Alignments for a candidate for metH in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Xenophilus azovorans DSM 13620

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_084217489.1 Q392_RS29470 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000745855.1:WP_084217489.1
          Length = 914

 Score = 1028 bits (2658), Expect = 0.0
 Identities = 551/918 (60%), Positives = 672/918 (73%), Gaps = 34/918 (3%)

Query: 333  LPEIPVA-CRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQV 391
            +P  PVA  +LSGLEP+ +GE SLFVN+GERTNVTGS  F R+I   ++ EAL VARQQV
Sbjct: 3    IPTPPVAPMKLSGLEPVTLGEGSLFVNIGERTNVTGSKAFARMILNGRFEEALAVARQQV 62

Query: 392  ENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGK 451
            ENGAQ+ID+NMDE MLD++AAMVRFLNLIA EPDIARVPIM+DSSKW+VIE GL+CIQGK
Sbjct: 63   ENGAQVIDVNMDEAMLDSKAAMVRFLNLIASEPDIARVPIMVDSSKWEVIEAGLRCIQGK 122

Query: 452  GIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEE 511
            GIVNSISMKEG++ F H A+L+RRYGAA VVMAFDE GQADT  RKIEIC RAY++L +E
Sbjct: 123  GIVNSISMKEGIEKFKHEARLVRRYGAAAVVMAFDEVGQADTYQRKIEICERAYRVLVDE 182

Query: 512  VGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRG 571
            VGFPPEDIIFDPNIFA+ATGIEEHNNYA DFI A   IK+ LP A +SGGVSNVSFSFRG
Sbjct: 183  VGFPPEDIIFDPNIFAIATGIEEHNNYAVDFIEATRWIKQNLPGAKVSGGVSNVSFSFRG 242

Query: 572  NDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERL 631
            NDPVREAIH VFLY+AIR GMDMGIVNAG + +YD++  +LR+ VEDV+LNRR D  ERL
Sbjct: 243  NDPVREAIHTVFLYHAIRAGMDMGIVNAGMVGVYDEVEPQLRERVEDVVLNRRPDAGERL 302

Query: 632  LELAEKYRGSKTDDTANAQQAEWRSW-----EVNKRLEYSLVKGITEFIEQDTEEARQQA 686
            +E+AE  +G+  D+   +++ EWR        V +RL ++LV GIT+FI +DTEEA ++ 
Sbjct: 303  VEIAESAKGAARDE---SRKLEWRGTPEQPVPVAQRLSHALVHGITDFIVEDTEEAYREI 359

Query: 687  T----RPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQ 742
                 RP+ VIEGPLMDGMNVVGDLFG GKMFLPQVVKSARVMKQAVA+L P+IE  K++
Sbjct: 360  VARGGRPLHVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPYIEEEKKR 419

Query: 743  G-------KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKE 795
                    ++ GK+VIATVKGDVHDIGKNIV VVLQCNN+E+V++GVMVP  +IL  A+ 
Sbjct: 420  DEAAGRDVRSKGKIVIATVKGDVHDIGKNIVTVVLQCNNFEVVNMGVMVPCHEILARARI 479

Query: 796  VNADLIGLSGLITPSLDEMVNVAKEMERQGF----TIPLLIGGATTSKAHTAVKIEQNYS 851
              AD++GLSGLITPSL+EM  VA EM++        IPLLIGGATTS+ HTAVKI  +Y 
Sbjct: 480  EGADIVGLSGLITPSLEEMQYVAGEMQKDEHFRIRKIPLLIGGATTSRVHTAVKIAPHYE 539

Query: 852  GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARD 911
            GP VYV +ASR+VGV   LLS+ Q   ++A    +YE VR QH  +K + P   L  AR 
Sbjct: 540  GPVVYVPDASRSVGVAQNLLSE-QAAQYIAEVNADYERVRHQHANRK-QVPLWPLAKARA 597

Query: 912  NDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVG 970
            N    DW+ Y P      G +      +  L   IDW PFF TW LAG +P+IL+DE+VG
Sbjct: 598  NKTPVDWRGYQPTRPKFTGRRIFRNYDLSELAAAIDWGPFFQTWDLAGPFPQILKDEIVG 657

Query: 971  VEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPAN-RVGDDIEIYRDETRTHVINVSHHL 1029
             EAQR+F D   ML +L   + L   GVVG +PAN    DDI +Y DE R   +   + +
Sbjct: 658  SEAQRVFSDGKRMLQRLIEGRWLTANGVVGFWPANTEHDDDIVLYADEGRERKVLTWYGM 717

