Alignments for a candidate for metH in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Echinicola vietnamensis KMM 6221, DSM 17526

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate Echvi_3638 Echvi_3638 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Cola:Echvi_3638
          Length = 902

 Score = 1033 bits (2672), Expect = 0.0
 Identities = 528/891 (59%), Positives = 659/891 (73%), Gaps = 13/891 (1%)

Query: 341  RLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDI 400
            +LSGLEPL    +  FVN+GERTNVTGS KF RLI   ++ EAL+VA  QV  GAQ++D+
Sbjct: 11   KLSGLEPLVFTPELNFVNIGERTNVTGSKKFARLILNGQFDEALEVALDQVRGGAQVLDV 70

Query: 401  NMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMK 460
             MDEGMLD EAAMV++LNLIA EP+I+R+PI++DSSKW++I  GLKCIQGKGIVNSIS+K
Sbjct: 71   CMDEGMLDGEAAMVKYLNLIASEPEISRIPIVVDSSKWNIILAGLKCIQGKGIVNSISLK 130

Query: 461  EGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDII 520
             G D FIH AK ++++GAAVVVMAFDE GQADT  R+++IC+R+Y IL E V F P DII
Sbjct: 131  NGEDEFIHQAKTIKKFGAAVVVMAFDEDGQADTYQRRVDICKRSYDILVETVKFNPNDII 190

Query: 521  FDPNIFAVATGIEEHNNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIH 580
            FDPNIF VATG+EEH + A DF  A + IK  LP A +SGGVSNVSFSFRGN+PVREA+H
Sbjct: 191  FDPNIFPVATGMEEHRSNAIDFFKATKWIKENLPGAKVSGGVSNVSFSFRGNNPVREAMH 250

Query: 581  AVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG 640
            A FLY+AI++GMDMGIVN   L +YDD+P +L + VEDV+ +RRDD TERLL+ AE  + 
Sbjct: 251  AAFLYHAIQHGMDMGIVNPTMLEVYDDIPKDLLEHVEDVLWDRRDDATERLLDFAETVKS 310

Query: 641  SKTDDTANAQQAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDG 700
            S   + A+     WR+  V KR+E+SLVKGI + IE D EEARQ    P++VIEGPLMDG
Sbjct: 311  SGKKEVAS---EAWRAESVEKRIEHSLVKGIIDHIESDAEEARQHLKSPLKVIEGPLMDG 367

Query: 701  MNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEAS-----KEQGKTNGKMVIATVK 755
            MNVVGDLFG GKMFLPQVVKSARVMK+AVAYLEPF+  +      E+  +  K+++ATVK
Sbjct: 368  MNVVGDLFGSGKMFLPQVVKSARVMKKAVAYLEPFMPKAGDADFNEEKSSIKKVLLATVK 427

Query: 756  GDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMV 815
            GDVHDIGKNIVGVVL CN+Y+I+DLGVMV A+ I+  A + + D+IGLSGLITPSLDEMV
Sbjct: 428  GDVHDIGKNIVGVVLACNSYQIIDLGVMVDAQTIIDEAIKQDVDIIGLSGLITPSLDEMV 487

Query: 816  NVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQ 875
            NVA EMERQG  IPLLIGGATTS+ HTAVKI+  YSG  V+V +AS++V V    +S+  
Sbjct: 488  NVASEMERQGLKIPLLIGGATTSRIHTAVKIDPVYSGTVVHVLDASKSVPVAGEAISEDT 547

Query: 876  RDDFVARTRKEYETVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE 935
            RD +  + +  Y  +R  H  K+      T E A+ N    DW  Y P    +LG   ++
Sbjct: 548  RDAYHEQIKATYAELRESHQAKQEAKKLATYEEAKANPVVIDWDHYAPTKPAKLGRTILD 607

Query: 936  ASIETLRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNP 995
              I+TLRNYIDWTPFF TW L+GKYP+IL+DEVVGV+AQ+LF +AN MLDK+  E  L  
Sbjct: 608  LDIKTLRNYIDWTPFFSTWMLSGKYPKILKDEVVGVQAQKLFDEANAMLDKVIDENWLQA 667

Query: 996  RGVVGLFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGK 1054
            + VVGL+P  R GDD+ I  DE         H LRQQ +K  G  N  LAD++ P+   +
Sbjct: 668  KAVVGLYPVKRSGDDLAIL-DENLHETGTTFHFLRQQGKKGKGVPNRSLADYLHPE---Q 723

Query: 1055 ADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGY 1114
             DY G FAVT GL  D   DAF+A+ DDYN+IM KA+ DRLAEA AEY+HE VRK  WGY
Sbjct: 724  VDYFGGFAVTAGLNMDKKVDAFKAEGDDYNEIMFKAIGDRLAEAAAEYMHEVVRKELWGY 783

Query: 1115 APNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPG 1174
            AP E L N++LI+E+Y GIRPAPGYPACPEH+EK T++ELL+ +    + LT+SFAM P 
Sbjct: 784  APKEKLENDDLIKESYAGIRPAPGYPACPEHSEKVTLFELLDAQNSIDVHLTDSFAMLPT 843

