Alignments for a candidate for metH in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Polaromonas naphthalenivorans CJ2

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_011799552.1 PNAP_RS00580 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000015505.1:WP_011799552.1
          Length = 939

 Score = 1053 bits (2724), Expect = 0.0
 Identities = 572/938 (60%), Positives = 673/938 (71%), Gaps = 57/938 (6%)

Query: 335  EIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENG 394
            E+P   +LSGLEP+ IG DSLFVN+GERTNVTGS  F R+I    Y +AL VARQQVENG
Sbjct: 9    EVP-PMKLSGLEPVTIGSDSLFVNIGERTNVTGSKAFARMILNGDYEQALTVARQQVENG 67

Query: 395  AQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIV 454
            AQIIDINMDE MLD++AAMVRFLNLIAGEPDIARVPIMIDSSKW VIE GL+CIQGKGIV
Sbjct: 68   AQIIDINMDEAMLDSQAAMVRFLNLIAGEPDIARVPIMIDSSKWSVIEAGLRCIQGKGIV 127

Query: 455  NSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGF 514
            NSISMKEGVDAF H AKLL+RYGAA VVMAFDE+GQADT  RKI IC RAY++L +E+GF
Sbjct: 128  NSISMKEGVDAFKHQAKLLKRYGAAAVVMAFDEKGQADTYERKISICERAYRVLVDEIGF 187

Query: 515  PPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDP 574
            PPEDIIFDPNIFA+ATGI+EHNNYA DFI A   IK  LP A +SGGVSNVSFSFRGNDP
Sbjct: 188  PPEDIIFDPNIFAIATGIDEHNNYAVDFIEATRWIKANLPGAKVSGGVSNVSFSFRGNDP 247

Query: 575  VREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRD--------- 625
            VREAIH VFLY+AI+ GMDMGIVNAG + +YD+L   LR+ VEDV+LNR+          
Sbjct: 248  VREAIHTVFLYHAIQAGMDMGIVNAGMMGVYDELEPVLRERVEDVVLNRQPVYKPGEAHL 307

Query: 626  DGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQ- 684
               ERL+E+AE  +    DD   +++ EWR+  +  RL ++LV G  EFI +DTEE  Q 
Sbjct: 308  TPGERLIEVAETAKSGARDD---SKKYEWRALPIRARLSHALVHGNNEFITEDTEEVWQA 364

Query: 685  ---QATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASK- 740
               +  RP+ VIEGPLMDGMNVVGDLFG+GKMFLPQVVKSARVMKQAVA+L P+IEA K 
Sbjct: 365  IKAEGGRPLHVIEGPLMDGMNVVGDLFGQGKMFLPQVVKSARVMKQAVAHLLPYIEAEKL 424

Query: 741  ------EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAK 794
                     KT GK++IATVKGDVHDIGKNIV VVLQCNN+E+V++GVMVP  +IL  AK
Sbjct: 425  LLEAAGGDVKTKGKIIIATVKGDVHDIGKNIVTVVLQCNNFEVVNMGVMVPCHEILALAK 484

Query: 795  EVNADLIGLSGLITPSLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNY 850
               A ++GLSGLITPSL+EM  VA EM++        IPL+IGGATTS+ HTAVKI  +Y
Sbjct: 485  AEGAHIVGLSGLITPSLEEMQYVAAEMQKDDHFRLNKIPLMIGGATTSRVHTAVKISPHY 544

Query: 851  SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAAR 910
             GP VYV +ASR+V V  +LLS+ Q   ++A    +Y+ VR QH  KK +TP   L  AR
Sbjct: 545  EGPVVYVPDASRSVSVAQSLLSE-QAAKYIAELNADYDKVRTQHANKK-QTPMWPLAKAR 602

Query: 911  DNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVV 969
             N    DW  YTPPV   +G +  +   +  L  +IDW PFF TW LAG +P IL DEVV
Sbjct: 603  ANATPIDWTNYTPPVPKFIGRRVFKNFDLAELAQFIDWGPFFQTWDLAGPFPAILTDEVV 662

Query: 970  GVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSHHL 1029
            GVEA R+++DA  ML +L   + L   GV+ L PAN VGDDIEIY DETRT V    H L
Sbjct: 663  GVEATRVYEDAQKMLKRLIEGRWLTASGVMALLPANSVGDDIEIYTDETRTEVAMTWHGL 722

Query: 1030 RQQTEKTGF-----ANYCLADFVAPKL-------------SGK-------ADYIGAFAVT 1064
            RQQTEKT        + CLADFVAPK+             S K       ADYIG FAVT
Sbjct: 723  RQQTEKTAVDGVMRPSRCLADFVAPKVLTPELIAARTRAASAKGQNDLKIADYIGVFAVT 782

