Alignments for a candidate for metH in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Hydrogenophaga taeniospiralis NBRC 102512

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_084235998.1 HTA01S_RS09875 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_001592305.1:WP_084235998.1
          Length = 917

 Score = 1058 bits (2735), Expect = 0.0
 Identities = 556/904 (61%), Positives = 670/904 (74%), Gaps = 31/904 (3%)

Query: 342  LSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDIN 401
            LSGLEPL IG+DSLFVNVGERTNVTGS  F R+I   +Y +AL VARQQVENGAQ+IDIN
Sbjct: 22   LSGLEPLRIGDDSLFVNVGERTNVTGSKAFARMILNGEYEQALAVARQQVENGAQVIDIN 81

Query: 402  MDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKE 461
            MDE MLD++AAMV+FLNLIAGEPDIARVP+M+DSSKW+VIE GL+C+QGKG+VNSISMKE
Sbjct: 82   MDEAMLDSKAAMVKFLNLIAGEPDIARVPVMVDSSKWEVIEAGLRCVQGKGVVNSISMKE 141

Query: 462  GVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIF 521
            GVD F   A+L++RYGAA VVMAFDE+GQADT  RK+EIC RAY+IL +EVGFPPEDIIF
Sbjct: 142  GVDEFKRQARLVKRYGAAAVVMAFDEKGQADTYERKVEICERAYRILVDEVGFPPEDIIF 201

Query: 522  DPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHA 581
            DPNIFA+ATGIEEHNNYA DFI A   IK+ LP A +SGGVSNVSFSFRGNDPVREAIH 
Sbjct: 202  DPNIFAIATGIEEHNNYAVDFINATRWIKQHLPGAKVSGGVSNVSFSFRGNDPVREAIHT 261

Query: 582  VFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGS 641
            VFLY+AI+ GMDMGIVNAG + +YD+L  ELR+ VEDV+LNRR D  ERL+E+AE  +G+
Sbjct: 262  VFLYHAIKAGMDMGIVNAGMVGVYDELEPELRERVEDVVLNRRPDAGERLVEVAENAKGA 321

Query: 642  KTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTE----EARQQATRPIEVIEGPL 697
              DD   +++ EWR+  + +RL ++LV+G+ EFI +DTE    E   +  RP+ VIEGPL
Sbjct: 322  AKDD---SKKNEWRALPIRERLAHALVRGMNEFISEDTEEMWREIEAEGGRPLNVIEGPL 378

Query: 698  MDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASK-------EQGKTNGKMV 750
            MDGMNVVGDLFG+GKMFLPQVVKSARVMKQAVA+L P+IEA K          K  GK+V
Sbjct: 379  MDGMNVVGDLFGQGKMFLPQVVKSARVMKQAVAHLLPYIEAEKLAQQAAGADVKPKGKIV 438

Query: 751  IATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPS 810
            IATVKGDVHDIGKNIV VVLQCNN+E+V++GVMVP  +IL  AKE  AD++GLSGLITPS
Sbjct: 439  IATVKGDVHDIGKNIVTVVLQCNNFEVVNMGVMVPCHEILAKAKEEGADIVGLSGLITPS 498

Query: 811  LDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGV 866
            L+EM  VA EM++        IPLLIGGATTS+ HTAVKI  +Y GP VYV +ASR+V V
Sbjct: 499  LEEMQYVAGEMQKDAHFREKGIPLLIGGATTSRVHTAVKISPHYEGPVVYVPDASRSVSV 558

Query: 867  VAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVA 926
              +L+ D+ R  ++A    +Y  VR QH  KK + P   L  AR N    DW  + P   
Sbjct: 559  AQSLIGDS-RVKYIAELNADYHRVRTQHANKK-QVPLWPLAQARANKTPIDWAGFKPMKP 616

Query: 927  HRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLD 985
              +G ++ +   +  +  YIDW PFF TW LAG YP IL DEVVG +A ++F D   ML 
Sbjct: 617  KVIGKRQFKNFDLAEIAKYIDWGPFFQTWDLAGPYPAILTDEVVGEQASKVFADGQAMLK 676

Query: 986  KLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDETRTHVINVSHHLRQQTEKTGF-----A 1039
            K+   + L   GV+GL+PAN V  DDI++Y DE+R+ V    H LRQQTEK         
Sbjct: 677  KIIEGRWLQANGVIGLYPANTVNDDDIQLYTDESRSQVALTWHGLRQQTEKQEVDGVLRP 736

Query: 1040 NYCLADFVAPKLSGKA-DYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEA 1098
            + CLADFVAPK  G A DY+G FAVT GL  D     F   HDDYN I+ K+LADRLAEA
Sbjct: 737  SRCLADFVAPK--GVADDYVGLFAVTAGLGIDKKEQQFLDAHDDYNAILFKSLADRLAEA 794

