Alignments for a candidate for metH in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Derxia gummosa DSM 723

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_084544571.1 H566_RS21925 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000482785.1:WP_084544571.1
          Length = 911

 Score = 1012 bits (2617), Expect = 0.0
 Identities = 554/894 (61%), Positives = 647/894 (72%), Gaps = 40/894 (4%)

Query: 341  RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400
            RLSGLE L+I +D+LFVNVGERTNVTGS  F RLI   +Y +AL VARQQVENGAQIID+
Sbjct: 22   RLSGLEALSIDDDTLFVNVGERTNVTGSKMFARLILNGEYDQALAVARQQVENGAQIIDV 81

Query: 401  NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460
            NMDE MLD++AAM RFLNLIA EPDIARVPIMIDSSKW+VIE GLKC+QGK IVNSIS+K
Sbjct: 82   NMDEAMLDSKAAMTRFLNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKSIVNSISLK 141

Query: 461  EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520
            EG   FIH AKL RRYGAAV+VMAFDE+GQADT ARK EIC RAYK+LTE+VGF PEDII
Sbjct: 142  EGEANFIHQAKLCRRYGAAVIVMAFDEKGQADTFARKTEICARAYKVLTEKVGFAPEDII 201

Query: 521  FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580
            FDPNIFA+ATGIEEH+NYA DFI AC  I+  LPHA ISGGVSNVSFSFRGN+PVREAIH
Sbjct: 202  FDPNIFAIATGIEEHDNYAVDFIEACRWIRANLPHARISGGVSNVSFSFRGNEPVREAIH 261

Query: 581  AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNR---------RDDGTERL 631
             VFLY+AIR GM MGIVNAGQL +Y DL  ELR+ VEDV+LNR             TERL
Sbjct: 262  TVFLYHAIRAGMTMGIVNAGQLGVYADLDPELRERVEDVVLNRVPKQAEGEEPKTATERL 321

Query: 632  LELAEKYRGSKTDDTANAQQAEWRSW-----EVNKRLEYSLVKGITEFIEQDTEEAR--- 683
            LE+AE+++G+      N    +WR        V +RL ++LV GIT FI +DTEEAR   
Sbjct: 322  LEIAERFKGAGGKKEEN---LDWRGTPDNPVPVEQRLSHALVHGITNFITEDTEEARAAI 378

Query: 684  -QQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQ 742
              +  RPIEVIEGPLM GMNVVGDLFG+GKMFLPQVVKSARVMKQAVA+L PFIE  K Q
Sbjct: 379  AARGGRPIEVIEGPLMAGMNVVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPFIEEEKRQ 438

Query: 743  -------GKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKE 795
                    ++ GK+VIATVKGDVHDIGKNIV VVLQCNN+E+V++GVMVP  +IL  AK 
Sbjct: 439  IEAAGGDVRSKGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVPCSEILAKAKV 498

Query: 796  VNADLIGLSGLITPSLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYS 851
              AD+IGLSGLITPSL+EM  VA EM+R  F     IPLLIGGATTS+ HTAVKI  +Y 
Sbjct: 499  EGADIIGLSGLITPSLEEMAYVATEMQRDDFFRVKKIPLLIGGATTSRVHTAVKIAPHYD 558

Query: 852  GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARD 911
            GP VYV +ASR+V V  +LLSD     +++    EY+ VR  H  KK  TP + L  AR 
Sbjct: 559  GPVVYVPDASRSVSVAQSLLSDEGAARYISELEAEYDRVRTAHANKK-ATPLLPLAEARA 617

Query: 912  NDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVG 970
            +  A DW+A  P     LG +E     +  L  YIDW PFF TW L G +P +L+D VVG
Sbjct: 618  HKPAIDWRAAAPVKPKFLGRREFRNYDLAELARYIDWGPFFQTWDLHGAFPALLDDPVVG 677

Query: 971  VEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDE---TRTHVINVS 1026
              A+++F D   ML KL   + LN   VVG +PAN  G + I +Y D+      HV+   
Sbjct: 678  ESARKVFADGQAMLKKLIDGRQLNASAVVGFWPANSDGAETITLYTDDDARDEAHVLFRW 737

Query: 1027 HHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNK 1085
             +LRQQT K  G  N CLAD++AP  SG  DYIG FAVT GL  D LA+ +EA HDDY+ 
Sbjct: 738  KNLRQQTAKREGVENKCLADYIAPLDSGVRDYIGVFAVTAGLGADKLAERYEAAHDDYSA 797

Query: 1086 IMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEH 1145
            IMVKALADRLAEAFAE +HERVRK  WGYAP+E L+NEELI+E Y GIRPAPGYPACP H
Sbjct: 798  IMVKALADRLAEAFAEAMHERVRKDLWGYAPDEALTNEELIKEKYVGIRPAPGYPACPRH 857