Query: 1030 RQQTEKTGF-----ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYN 1084
            RQQTEK         N CLADFVAP+ +G ADY+GAFAVT G+  +     F    DDY+
Sbjct: 718  RQQTEKQEVNGVMRPNRCLADFVAPRDAGIADYVGAFAVTAGIGAEKKEKYFLDDLDDYS 777

Query: 1085 KIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPE 1144
             IM KALADRLAEAFAE LH RVR   WGYAP+E L  E+LI+E Y+GIRPAPGYPACP+
Sbjct: 778  AIMFKALADRLAEAFAEVLHRRVRMDLWGYAPDEQLGLEQLIKEQYRGIRPAPGYPACPD 837

Query: 1145 HTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYA 1204
            H+ K  ++ELL+ E+  GM LTES AM P ASVSG+Y  HP++KY++V +I  DQ+ D A
Sbjct: 838  HSVKGPLFELLQCEE-IGMGLTESLAMTPAASVSGFYLGHPEAKYFSVGRIGPDQLADLA 896

Query: 1205 RRKGMSVTEVERWLAPNL 1222
             R+ ++  +++R LAPNL
Sbjct: 897  ARRQVAEADLQRLLAPNL 914


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: 2757
Number of extensions: 128
Number of successful extensions: 11
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: 914
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 869
Effective search space:  1027158
Effective search space used:  1027158
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_038217728.1 Q392_RS29445 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000745855.1:WP_038217728.1
          Length = 348

 Score =  376 bits (966), Expect = e-108
 Identities = 191/338 (56%), Positives = 247/338 (73%), Gaps = 5/338 (1%)

Query: 3   SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
           ++  +L   L ERI +LDG MGTMIQ  RL+E  +RGERF D P D+KGNN+LL L++P+
Sbjct: 7   TRARELPGILAERIAILDGAMGTMIQRLRLSEEQYRGERFRDAPKDVKGNNELLSLTRPD 66

Query: 63  VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
           VI  IH  Y  AGAD++ETNTF +TTIA  DY+M  L+ E+N A+A+LAR   D+++  T
Sbjct: 67  VIRDIHEGYLAAGADLVETNTFGATTIAQEDYEMAHLAREMNLASARLAREACDKFS--T 124

Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
           P++PR+VAG LGPT +TASISPDVNDP  RN+ F+ L AAY + T AL+EGGAD++L+ET
Sbjct: 125 PDRPRFVAGALGPTPKTASISPDVNDPGARNVDFEQLRAAYHQQTAALIEGGADVLLVET 184

Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
           +FDTLNAKAA+FA+   FEA G  LPI+ISGT+TDASGR LSGQT  AF++S+RHA  L 
Sbjct: 185 IFDTLNAKAALFAIDEVFEATGECLPIIISGTVTDASGRILSGQTVTAFWHSVRHARPLA 244

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

Query: 300 QAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIP 337
             G +NIVGGCCGTTP HIAA+  AV  +  R +   P
Sbjct: 305 AEGLVNIVGGCCGTTPDHIAAIGAAVAPMRARAVAAGP 342


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: 991
Number of extensions: 35
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_084217489.1 Q392_RS29470 (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.9653.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 1203.1   0.0          0 1202.9   0.0    1.0  1  lcl|NCBI__GCF_000745855.1:WP_084217489.1  Q392_RS29470 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745855.1:WP_084217489.1  Q392_RS29470 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1202.9   0.0         0         0     326    1182 .]      10     884 ..       4     884 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1202.9 bits;  conditional E-value: 0
                                 TIGR02082  326 ksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDev 392 
                                                ++ lsgle++++++ s fvniGeRtnv+Gsk f+++i ++ +eeal +a+qqve+Gaq++D+n+De+
  lcl|NCBI__GCF_000745855.1:WP_084217489.1   10 PMKLSGLEPVTLGEGSLFVNIGERTNVTGSKAFARMILNGRFEEALAVARQQVENGAQVIDVNMDEA 76  
                                                7899*************************************************************** PP

                                 TIGR02082  393 llDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekakl 459 
                                                +lD++a+m+++l+l+asepdia+vP+m+Dss++ev+eaGL++iqGk+ivnsis+k+G e+F ++a+l
  lcl|NCBI__GCF_000745855.1:WP_084217489.1   77 MLDSKAAMVRFLNLIASEPDIARVPIMVDSSKWEVIEAGLRCIQGKGIVNSISMKEGIEKFKHEARL 143 
                                                ******************************************************************* PP

                                 TIGR02082  460 ikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdrya 526 
                                                +++yGaa+vvmafDe Gqa+t+++kiei++Ray++l+++vgfppediifDpni++iatGieeh++ya
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  144 VRRYGAAAVVMAFDEVGQADTYQRKIEICERAYRVLVDEVGFPPEDIIFDPNIFAIATGIEEHNNYA 210 
                                                ******************************************************************* PP