Query: 1175 ASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
            +SVSG+YF HP+S+Y+ + +I  DQVE YA+RKG+S  + E+WL+PNL Y+
Sbjct: 844  SSVSGFYFGHPESRYFGLGKIGEDQVESYAKRKGVSKEQAEKWLSPNLAYN 894


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: 2652
Number of extensions: 92
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: 902
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 857
Effective search space:  1012974
Effective search space used:  1012974
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 Echvi_3639 Echvi_3639 Methionine synthase I (cobalamin-dependent), methyltransferase domain

Query= CharProtDB::CH_090726
         (1227 letters)



>FitnessBrowser__Cola:Echvi_3639
          Length = 347

 Score =  383 bits (983), Expect = e-110
 Identities = 190/340 (55%), Positives = 248/340 (72%), Gaps = 7/340 (2%)

Query: 1   MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK 60
           M+++ + L  Q++++IL+LDG MGTMIQ Y L E DFR    A+ P  LKGNNDLL LS+
Sbjct: 1   MNTRTDILLQQVDKKILILDGAMGTMIQRYTLEEEDFRTPELANHPKALKGNNDLLSLSR 60

Query: 61  PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA 120
           P++I  IH+ Y EAGADIIETNTF+ST+IA  DY +  L+ E+N  +A++AR  A  ++ 
Sbjct: 61  PKIIRDIHDTYLEAGADIIETNTFSSTSIAQEDYDLSQLAYELNVESARIAREAALSYSE 120

Query: 121 RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180
           +TP++PR+VAG +GPTNRTASISPDVNDP +R I FD L  AY E  + L++GG D++L+
Sbjct: 121 KTPDQPRFVAGAIGPTNRTASISPDVNDPGYRAINFDQLSEAYAEQVRGLLDGGVDILLV 180

Query: 181 ETVFDTLNAKAAVFAVKTEFEALGVEL-------PIMISGTITDASGRTLSGQTTEAFYN 233
           ET+FDTLNAKAA+FA++  FE  G+ L       PIMISGTITDASGRTLSGQTTEAF  
Sbjct: 181 ETIFDTLNAKAALFAIQEVFEEKGLPLSPEEGGIPIMISGTITDASGRTLSGQTTEAFLI 240

Query: 234 SLRHAEALTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAK 293
           S+ H   ++ GLNCALG  ELR Y++ L+  A  YV+A+PNAGLPN FG+YD  A  MA 
Sbjct: 241 SVSHVPLMSIGLNCALGAKELRPYLKVLAENAPFYVSAYPNAGLPNEFGQYDQTAQEMAD 300

Query: 294 QIREWAQAGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKL 333
           Q+ E+ + G +NI+GGCCGTTP+HI  +    +   PRKL
Sbjct: 301 QVEEFLKDGLINILGGCCGTTPEHIRVIGDVSKKYKPRKL 340


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: 997
Number of extensions: 43
Number of successful extensions: 2
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: 347
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 309
Effective search space:   367401
Effective search space used:   367401
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 Echvi_3638 Echvi_3638 (5-methyltetrahydrofolate--homocysteine methyltransferase)
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.26890.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 1191.8   0.6          0 1191.5   0.6    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3638  Echvi_3638 5-methyltetrahydrofol


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3638  Echvi_3638 5-methyltetrahydrofolate--homocysteine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1191.5   0.6         0         0     323    1181 ..       6     860 ..       2     861 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1191.5 bits;  conditional E-value: 0
                            TIGR02082  323 leeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevll 394 
                                            ++++ lsgle+l +++e +fvniGeRtnv+Gskkf++li +++++eal++a +qv+ Gaq+lD+++De++l
  lcl|FitnessBrowser__Cola:Echvi_3638    6 KHNQLKLSGLEPLVFTPELNFVNIGERTNVTGSKKFARLILNGQFDEALEVALDQVRGGAQVLDVCMDEGML 77  
                                           5678899***************************************************************** PP

                            TIGR02082  395 DgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaa 466 
                                           Dgea+m+k+l+l+asep+i+++P+++Dss+++++ aGLk+iqGk+ivnsislk+Ge++F+++ak ik++Gaa
  lcl|FitnessBrowser__Cola:Echvi_3638   78 DGEAAMVKYLNLIASEPEISRIPIVVDSSKWNIILAGLKCIQGKGIVNSISLKNGEDEFIHQAKTIKKFGAA 149 
                                           ************************************************************************ PP

                            TIGR02082  467 vvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireike 538 
                                           vvvmafDe+Gqa+t++++++i+kR y++l+e v+f+p+diifDpni+++atG+eeh+ +aidf +a+++ike
  lcl|FitnessBrowser__Cola:Echvi_3638  150 VVVMAFDEDGQADTYQRRVDICKRSYDILVETVKFNPNDIIFDPNIFPVATGMEEHRSNAIDFFKATKWIKE 221 
                                           ************************************************************************ PP

