Alignments for a candidate for metH in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Paraburkholderia bryophila 376MFSha3.1

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate H281DRAFT_02076 H281DRAFT_02076 methionine synthase (B12-dependent)

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Burk376:H281DRAFT_02076
          Length = 900

 Score = 1064 bits (2752), Expect = 0.0
 Identities = 560/904 (61%), Positives = 664/904 (73%), Gaps = 27/904 (2%)

Query: 341  RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400
            RL+GLEP N+   +LF+NVGERTNVTGS  F R+I  +++ EA+ VARQQVENGAQ+ID+
Sbjct: 2    RLAGLEPFNVTSGTLFINVGERTNVTGSKAFARMILNDQFDEAIAVARQQVENGAQVIDV 61

Query: 401  NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460
            NMDE MLD++AAMVRF+NLIA EPDIARVPIMIDSSKW+VIE GLKC+QGK IVNSIS+K
Sbjct: 62   NMDEAMLDSKAAMVRFMNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKAIVNSISLK 121

Query: 461  EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520
            EG +AF HHA L+RRYGAA VVMAFDEQGQADT  RK +IC+R+Y  L  EVGFPPEDII
Sbjct: 122  EGEEAFRHHANLIRRYGAAAVVMAFDEQGQADTFERKTQICKRSYDFLVNEVGFPPEDII 181

Query: 521  FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580
            FDPNIFA+ATGIEEHNNYA DFI A   IK  LP+A +SGGVSNVSFSFRGNDPVREAIH
Sbjct: 182  FDPNIFAIATGIEEHNNYAVDFINATRWIKENLPYAKVSGGVSNVSFSFRGNDPVREAIH 241

Query: 581  AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG 640
             VFLY+AI+ GMDMGIVNAGQL +Y DL  ELR+ VEDV+LNRR DGT+RLLE+A+K+  
Sbjct: 242  TVFLYHAIQAGMDMGIVNAGQLGVYADLDPELRERVEDVVLNRRPDGTDRLLEIADKF-- 299

Query: 641  SKTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQAT----RPIEVIEGP 696
             KT      +  EWR+  V KRL ++LV GIT FI +DTEE R +      RPI VIEGP
Sbjct: 300  -KTGAAKKEENLEWRNQPVEKRLSHALVHGITNFIVEDTEEVRAKIAAAGGRPINVIEGP 358

Query: 697  LMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQ-------GKTNGKM 749
            LMDGMN+VGDLFG+GKMFLPQVVKSARVMKQAVA+L PFIE  K+Q        +  GK+
Sbjct: 359  LMDGMNIVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPFIEEEKKQLAAAGGDVRAKGKI 418

Query: 750  VIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITP 809
            VIATVKGDVHDIGKNIV VVLQCNN+E+V++GVMVP   IL  AK   AD+IGLSGLITP
Sbjct: 419  VIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVPCNDILAKAKVEGADIIGLSGLITP 478

Query: 810  SLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVG 865
            SL+EM  VA EM+R  +     IPLLIGGATTS+ HTAVKI  +Y GP VYV +ASR+V 
Sbjct: 479  SLEEMAYVASEMQRDDYFRVKKIPLLIGGATTSRVHTAVKIAPHYEGPVVYVPDASRSVS 538

Query: 866  VVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPV 925
            V ++LLSD     ++   + +YE +R QH  KK   P VTL  AR N    DW+ Y P  
Sbjct: 539  VASSLLSDEGATKYLDELKSDYERIRNQHANKK-ALPMVTLAEARANKTPIDWKGYQPVK 597

Query: 926  AHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDML 984
               +G +  +   +  L NYIDW PFF TW LAG YP IL DE+VG  A+R+F D   ML
Sbjct: 598  PKFIGRRVFKNFDLNELANYIDWGPFFQTWDLAGPYPAILNDEIVGESARRVFSDGKSML 657

Query: 985  DKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDETRTHVINVSHHLRQQTEKTGF----- 1038
             +L   + L   GV+ L PAN V  DDIEIY DE+RT V     +LRQQ+ +        
Sbjct: 658  ARLIQGRWLQANGVIALLPANTVNDDDIEIYTDESRTEVALTWRNLRQQSVRPVVDGVMR 717

