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.11007.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: 0.09u 0.02s 00:00:00.11 Elapsed: 00:00:00.11
# Mc/sec: 9.16
//
[ok]

This GapMind analysis is from Apr 09 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:

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