Alignments for a candidate for metH in Hyphomicrobium sulfonivorans WDL6

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Hyphomicrobium sulfonivorans WDL6

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_083509711.1 APY04_RS10635 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_001541235.1:WP_083509711.1
          Length = 913

 Score = 1107 bits (2862), Expect = 0.0
 Identities = 571/882 (64%), Positives = 673/882 (76%), Gaps = 13/882 (1%)

Query: 356  FVNVGERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVR 415
            F+NVGERTNVTGSA+F++LI+   Y  AL VAR QVENGAQ+IDINMDEG+LD+E AM  
Sbjct: 24   FINVGERTNVTGSARFRKLIEANDYPAALAVARSQVENGAQVIDINMDEGLLDSEKAMTT 83

Query: 416  FLNLIAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRR 475
            FLNLIA EPDIARVP+MIDSSKW VIE GLKC+QGK IVNSIS+KEG + F+ HAK + R
Sbjct: 84   FLNLIASEPDIARVPVMIDSSKWSVIEAGLKCVQGKPIVNSISLKEGEEQFLDHAKKVLR 143

Query: 476  YGAAVVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEH 535
            YGAAVVVMAFDE GQADT  RK EIC RAYKILTE+VGFPPEDIIFDPNIFAVATGIEEH
Sbjct: 144  YGAAVVVMAFDEVGQADTEDRKFEICHRAYKILTEQVGFPPEDIIFDPNIFAVATGIEEH 203

Query: 536  NNYAQDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMG 595
            N Y   FI A   IK  +P   ISGGVSN+SF+FRGN+PVR A+H+VFLYYAI  GMDMG
Sbjct: 204  NGYGIAFIEAVRRIKEVMPLVHISGGVSNLSFAFRGNEPVRAAMHSVFLYYAIAAGMDMG 263

Query: 596  IVNAGQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG-SKTDDTANAQQAEW 654
            IVNAGQL  YD +  ELRD  EDV+LN+R D T+RLL+ A +++G   T      +   W
Sbjct: 264  IVNAGQLTPYDAIDPELRDLCEDVVLNKRPDATDRLLDAAPRFKGDGSTGAKPKEKDLSW 323

Query: 655  RSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMF 714
            R+  V +RL +SLV GIT+FIE+DTEEARQQA +P+ VIEGPLM GMNVVGDLFG GKMF
Sbjct: 324  RNQPVQERLTHSLVNGITDFIEEDTEEARQQAAKPLHVIEGPLMAGMNVVGDLFGAGKMF 383

Query: 715  LPQVVKSARVMKQAVAYLEPFIEASK-----EQGKTNGKMVIATVKGDVHDIGKNIVGVV 769
            LPQVVKSARVMKQAVAYL+PF+E  K     +Q    GK+V+ATVKGDVHDIGKNIVGVV
Sbjct: 384  LPQVVKSARVMKQAVAYLQPFLEEEKRASGVDQMPAAGKIVMATVKGDVHDIGKNIVGVV 443

Query: 770  LQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIP 829
            LQCNNYE++DLGVMVPA KIL  AK+  AD+IGLSGLITPSLDEM  VA EMER+GF  P
Sbjct: 444  LQCNNYEVIDLGVMVPAAKILEAAKKEKADMIGLSGLITPSLDEMCFVAAEMEREGFDCP 503

Query: 830  LLIGGATTSKAHTAVKIEQNYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYE 888
            LLIGGATTS+ HTAVKI  NYS G  +YV +ASR VGVV+ LLS+T R D+VA  + EY 
Sbjct: 504  LLIGGATTSRVHTAVKISPNYSKGQAIYVLDASRAVGVVSKLLSETDRQDYVAEIQTEYV 563

Query: 889  TVRIQHGRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDW 947
             VR  H + +     + L AAR+N F  DW  YTPP    LG ++ E   +  L  YIDW
Sbjct: 564  KVRENHLKNEASKKRIPLSAARENKFNIDWPNYTPPKPTFLGTRKFENYPLAELVPYIDW 623

Query: 948  TPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV 1007
            TPFF TW LAG+YP IL+D  VG EAQ+LF DA +ML  + A   +   GVVG +PAN +
Sbjct: 624  TPFFQTWELAGRYPAILKDNKVGAEAQKLFNDAQEMLRAMVAGNWVRASGVVGFWPANAI 683

Query: 1008 GDDIEIYRDETRTHVINVSHHLRQQ---TEKTGFANYCLADFVAPKLSGKADYIGAFAVT 1064
            GDDI +Y D++R+  I   H LRQQ     K   A+  L+DF+AP+ SG ADY+G FAVT
Sbjct: 684  GDDIAVYADDSRSEQIATFHTLRQQIARDPKRDRAHTALSDFIAPQGSGIADYVGGFAVT 743

Query: 1065 GGL-EEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNE 1123
             GL EEDA+A   +A  DDY++I++KAL+DRLAEAFAE +H RVR+  WGYA +E LSN+
Sbjct: 744  AGLGEEDAIAKHVKAT-DDYSRILLKALSDRLAEAFAECMHARVRRELWGYAADEKLSND 802

Query: 1124 ELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFS 1183
            +LI E Y GIRPAPGYPA P+HTEK TIWEL++VE   GM+LTES+AMWPGA+V+G YFS
Sbjct: 803  DLILEKYSGIRPAPGYPAQPDHTEKGTIWELMDVENAIGMQLTESYAMWPGAAVAGLYFS 862