Query: 1146 TEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQ 1199
              K  ++  L+     GM LTESFAM P +SVSG+Y SHP ++Y+ V +I  +Q
Sbjct: 858  EVKREMFAALDATA-IGMGLTESFAMTPASSVSGFYLSHPKAQYFNVGEIGDEQ 910


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: 2641
Number of extensions: 100
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: 911
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 866
Effective search space:  1023612
Effective search space used:  1023612
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_051377698.1 H566_RS21930 homocysteine S-methyltransferase family protein

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000482785.1:WP_051377698.1
          Length = 353

 Score =  397 bits (1021), Expect = e-115
 Identities = 201/346 (58%), Positives = 259/346 (74%), Gaps = 13/346 (3%)

Query: 2   SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADW-PCDL--------KGN 52
           S    +L   ++ RIL+LDG MGTMIQ Y+L+EA +RG RFADW P DL        KGN
Sbjct: 5   SDLAARLADAMSRRILILDGAMGTMIQRYKLDEAAYRGARFADWQPADLAPGKQLFLKGN 64

Query: 53  NDLLVLSKPEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLAR 112
           NDLLVL++PEVIA IH  Y  AGADIIETNTF +T++A ADY M  L+ E+N AAA+LAR
Sbjct: 65  NDLLVLTQPEVIAEIHGKYLAAGADIIETNTFGATSVAQADYHMADLAYEMNLAAARLAR 124

Query: 113 ACADEWTARTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVE 172
           A  D+++  T +KPR+VAG LGPT +TASISPDVNDP  RN++FD LVAAY E  + L +
Sbjct: 125 AECDKYS--TADKPRFVAGALGPTPKTASISPDVNDPGARNVSFDELVAAYHEQARGLWD 182

Query: 173 GGADLILIETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFY 232
           GGADL L+ET+FDTLNAKAA+FA+   FE  G  LPIMISGT+TDASGR LSGQT  AF+
Sbjct: 183 GGADLFLVETIFDTLNAKAALFAIDQLFEERGATLPIMISGTVTDASGRILSGQTVAAFW 242

Query: 233 NSLRHAEALTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGE--YDLDADT 290
           +S+RHA  +T GLNCALG   +R Y+ ELS+IA+  +  +PNAGLPN   +  +D   D 
Sbjct: 243 HSVRHARPITIGLNCALGAALMRPYIAELSKIADTRICVYPNAGLPNPMSDTGFDETPDV 302

Query: 291 MAKQIREWAQAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEI 336
            ++ ++E+A+AGF+NI GGCCGTTP+HIAA+++AV  + PR++P++
Sbjct: 303 TSRLLKEFAEAGFVNIAGGCCGTTPEHIAAIAQAVATVTPRRVPDL 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: 1004
Number of extensions: 37
Number of successful extensions: 4
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: 353
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 315
Effective search space:   374535
Effective search space used:   374535
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_084544571.1 H566_RS21925 (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.3724261.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 1211.0   0.0          0 1210.8   0.0    1.0  1  NCBI__GCF_000482785.1:WP_084544571.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000482785.1:WP_084544571.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1210.8   0.0         0         0     320    1182 .]      14     903 ..       3     903 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1210.8 bits;  conditional E-value: 0
                             TIGR02082  320 rqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvD 390 
                                             ++   +++lsgleal+i++++ fvn+GeRtnv+Gsk f++li +++y++al +a+qqve+Gaqi+D+n+D
  NCBI__GCF_000482785.1:WP_084544571.1   14 PPRRSRPLRLSGLEALSIDDDTLFVNVGERTNVTGSKMFARLILNGEYDQALAVARQQVENGAQIIDVNMD 84  
                                            555678899************************************************************** PP

                             TIGR02082  391 evllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklik 461 
                                            e++lD++a+m+++l+l+asepdia+vP+m+Dss++ev+eaGLk++qGk+ivnsislk+Ge++F+++akl +
  NCBI__GCF_000482785.1:WP_084544571.1   85 EAMLDSKAAMTRFLNLIASEPDIARVPIMIDSSKWEVIEAGLKCVQGKSIVNSISLKEGEANFIHQAKLCR 155 
                                            *********************************************************************** PP

                             TIGR02082  462 eyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfiea 532 
                                            +yGaav+vmafDe+Gqa+t ++k ei+ Rayk+ltekvgf pediifDpni++iatGieehd+ya+dfiea
  NCBI__GCF_000482785.1:WP_084544571.1  156 RYGAAVIVMAFDEKGQADTFARKTEICARAYKVLTEKVGFAPEDIIFDPNIFAIATGIEEHDNYAVDFIEA 226 
                                            *********************************************************************** PP