Query: 1099 FAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVE 1158
            FAE LH+RVR   WGYA +E L+N+ELI+E YQGIRPAPGYPACP+H+ K  ++ LL+ E
Sbjct: 795  FAECLHQRVRTDLWGYAADEQLANDELIKEKYQGIRPAPGYPACPDHSVKRAMFALLQAE 854

Query: 1159 KHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWL 1218
            +  GM LT+S AM P ASVSG+Y  HPDS Y+ V +I  DQVED A R G++ +E+ RWL
Sbjct: 855  E-IGMALTDSLAMTPAASVSGFYLGHPDSSYFNVGKIGEDQVEDLAERSGVAASELRRWL 913

Query: 1219 APNL 1222
             PNL
Sbjct: 914  GPNL 917


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: 2703
Number of extensions: 118
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: 917
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 872
Effective search space:  1030704
Effective search space used:  1030704
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_068170213.1 HTA01S_RS10005 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_001592305.1:WP_068170213.1
          Length = 349

 Score =  378 bits (971), Expect = e-109
 Identities = 189/332 (56%), Positives = 248/332 (74%), Gaps = 5/332 (1%)

Query: 3   SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
           ++ + L A L++RI +LDG MGTMIQ ++L EA +RGERF D+  D+KGNN+LL L++P+
Sbjct: 7   TRAQALPAILSQRIAILDGAMGTMIQRFKLGEAQYRGERFKDFHKDVKGNNELLSLTRPD 66

Query: 63  VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
           VI  IH  Y  AGADIIETNTF +TTIA  DY M SL+ E+N A+A++AR   D+++  T
Sbjct: 67  VIRDIHEGYLAAGADIIETNTFGATTIAQEDYDMASLAREMNLASARIAREACDKFS--T 124

Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
           P+KPR+VAG LGPT +TASISPDVND   RN+TF+ L AAY E  +ALVEGGADL+L+ET
Sbjct: 125 PDKPRFVAGALGPTPKTASISPDVNDAGARNVTFEQLRAAYYEQMEALVEGGADLLLVET 184

Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
           +FDTLNAKAA+FA+   FE  G  LP++ISGT+TDASGR LSGQT  AF+ S+RH + L 
Sbjct: 185 IFDTLNAKAALFAIDEYFENSGERLPVIISGTVTDASGRILSGQTVTAFWASVRHIQPLA 244

Query: 243 FGLNCALGPDELRQYVQELSRIA-ECYVTAHPNAGLPNAFGE--YDLDADTMAKQIREWA 299
            GLNCALG   +R Y+QEL+++A + +++ +PNAGLPN   +  +D   D  ++ +RE+A
Sbjct: 245 VGLNCALGATLMRPYIQELAKVAGDTFISCYPNAGLPNPMSDTGFDETPDVTSRLLREFA 304

Query: 300 QAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPR 331
             G +NIVGGCCGTTPQHI A+  AV    PR
Sbjct: 305 AEGLVNIVGGCCGTTPQHIGAIHEAVASQTPR 336


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: 989
Number of extensions: 32
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: 349
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 311
Effective search space:   369779
Effective search space used:   369779
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_084235998.1 HTA01S_RS09875 (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.21184.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 1204.6   0.0          0 1204.5   0.0    1.0  1  lcl|NCBI__GCF_001592305.1:WP_084235998.1  HTA01S_RS09875 methionine syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_084235998.1  HTA01S_RS09875 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1204.5   0.0         0         0     319    1182 .]      12     887 ..       1     887 [. 0.96

  Alignments for each domain:
  == domain 1  score: 1204.5 bits;  conditional E-value: 0
                                 TIGR02082  319 krqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqil 385 
                                                   +  ++++lsgle+l+i+++s fvn+GeRtnv+Gsk f+++i +++ye+al +a+qqve+Gaq++
  lcl|NCBI__GCF_001592305.1:WP_084235998.1   12 SSSAAVPPMLLSGLEPLRIGDDSLFVNVGERTNVTGSKAFARMILNGEYEQALAVARQQVENGAQVI 78  
                                                455677899********************************************************** PP

                                 TIGR02082  386 DinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeer 452 
                                                Din+De++lD++a+m+k+l+l+a+epdia+vP+m+Dss++ev+eaGL+++qGk++vnsis+k+G+++
  lcl|NCBI__GCF_001592305.1:WP_084235998.1   79 DINMDEAMLDSKAAMVKFLNLIAGEPDIARVPVMVDSSKWEVIEAGLRCVQGKGVVNSISMKEGVDE 145 
                                                ******************************************************************* PP

                                 TIGR02082  453 FlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGi 519 
                                                F ++a+l+k+yGaa+vvmafDe+Gqa+t+++k+ei++Ray++l+++vgfppediifDpni++iatGi
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  146 FKRQARLVKRYGAAAVVMAFDEKGQADTYERKVEICERAYRILVDEVGFPPEDIIFDPNIFAIATGI 212 
                                                ******************************************************************* PP