Query: 1065 GGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEE 1124
             GL  D    AF+A HDDY+ IM K+LADRLAEAFAE LH+RVR+  WGYAP E+L ++ 
Sbjct: 783  AGLGADKKEKAFQADHDDYSSIMFKSLADRLAEAFAEALHQRVRRDLWGYAPAESLGHDA 842

Query: 1125 LIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSH 1184
            LI E YQGIRPAPGYPACP+H+ K  ++ELL      GM LTES AM P ASVSG+Y SH
Sbjct: 843  LIAEQYQGIRPAPGYPACPDHSVKKEMFELLHA-GDIGMALTESLAMTPAASVSGFYLSH 901

Query: 1185 PDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNL 1222
            P S Y++V +I  DQ++D ARR+G    ++ R LAPNL
Sbjct: 902  PQSTYFSVGKIGDDQLQDLARRRGAKAEDLARLLAPNL 939


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: 2692
Number of extensions: 138
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1227
Length of database: 939
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 894
Effective search space:  1056708
Effective search space used:  1056708
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_041376875.1 PNAP_RS00570 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000015505.1:WP_041376875.1
          Length = 348

 Score =  379 bits (973), Expect = e-109
 Identities = 188/334 (56%), Positives = 254/334 (76%), Gaps = 5/334 (1%)

Query: 3   SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
           ++ +QL A L +RIL+LDG MGTMIQ +RLNEA +RGERF D+  D+KGNN+LL L++P+
Sbjct: 7   TRAQQLPALLAQRILILDGAMGTMIQRFRLNEAQYRGERFKDFHKDVKGNNELLSLTRPD 66

Query: 63  VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
           +I  IH  Y  AGAD+IETNTF +TT+A ADY M  L+ E+N+ +A++ARA  D+++  T
Sbjct: 67  MIRDIHEGYLAAGADMIETNTFGATTVAQADYDMADLAVEMNYESARIARAACDKFS--T 124

Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
           PEKPR+V G LGPT +TASISPDVND   RN +F+ L  AY E T+ALV+GGAD++L+ET
Sbjct: 125 PEKPRFVVGALGPTPKTASISPDVNDAGARNTSFEELRKAYYEQTEALVKGGADVLLVET 184

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

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

Query: 300 QAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKL 333
             G +NIVGGCCGTTP+HIAA+++AV  +  R+L
Sbjct: 305 AEGLVNIVGGCCGTTPEHIAAIAQAVAPMDGRRL 338


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: 990
Number of extensions: 38
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: 348
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 310
Effective search space:   368590
Effective search space used:   368590
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_011799552.1 PNAP_RS00580 (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.20091.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 1167.4   0.0          0 1167.0   0.0    1.1  1  lcl|NCBI__GCF_000015505.1:WP_011799552.1  PNAP_RS00580 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011799552.1  PNAP_RS00580 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1167.0   0.0         0         0     324    1182 .]      10     909 ..       2     909 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1167.0 bits;  conditional E-value: 0
                                 TIGR02082  324 eeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvD 390 
                                                 +++ lsgle+++i+ +s fvniGeRtnv+Gsk f+++i ++dye+al++a+qqve+Gaqi+Din+D
  lcl|NCBI__GCF_000015505.1:WP_011799552.1   10 VPPMKLSGLEPVTIGSDSLFVNIGERTNVTGSKAFARMILNGDYEQALTVARQQVENGAQIIDINMD 76  
                                                57899************************************************************** PP

                                 TIGR02082  391 evllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFleka 457 
                                                e++lD++a+m+++l+l+a+epdia+vP+m+Dss++ v+eaGL++iqGk+ivnsis+k+G+++F ++a
  lcl|NCBI__GCF_000015505.1:WP_011799552.1   77 EAMLDSQAAMVRFLNLIAGEPDIARVPIMIDSSKWSVIEAGLRCIQGKGIVNSISMKEGVDAFKHQA 143 
                                                ******************************************************************* PP

                                 TIGR02082  458 klikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdr 524 
                                                kl+k+yGaa+vvmafDe+Gqa+t+++ki i++Ray++l++++gfppediifDpni++iatGi+eh++
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  144 KLLKRYGAAAVVMAFDEKGQADTYERKISICERAYRVLVDEIGFPPEDIIFDPNIFAIATGIDEHNN 210 
                                                ******************************************************************* PP

