVAVARQQVENGAQVIDVNMDEAM 69  
                                               5899**************************************************************** PP

                                TIGR02082  394 lDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklik 461 
                                               lD++a+m+++++l+asepdia+vP+m+Dss++ev+eaGLk++qGkaivnsislk+Gee+F ++a+li+
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305   70 LDSKAAMVRFMNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKAIVNSISLKEGEEAFRHHANLIR 137 
                                               ******************************************************************** PP

                                TIGR02082  462 eyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidf 529 
                                               +yGaa+vvmafDe+Gqa+t ++k +i+kR y+ l+++vgfppediifDpni++iatGieeh++ya+df
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  138 RYGAAAVVMAFDEQGQADTFERKTQICKRSYDFLVNEVGFPPEDIIFDPNIFAIATGIEEHNNYAVDF 205 
                                               ******************************************************************** PP

                                TIGR02082  530 ieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidk 597 
                                               i+a+r+ike+lP+ak+sgGvsnvsFs+rgnd+vRea+h+vFLy+ai+aG+Dmgivnag+l vy+d+d+
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  206 INATRWIKENLPYAKVSGGVSNVSFSFRGNDPVREAIHTVFLYHAIQAGMDMGIVNAGQLGVYADLDP 273 
                                               ******************************************************************** PP

                                TIGR02082  598 elrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieed 665 
                                               elre ved++l+rr++ t++Lle+a+++k   +k   ++++ ewrn+pve+RL++alv+G++++i ed
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  274 ELRERVEDVVLNRREDGTDRLLEIADKFKTGAAK---KEENLEWRNQPVEKRLSHALVHGITNFIVED 338 
                                               ****************************987777...56789************************** PP

                                TIGR02082  666 leear....kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekee 729 
                                               +ee r     +  +p+++iegpL+dGm++vGdLFG+GkmfLPqvvksarvmk+ava+L+Py+e+ek+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  339 TEEVRakiaAEGGRPINVIEGPLMDGMNIVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPYIEEEKKL 406 
                                               ***99544445679***************************************************964 PP

                                TIGR02082  730 d.......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDvigl 790 
                                                       ++kGkiv+atvkGDvhDiGkniv+vvL+cn++evv++Gv+v ++ il +ak + aD+igl
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  407 LaeagadvRAKGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVSCNDILAKAKVEGADIIGL 474 
                                               466788899*********************************************************** PP

                                TIGR02082  791 sGLivksldemvevaeemerrgvk....iPlllGGaalskahvavkiaekYkgevvyvkdaseavkvv 854 
                                               sGLi++sl+em++va em+r        iPll+GGa++s+ h+avkia++Y+g+vvyv das++v+v+
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  475 SGLITPSLEEMAYVASEMQRDDYFrvkkIPLLIGGATTSRVHTAVKIAPHYEGPVVYVPDASRSVSVA 542 
                                               ********************87422446**************************************** PP

                                TIGR02082  855 dkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvl 922 
                                               ++lls++  a++l+++k++ye ir ++ + k+ l  +++++ar ++ ++d+   +++++pkf+G++v+
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  543 SSLLSDEGAAKYLDELKSDYERIRVQHAN-KKALPMVTLAEARANKTKVDWA-SYQPVKPKFIGRRVF 608 
                                               ***************************98.7889******************.9************** PP

                                TIGR02082  923 eas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGl 989 
                                               ++  + el +yiDw ++F +W+l+g yp il+de++g+ ar++f+d k++l +l++ + l+a+gv+ l
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  609 KNFdLSELANYIDWGPFFQTWDLAGPYPAILNDEIVGESARRVFSDGKSMLARLIQGRWLQANGVIAL 676 
                                               ******************************************************************** PP

                                TIGR02082  990 fPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdr....ylclaDfiaskesGikDylgal 1052
                                                Pa++v+ ddieiytde++s  + +   +r  ++ +r   d     + +laDfia+k+sG +Dy+g++
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  677 LPANTVNdDDIEIYTDESRSEVALTWRNLR--QQSVRPVVDGvmrpNRSLADFIAPKDSGVADYIGMF 742 
                                               ****876268*******9955444444443..333333333256789********************* PP

                                TIGR02082 1053 lvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllker 1120
                                               +vtaglg++   k++e+++ddy++i++kaladr+aea+ae lh rvR++lwgya+ e l+++dl+ e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  743 AVTAGLGVDVKEKQFEKDHDDYSAIMLKALADRFAEAFAEALHARVRRDLWGYANAETLSNDDLIAEK 810 
                                               ******************************************************************** PP

                                TIGR02082 1121 YrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                               Y+Girpa+GYpacPdh  k+ ++++l+a +iG+ +tesla+ P+asvsg+y+ahp++ Yf+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS02305  811 YHGIRPAPGYPACPDHLVKRDMFDVLHATEIGMSVTESLAMLPAASVSGFYLAHPDSTYFSV 872 
                                               ************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (902 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: 00:00:00.11
# Mc/sec: 9.23
//
[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