                                 TIGR02082  520 eehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivna 586 
                                                eeh++ya+dfi+a+r+ik++lP ak+sgGvsnvsFs+rgnd+vRea+h+vFLy+aikaG+Dmgivna
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  213 EEHNNYAVDFINATRWIKQHLPGAKVSGGVSNVSFSFRGNDPVREAIHTVFLYHAIKAGMDMGIVNA 279 
                                                ******************************************************************* PP

                                 TIGR02082  587 gklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLera 653 
                                                g++ vyd++++elre ved++l+rr++a e+L+e+ae+ kg  +++sk   ++ewr lp++eRL++a
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  280 GMVGVYDELEPELRERVEDVVLNRRPDAGERLVEVAENAKGAAKDDSK---KNEWRALPIRERLAHA 343 
                                                **************************************9999999555...99************** PP

                                 TIGR02082  654 lvkGeregieedleear....kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkav 716 
                                                lv+G++e+i ed+ee       +  +pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmk+av
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  344 LVRGMNEFISEDTEEMWreieAEGGRPLNVIEGPLMDGMNVVGDLFGQGKMFLPQVVKSARVMKQAV 410 
                                                ***************98333334568***************************************** PP

                                 TIGR02082  717 ayLePylekekeed.......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPveki 776 
                                                a+L Py+e+ek ++       k kGkiv+atvkGDvhDiGkniv vvL+cn++evv++Gv+vP+++i
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  411 AHLLPYIEAEKLAQqaagadvKPKGKIVIATVKGDVHDIGKNIVTVVLQCNNFEVVNMGVMVPCHEI 477 
                                                ***********888899999999******************************************** PP

                                 TIGR02082  777 leaakkkkaDviglsGLivksldemvevaeemerrgvk....iPlllGGaalskahvavkiaekYkg 839 
                                                l +ak++ aD++glsGLi++sl+em++va em++ +      iPll+GGa++s+ h+avki ++Y+g
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  478 LAKAKEEGADIVGLSGLITPSLEEMQYVAGEMQKDAHFrekgIPLLIGGATTSRVHTAVKISPHYEG 544 
                                                ********************************9987433778************************* PP

                                 TIGR02082  840 evvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrs 906 
                                                +vvyv das++v+v+++l+ + +  +++++++++y+ +r+++ + k+++   ++++ar ++  +d+ 
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  545 PVVYVPDASRSVSVAQSLIGDSR-VKYIAELNADYHRVRTQHAN-KKQVPLWPLAQARANKTPIDWA 609 
                                                *********************95.99****************98.7889999*************** PP

                                 TIGR02082  907 edlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakell 972 
                                                   ++ +pk +G++++++  ++e+ kyiDw ++F +W+l+g yp il+de++g++a k+f+d +++l
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  610 -GFKPMKPKVIGKRQFKNFdLAEIAKYIDWGPFFQTWDLAGPYPAILTDEVVGEQASKVFADGQAML 675 
                                                .9***************************************************************** PP

                                 TIGR02082  973 dklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiatvrekleqlrqqsdr....ylcl 1034
                                                +k+++ + l+a+gv+Gl+Pa++v+ ddi++ytde++sq + +   +r  +++ +q+ d       cl
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  676 KKIIEGRWLQANGVIGLYPANTVNdDDIQLYTDESRSQVALTWHGLR--QQTEKQEVDGvlrpSRCL 740 
                                                *********************876268*********77776666665..4444555554677899** PP

                                 TIGR02082 1035 aDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRke 1101
                                                aDf+a+k +   Dy+g+++vtaglg+++  +++ + +ddy++il+k+ladrlaea+ae lh+rvR +
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  741 ADFVAPKGV-ADDYVGLFAVTAGLGIDKKEQQFLDAHDDYNAILFKSLADRLAEAFAECLHQRVRTD 806 
                                                ******765.679****************************************************** PP

                                 TIGR02082 1102 lwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvs 1168
                                                lwgya++e+l++++l+ke+Y+Girpa+GYpacPdh+ k+ +++Ll+ae+iG+ lt+sla++P+asvs
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  807 LWGYAADEQLANDELIKEKYQGIRPAPGYPACPDHSVKRAMFALLQAEEIGMALTDSLAMTPAASVS 873 
                                                ******************************************************************* PP

                                 TIGR02082 1169 glyfahpeakYfav 1182
                                                g+y+ hp++ Yf+v
  lcl|NCBI__GCF_001592305.1:WP_084235998.1  874 GFYLGHPDSSYFNV 887 
                                                ************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (917 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 13.34
//
[ok]

This GapMind analysis is from Apr 10 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