                                 TIGR02082  525 yaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklav 591 
                                                ya+dfiea+r+ik +lP ak+sgGvsnvsFs+rgnd+vRea+h+vFLy+ai+aG+Dmgivnag++ v
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  211 YAVDFIEATRWIKANLPGAKVSGGVSNVSFSFRGNDPVREAIHTVFLYHAIQAGMDMGIVNAGMMGV 277 
                                                ******************************************************************* PP

                                 TIGR02082  592 yddidkelrevvedlildrr.........reatekLlelaelykgtkeksskeaqeaewrnlpveeR 649 
                                                yd++++ lre ved++l+r+             e+L e+ae+ k   ++   ++++ ewr lp++ R
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  278 YDELEPVLRERVEDVVLNRQpvykpgeahLTPGERLIEVAETAKSGARD---DSKKYEWRALPIRAR 341 
                                                ********************99988765545579999999996666666...45699********** PP

                                 TIGR02082  650 LeralvkGeregieedleear....kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvm 712 
                                                L++alv+G++e+i ed+ee       +  +pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvm
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  342 LSHALVHGNNEFITEDTEEVWqaikAEGGRPLHVIEGPLMDGMNVVGDLFGQGKMFLPQVVKSARVM 408 
                                                *******************88333234568************************************* PP

                                 TIGR02082  713 kkavayLePylekekeed.......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvP 772 
                                                k+ava+L Py+e+ek          k+kGki++atvkGDvhDiGkniv vvL+cn++evv++Gv+vP
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  409 KQAVAHLLPYIEAEKLLLeaaggdvKTKGKIIIATVKGDVHDIGKNIVTVVLQCNNFEVVNMGVMVP 475 
                                                **************95435578899****************************************** PP

                                 TIGR02082  773 vekileaakkkkaDviglsGLivksldemvevaeemerrg.vk...iPlllGGaalskahvavkiae 835 
                                                +++il  ak + a ++glsGLi++sl+em++va em++   ++   iPl++GGa++s+ h+avki +
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  476 CHEILALAKAEGAHIVGLSGLITPSLEEMQYVAAEMQKDDhFRlnkIPLMIGGATTSRVHTAVKISP 542 
                                                ************************************9975233556********************* PP

                                 TIGR02082  836 kYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfa 902 
                                                +Y+g+vvyv das++v+v+++llse++ a+++++++++y+++r+++ + k+++   ++++ar +   
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  543 HYEGPVVYVPDASRSVSVAQSLLSEQA-AKYIAELNADYDKVRTQHAN-KKQTPMWPLAKARANATP 607 
                                                *************************96.99****************98.7789999*********** PP

                                 TIGR02082  903 ldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkda 968 
                                                +d++ ++++p+pkf+G++v+++  ++el ++iDw ++F +W+l+g +p il+de++g+ea+++++da
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  608 IDWT-NYTPPVPKFIGRRVFKNFdLAELAQFIDWGPFFQTWDLAGPFPAILTDEVVGVEATRVYEDA 673 
                                                ****.9************************************************************* PP

                                 TIGR02082  969 kelldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdr..... 1030
                                                +++l++l++ + l+a+gv+ l Pa+svgddieiytdet+   t++  t     + lrqq+++     
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  674 QKMLKRLIEGRWLTASGVMALLPANSVGDDIEIYTDETR---TEVAMTW----HGLRQQTEKtavdg 733 
                                                **************************************9...3333333....33333333333346 PP

                                 TIGR02082 1031 ....ylclaDfiask............es........GikDylgallvtaglgaeelakkleakedd 1073
                                                      claDf+a+k            ++         i+Dy+g+++vtaglga++  k+++a++dd
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  734 vmrpSRCLADFVAPKvltpeliaartrAAsakgqndlKIADYIGVFAVTAGLGADKKEKAFQADHDD 800 
                                                678899********988877766555411566333334689************************** PP

                                 TIGR02082 1074 ydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhteka 1140
                                                y+si++k+ladrlaea+ae lh+rvR++lwgya  e+l ++ l+ e+Y+Girpa+GYpacPdh+ k+
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  801 YSSIMFKSLADRLAEAFAEALHQRVRRDLWGYAPAESLGHDALIAEQYQGIRPAPGYPACPDHSVKK 867 
                                                ******************************************************************* PP

                                 TIGR02082 1141 tlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                                +++eLl+a  iG+ ltesla++P+asvsg+y++hp++ Yf+v
  lcl|NCBI__GCF_000015505.1:WP_011799552.1  868 EMFELLHAGDIGMALTESLAMTPAASVSGFYLSHPQSTYFSV 909 
                                                ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (939 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: 00:00:00.13
# Mc/sec: 8.51
//
[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