                                 TIGR02082  527 idfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyd 593 
                                                +dfiea+r+ik++lP ak+sgGvsnvsFs+rgnd+vRea+h+vFLy+ai+aG+Dmgivnag++ vyd
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  211 VDFIEATRWIKQNLPGAKVSGGVSNVSFSFRGNDPVREAIHTVFLYHAIRAGMDMGIVNAGMVGVYD 277 
                                                ******************************************************************* PP

                                 TIGR02082  594 didkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrn.....lpveeRLeralv 655 
                                                +++++lre ved++l+rr++a e+L+e+ae  kg  +++s   ++ ewr+     +pv +RL++alv
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  278 EVEPQLRERVEDVVLNRRPDAGERLVEIAESAKGAARDES---RKLEWRGtpeqpVPVAQRLSHALV 341 
                                                *******************************999999844...4556654111225799******** PP

                                 TIGR02082  656 kGeregieedleearkkl....kapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavay 718 
                                                +G++++i ed+eea+++      +pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmk+ava+
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  342 HGITDFIVEDTEEAYREIvargGRPLHVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAH 408 
                                                ***************765222268******************************************* PP

                                 TIGR02082  719 LePylekekeed.......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekile 778 
                                                L+Py+e+ek+ d       +skGkiv+atvkGDvhDiGkniv vvL+cn++evv++Gv+vP+++il 
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  409 LIPYIEEEKKRDeaagrdvRSKGKIVIATVKGDVHDIGKNIVTVVLQCNNFEVVNMGVMVPCHEILA 475 
                                                *********999999**999*********************************************** PP

                                 TIGR02082  779 aakkkkaDviglsGLivksldemvevaeemerrg.vk...iPlllGGaalskahvavkiaekYkgev 841 
                                                 a+ + aD++glsGLi++sl+em++va em++   ++   iPll+GGa++s+ h+avkia++Y+g+v
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  476 RARIEGADIVGLSGLITPSLEEMQYVAGEMQKDEhFRirkIPLLIGGATTSRVHTAVKIAPHYEGPV 542 
                                                ******************************9864243446*************************** PP

                                 TIGR02082  842 vyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsed 908 
                                                vyv das++v v+++llse++ a+++++++++ye +r+++ + ++++   ++++ar ++  +d++  
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  543 VYVPDASRSVGVAQNLLSEQA-AQYIAEVNADYERVRHQHAN-RKQVPLWPLAKARANKTPVDWR-G 606 
                                                *******************96.99****************98.7889999***************.9 PP

                                 TIGR02082  909 levpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldk 974 
                                                ++++ pkf G+++++++ + el   iDw ++F +W+l+g +p+ilkde++g ea+++f+d k +l++
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  607 YQPTRPKFTGRRIFRNYdLSELAAAIDWGPFFQTWDLAGPFPQILKDEIVGSEAQRVFSDGKRMLQR 673 
                                                ******************************************************************* PP

                                 TIGR02082  975 lsaekllrargvvGlfPaq.svgddieiytdetvsqetkpiatvrekleqlrqqsdr.....ylcla 1035
                                                l++ + l+a+gvvG++Pa+   +ddi++y+de++  e k++ t +  ++q+++q+ +     + cla
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  674 LIEGRWLTANGVVGFWPANtEHDDDIVLYADEGR--ERKVL-TWYGMRQQTEKQEVNgvmrpNRCLA 737 
                                                *******************445679********9..44444.44444455555544447889***** PP

                                 TIGR02082 1036 DfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkel 1102
                                                Df+a++++Gi+Dy+ga++vtag+gae+  k + ++ ddy++i++kaladrlaea+ae lh+rvR +l
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  738 DFVAPRDAGIADYVGAFAVTAGIGAEKKEKYFLDDLDDYSAIMFKALADRLAEAFAEVLHRRVRMDL 804 
                                                ******************************************************************* PP

                                 TIGR02082 1103 wgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsg 1169
                                                wgya +e+l  e+l+ke+YrGirpa+GYpacPdh+ k  l+eLl+ e+iG+ ltesla++P+asvsg
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  805 WGYAPDEQLGLEQLIKEQYRGIRPAPGYPACPDHSVKGPLFELLQCEEIGMGLTESLAMTPAASVSG 871 
                                                ******************************************************************* PP

                                 TIGR02082 1170 lyfahpeakYfav 1182
                                                +y+ hpeakYf+v
  lcl|NCBI__GCF_000745855.1:WP_084217489.1  872 FYLGHPEAKYFSV 884 
                                                ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (914 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: 00:00:00.08
# Mc/sec: 12.46
//
[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