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.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 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: 0.09u 0.04s 00:00:00.13 Elapsed: 00:00:00.12
# Mc/sec: 8.43
//
[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