Query: 1039 ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEA 1098
             N  LADF+APK SG ADYIG FAVT GL  D     FE  HDDY+ IM+KALADR AEA
Sbjct: 718  PNRSLADFIAPKDSGVADYIGMFAVTAGLGVDVKEKQFEKDHDDYSAIMLKALADRFAEA 777

Query: 1099 FAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVE 1158
            FAE LH RVR+  WGYA  ENLS+++LI E Y+GIRPAPGYPACP+H  K  ++E+L+  
Sbjct: 778  FAEALHARVRRDLWGYANTENLSSDDLIAEKYRGIRPAPGYPACPDHLVKRDMFEVLQA- 836

Query: 1159 KHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWL 1218
               GM +TES AM P ASVSG+Y +HPDS Y++V +I +DQ+EDYA+R  +S  + ER L
Sbjct: 837  GDIGMSVTESLAMLPAASVSGFYLAHPDSTYFSVGKIGQDQLEDYAQRMSLSKADAERAL 896

Query: 1219 APNL 1222
            AP L
Sbjct: 897  APLL 900


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: 2593
Number of extensions: 110
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: 900
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 855
Effective search space:  1010610
Effective search space used:  1010610
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 H281DRAFT_02075 H281DRAFT_02075 methionine synthase (B12-dependent)

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Burk376:H281DRAFT_02075
          Length = 356

 Score =  405 bits (1041), Expect = e-117
 Identities = 203/330 (61%), Positives = 259/330 (78%), 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  LPALLKSRILILDGAMGTMIQRYKLDEARYRGERFKDYGRDIKGNNELLSITQPQIISEI 82

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

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

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

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

Query: 305 NIVGGCCGTTPQHIAAMSRAVEGLAPRKLP 334
           NI GGCCGTTP+HIAA+++A+  + PRK P
Sbjct: 320 NIAGGCCGTTPEHIAAIAKALAEVKPRKWP 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: 1014
Number of extensions: 34
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 H281DRAFT_02076 H281DRAFT_02076 (methionine synthase (B12-dependent))
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.28813.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 1208.1   0.1          0 1208.0   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  H281DRAFT_02076 methionine synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02076  H281DRAFT_02076 methionine synthase (B12-dependent)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1208.0   0.1         0         0     328    1182 .]       2     870 ..       1     870 [. 0.96

  Alignments for each domain:
  == domain 1  score: 1208.0 bits;  conditional E-value: 0
                                    TIGR02082  328 vlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDe 391 
                                                   +l+gle+++++  + f+n+GeRtnv+Gsk f+++i +++++ea+ +a+qqve+Gaq++D+n+De
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076    2 RLAGLEPFNVTSGTLFINVGERTNVTGSKAFARMILNDQFDEAIAVARQQVENGAQVIDVNMDE 65  
                                                   7899************************************************************ PP

                                    TIGR02082  392 vllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFle 455 
                                                   ++lD++a+m+++++l+asepdia+vP+m+Dss++ev+eaGLk++qGkaivnsislk+Gee+F +
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076   66 AMLDSKAAMVRFMNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKAIVNSISLKEGEEAFRH 129 
                                                   **************************************************************** PP

                                    TIGR02082  456 kaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGi 519 
                                                   +a+li++yGaa+vvmafDe+Gqa+t ++k +i+kR y+ l+++vgfppediifDpni++iatGi
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  130 HANLIRRYGAAAVVMAFDEQGQADTFERKTQICKRSYDFLVNEVGFPPEDIIFDPNIFAIATGI 193 
                                                   **************************************************************** PP

                                    TIGR02082  520 eehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgi 583 
                                                   eeh++ya+dfi+a+r+ike+lP+ak+sgGvsnvsFs+rgnd+vRea+h+vFLy+ai+aG+Dmgi
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  194 EEHNNYAVDFINATRWIKENLPYAKVSGGVSNVSFSFRGNDPVREAIHTVFLYHAIQAGMDMGI 257 
                                                   **************************************************************** PP