                            TIGR02082  539 elPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildr 610 
                                           +lP ak+sgGvsnvsFs+rgn++vRea+h+ FLy+ai+ G+Dmgivn+++l+vyddi+k+l+e ved+++dr
  lcl|FitnessBrowser__Cola:Echvi_3638  222 NLPGAKVSGGVSNVSFSFRGNNPVREAMHAAFLYHAIQHGMDMGIVNPTMLEVYDDIPKDLLEHVEDVLWDR 293 
                                           ************************************************************************ PP

                            TIGR02082  611 rreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiieg 682 
                                           r++ate+Ll++ae+ k   +k   e + ++wr  +ve+R+e++lvkG+ ++ie d+eear++lk+pl++ieg
  lcl|FitnessBrowser__Cola:Echvi_3638  294 RDDATERLLDFAETVKSSGKK---EVASEAWRAESVEKRIEHSLVKGIIDHIESDAEEARQHLKSPLKVIEG 362 
                                           **************7766666...88999******************************************* PP

                            TIGR02082  683 pLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.....kskGkivlatvkGDvhDiG 749 
                                           pL+dGm+vvGdLFGsGkmfLPqvvksarvmkkavayLeP++ k  ++d     +s  k++latvkGDvhDiG
  lcl|FitnessBrowser__Cola:Echvi_3638  363 PLMDGMNVVGDLFGSGKMFLPQVVKSARVMKKAVAYLEPFMPKAGDADfneekSSIKKVLLATVKGDVHDIG 434 
                                           *****************************************99877666766678889************** PP

                            TIGR02082  750 knivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGG 821 
                                           kniv+vvL+cn y+++dlGv+v +++i+++a k++ D+iglsGLi++sldemv+va emer+g+kiPll+GG
  lcl|FitnessBrowser__Cola:Echvi_3638  435 KNIVGVVLACNSYQIIDLGVMVDAQTIIDEAIKQDVDIIGLSGLITPSLDEMVNVASEMERQGLKIPLLIGG 506 
                                           ************************************************************************ PP

                            TIGR02082  822 aalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialse 893 
                                           a++s+ h+avki++ Y+g+vv+v das++v v+ + +se++++++ e+ik++y e+re+++ k+e ++ ++ 
  lcl|FitnessBrowser__Cola:Echvi_3638  507 ATTSRIHTAVKIDPVYSGTVVHVLDASKSVPVAGEAISEDTRDAYHEQIKATYAELRESHQAKQEAKKLATY 578 
                                           ************************************************************************ PP

                            TIGR02082  894 kaarkevfaldrsedlevpapkflGtkvleasieellkyiDwkalFvqWelrgkypkilkdeleglearklf 965 
                                           ++a+ + +++d+  ++ +++p +lG+ +l+  i++l++yiDw+++F +W l gkypkilkde++g++a+klf
  lcl|FitnessBrowser__Cola:Echvi_3638  579 EEAKANPVVIDWD-HYAPTKPAKLGRTILDLDIKTLRNYIDWTPFFSTWMLSGKYPKILKDEVVGVQAQKLF 649 
                                           ************9.9********************************************************* PP

                            TIGR02082  966 kdakelldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdr.....yl 1032
                                           ++a+++ldk++ e+ l+a++vvGl+P ++ gdd++i+++++      +  t+   +++lrqq ++     + 
  lcl|FitnessBrowser__Cola:Echvi_3638  650 DEANAMLDKVIDENWLQAKAVVGLYPVKRSGDDLAILDENLH-----ETGTT---FHFLRQQGKKgkgvpNR 713 
                                           *************************************97665.....33333...577777766666779** PP

                            TIGR02082 1033 claDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwg 1104
                                           +laD++ +    ++Dy+g ++vtagl++++  ++++a+ ddy++i++ka++drlaea ae++he vRkelwg
  lcl|FitnessBrowser__Cola:Echvi_3638  714 SLADYLHP---EQVDYFGGFAVTAGLNMDKKVDAFKAEGDDYNEIMFKAIGDRLAEAAAEYMHEVVRKELWG 782 
                                           *******9...689********************************************************** PP

                            TIGR02082 1105 yaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahp 1175
                                           ya +e+l+++dl+ke+Y Girpa+GYpacP+h+ek+tl+eLl+a++ i ++lt+s+a+ P++svsg+yf hp
  lcl|FitnessBrowser__Cola:Echvi_3638  783 YAPKEKLENDDLIKESYAGIRPAPGYPACPEHSEKVTLFELLDAQNsIDVHLTDSFAMLPTSSVSGFYFGHP 854 
                                           ********************************************999************************* PP

                            TIGR02082 1176 eakYfa 1181
                                           e++Yf 
  lcl|FitnessBrowser__Cola:Echvi_3638  855 ESRYFG 860 
                                           *****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (902 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.11
# Mc/sec: 9.50
//
[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:

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