                             TIGR02082  533 ireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603 
                                            +r+i+ +lP+a+isgGvsnvsFs+rgn++vRea+h+vFLy+ai+aG+ mgivnag+l vy+d+d+elre v
  NCBI__GCF_000482785.1:WP_084544571.1  227 CRWIRANLPHARISGGVSNVSFSFRGNEPVREAIHTVFLYHAIRAGMTMGIVNAGQLGVYADLDPELRERV 297 
                                            *********************************************************************** PP

                             TIGR02082  604 edlildrr.........reatekLlelaelykgtkeksskea..qeaewrnlpveeRLeralvkGeregie 663 
                                            ed++l+r          + ate+Lle+ae++kg   k++++   +   +  +pve+RL++alv+G++++i 
  NCBI__GCF_000482785.1:WP_084544571.1  298 EDVVLNRVpkqaegeepKTATERLLEIAERFKGAGGKKEENLdwRGTPDNPVPVEQRLSHALVHGITNFIT 368 
                                            *******999999999999**************998855443114444556789***************** PP

                             TIGR02082  664 edleear....kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed 730 
                                            ed+eear     +  +p+e+iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L+P++e+ek + 
  NCBI__GCF_000482785.1:WP_084544571.1  369 EDTEEARaaiaARGGRPIEVIEGPLMAGMNVVGDLFGQGKMFLPQVVKSARVMKQAVAHLIPFIEEEKRQI 439 
                                            ******9666556789****************************************************887 PP

                             TIGR02082  731 .......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLi 794 
                                                   +skGkiv+atvkGDvhDiGkniv+vvL+cn++evv++Gv+vP+ +il +ak + aD+iglsGLi
  NCBI__GCF_000482785.1:WP_084544571.1  440 eaaggdvRSKGKIVIATVKGDVHDIGKNIVSVVLQCNNFEVVNMGVMVPCSEILAKAKVEGADIIGLSGLI 510 
                                            89999999*************************************************************** PP

                             TIGR02082  795 vksldemvevaeemerrgvk....iPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsek 861 
                                            ++sl+em++va em+r  +     iPll+GGa++s+ h+avkia++Y+g+vvyv das++v+v+++lls++
  NCBI__GCF_000482785.1:WP_084544571.1  511 TPSLEEMAYVATEMQRDDFFrvkkIPLLIGGATTSRVHTAVKIAPHYDGPVVYVPDASRSVSVAQSLLSDE 581 
                                            ****************98744556*********************************************** PP

                             TIGR02082  862 kkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellk 931 
                                              a +++++++ey+ +r+ + + k+ +  l++++ar ++ a+d++ ++ +++pkflG+++++++ ++el  
  NCBI__GCF_000482785.1:WP_084544571.1  582 GAARYISELEAEYDRVRTAHAN-KKATPLLPLAEARAHKPAIDWR-AAAPVKPKFLGRREFRNYdLAELAR 650 
                                            *******************998.6788999***************.9************************ PP

                             TIGR02082  932 yiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg.ddiei 1001
                                            yiDw ++F +W+l+g +p  l+d+++g+ ark+f+d +++l+kl+  ++l+a++vvG++Pa+s g ++i++
  NCBI__GCF_000482785.1:WP_084544571.1  651 YIDWGPFFQTWDLHGAFPALLDDPVVGESARKVFADGQAMLKKLIDGRQLNASAVVGFWPANSDGaETITL 721 
                                            **************************************************************986379*** PP

                             TIGR02082 1002 ytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleake 1071
                                            ytd+    e++++   ++ ++q+ + ++  ++claD+ia+ +sG +Dy+g+++vtaglga++la+++ea +
  NCBI__GCF_000482785.1:WP_084544571.1  722 YTDDDARDEAHVLFRWKNLRQQTAKREGVeNKCLADYIAPLDSGVRDYIGVFAVTAGLGADKLAERYEAAH 792 
                                            **9988777777776665555444444436***************************************** PP

                             TIGR02082 1072 ddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatl 1142
                                            ddy++i+vkaladrlaea+ae +hervRk+lwgya +e+l +e+l+ke+Y Girpa+GYpacP h+ k+++
  NCBI__GCF_000482785.1:WP_084544571.1  793 DDYSAIMVKALADRLAEAFAEAMHERVRKDLWGYAPDEALTNEELIKEKYVGIRPAPGYPACPRHEVKREM 863 
                                            *********************************************************************** PP

                             TIGR02082 1143 leLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                            ++ l+a  iG+ ltes+a++P++svsg+y++hp+a+Yf+v
  NCBI__GCF_000482785.1:WP_084544571.1  864 FAALDATAIGMGLTESFAMTPASSVSGFYLSHPKAQYFNV 903 
                                            **************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (911 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 49.39
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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