                                    TIGR02082  584 vnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpve 647 
                                                   vnag+l vy+d+d+elre ved++l+rr++ t++Lle+a+++k   +k   ++++ ewrn+pve
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  258 VNAGQLGVYADLDPELRERVEDVVLNRRPDGTDRLLEIADKFKTGAAK---KEENLEWRNQPVE 318 
                                                   ******************************************987777...56789******** PP

                                    TIGR02082  648 eRLeralvkGeregieedleearkkl....kapleiiegpLldGmkvvGdLFGsGkmfLPqvvk 707 
                                                   +RL++alv+G++++i ed+ee r k      +p+++iegpL+dGm++vGdLFG+GkmfLPqvvk
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  319 KRLSHALVHGITNFIVEDTEEVRAKIaaagGRPINVIEGPLMDGMNIVGDLFGQGKMFLPQVVK 382 
                                                   *********************99655222268******************************** PP

                                    TIGR02082  708 sarvmkkavayLePylekekeed.......kskGkivlatvkGDvhDiGknivdvvLscngyev 764 
                                                   sarvmk+ava+L+P++e+ek++        ++kGkiv+atvkGDvhDiGkniv+vvL+cn++ev
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  383 SARVMKQAVAHLIPFIEEEKKQLaaaggdvRAKGKIVIATVKGDVHDIGKNIVSVVLQCNNFEV 446 
                                                   ********************8879999999********************************** PP

                                    TIGR02082  765 vdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvk....iPlllGGaal 824 
                                                   v++Gv+vP++ il +ak + aD+iglsGLi++sl+em++va em+r        iPll+GGa++
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  447 VNMGVMVPCNDILAKAKVEGADIIGLSGLITPSLEEMAYVASEMQRDDYFrvkkIPLLIGGATT 510 
                                                   **********************************************87422446********** PP

                                    TIGR02082  825 skahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkekl 888 
                                                   s+ h+avkia++Y+g+vvyv das++v+v+++lls++  +++l+++k++ye ir+++ + k+ l
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  511 SRVHTAVKIAPHYEGPVVYVPDASRSVSVASSLLSDEGATKYLDELKSDYERIRNQHAN-KKAL 573 
                                                   *********************************************************98.7889 PP

                                    TIGR02082  889 ialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypki 951 
                                                     +++++ar ++  +d++  +++++pkf+G++v+++  ++el +yiDw ++F +W+l+g yp i
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  574 PMVTLAEARANKTPIDWK-GYQPVKPKFIGRRVFKNFdLNELANYIDWGPFFQTWDLAGPYPAI 636 
                                                   ******************.9******************************************** PP

                                    TIGR02082  952 lkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpi 1014
                                                   l+de++g+ ar++f+d k++l +l++ + l+a+gv+ l Pa++v+ ddieiytde++   t++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  637 LNDEIVGESARRVFSDGKSMLARLIQGRWLQANGVIALLPANTVNdDDIEIYTDESR---TEVA 697 
                                                   ******************************************876268******999...4444 PP

                                    TIGR02082 1015 atvrekleqlrqqsdr.........ylclaDfiaskesGikDylgallvtaglgaeelakklea 1069
                                                    t r    +lrqqs r         + +laDfia+k+sG +Dy+g+++vtaglg++   k++e+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  698 LTWR----NLRQQSVRpvvdgvmrpNRSLADFIAPKDSGVADYIGMFAVTAGLGVDVKEKQFEK 757 
                                                   4443....333333333333467799************************************** PP

                                    TIGR02082 1070 keddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpac 1133
                                                   ++ddy++i++kaladr+aea+ae lh rvR++lwgya++enl+ +dl+ e+YrGirpa+GYpac
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  758 DHDDYSAIMLKALADRFAEAFAEALHARVRRDLWGYANTENLSSDDLIAEKYRGIRPAPGYPAC 821 
                                                   **************************************************************** PP

                                    TIGR02082 1134 PdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                                   Pdh  k+ ++e+l+a  iG+ +tesla+ P+asvsg+y+ahp++ Yf+v
  lcl|FitnessBrowser__Burk376:H281DRAFT_02076  822 PDHLVKRDMFEVLQAGDIGMSVTESLAMLPAASVSGFYLAHPDSTYFSV 870 
                                                   ***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (900 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: 00:00:00.09
# Mc/sec: 11.49
//
[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:

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