Query: 1184 HPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
            HPDS Y+ V +++RDQVEDYA RKG +V E ERWLAP L YD
Sbjct: 863  HPDSHYFGVGKVERDQVEDYAARKGWTVEETERWLAPVLNYD 904


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: 2634
Number of extensions: 104
Number of successful extensions: 6
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: 913
Length adjustment: 45
Effective length of query: 1182
Effective length of database: 868
Effective search space:  1025976
Effective search space used:  1025976
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_068462437.1 APY04_RS10640 5-methyltetrahydrofolate--homocysteine methyltransferase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_001541235.1:WP_068462437.1
          Length = 355

 Score =  430 bits (1105), Expect = e-124
 Identities = 212/340 (62%), Positives = 256/340 (75%)

Query: 8   LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67
           L A   ERIL++DG MGTMIQ Y+L+E  +RG RF DW  D+KGNNDLLVL++P++I AI
Sbjct: 11  LEAAAQERILIIDGAMGTMIQRYKLDEDGYRGVRFKDWHRDVKGNNDLLVLTQPQIIGAI 70

Query: 68  HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127
           H+ YF AGADIIETNTFN+  I++ADY ME L+ E+N AAA++AR  AD W  +TP+K R
Sbjct: 71  HDEYFAAGADIIETNTFNAQKISLADYGMEDLAYEVNLAAARIARDVADTWNKKTPDKLR 130

Query: 128 YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187
           +VAG +GPTNRTASISPDVN+P FRN+ FD L  AY+E  + L++GG D+ILIET+FDTL
Sbjct: 131 FVAGAIGPTNRTASISPDVNNPGFRNVDFDELREAYKEQMRGLMDGGVDIILIETIFDTL 190

Query: 188 NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247
           NAKAA  A    FE  GVELPIMISGTITD SGRTLSGQT EAF+ S+RH    + GLNC
Sbjct: 191 NAKAAGVATLEVFEEKGVELPIMISGTITDRSGRTLSGQTAEAFWYSMRHLRPFSIGLNC 250

Query: 248 ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIV 307
           ALG D +R Y+ ELS  A+  ++A+PNAGLPNA GEYD     MA  I  WA+ G LNIV
Sbjct: 251 ALGADLMRPYLAELSGFADTRISAYPNAGLPNAMGEYDETPHDMACAIEPWARDGILNIV 310

Query: 308 GGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEP 347
           GGCCG+TP+HIA +   V   APRK+P IP   RLSGLEP
Sbjct: 311 GGCCGSTPEHIAHVREHVSKFAPRKIPSIPPKLRLSGLEP 350


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: 1115
Number of extensions: 37
Number of successful extensions: 1
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: 355
Length adjustment: 38
Effective length of query: 1189
Effective length of database: 317
Effective search space:   376913
Effective search space used:   376913
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_083509711.1 APY04_RS10635 (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.24948.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 1256.2   0.0          0 1255.9   0.0    1.0  1  lcl|NCBI__GCF_001541235.1:WP_083509711.1  APY04_RS10635 methionine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001541235.1:WP_083509711.1  APY04_RS10635 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1255.9   0.0         0         0     335    1182 .]      16     871 ..       3     871 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1255.9 bits;  conditional E-value: 0
                                 TIGR02082  335 lkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmk 401 
                                                 + +  + f+n+GeRtnv+Gs++frkli+a+dy +al +a++qve+Gaq++Din+De+llD+e++m+
  lcl|NCBI__GCF_001541235.1:WP_083509711.1   16 TTANAAQAFINVGERTNVTGSARFRKLIEANDYPAALAVARSQVENGAQVIDINMDEGLLDSEKAMT 82  
                                                45566779*********************************************************** PP

                                 TIGR02082  402 kllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavv 468 
                                                ++l+l+asepdia+vP+m+Dss++ v+eaGLk++qGk ivnsislk+Gee+Fl++ak++ +yGaavv
  lcl|NCBI__GCF_001541235.1:WP_083509711.1   83 TFLNLIASEPDIARVPVMIDSSKWSVIEAGLKCVQGKPIVNSISLKEGEEQFLDHAKKVLRYGAAVV 149 
                                                ******************************************************************* PP

                                 TIGR02082  469 vmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaire 535 
                                                vmafDe Gqa+t d+k+ei++Rayk+lte+vgfppediifDpni+++atGieeh+ y+i+fiea+r+
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  150 VMAFDEVGQADTEDRKFEICHRAYKILTEQVGFPPEDIIFDPNIFAVATGIEEHNGYGIAFIEAVRR 216 
                                                ******************************************************************* PP

                                 TIGR02082  536 ikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrev 602 
                                                ike +P ++isgGvsn+sF++rgn++vR a+hsvFLy+ai aG+Dmgivnag+l++yd id+elr++
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  217 IKEVMPLVHISGGVSNLSFAFRGNEPVRAAMHSVFLYYAIAAGMDMGIVNAGQLTPYDAIDPELRDL 283 
                                                ******************************************************************* PP

                                 TIGR02082  603 vedlildrrreatekLlelaelykgtkeksskeaqea.ewrnlpveeRLeralvkGeregieedlee 668 
                                                +ed++l++r++at++Ll+ a ++kg  ++ +k ++++  wrn+pv+eRL+++lv+G++++ieed+ee
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  284 CEDVVLNKRPDATDRLLDAAPRFKGDGSTGAKPKEKDlSWRNQPVQERLTHSLVNGITDFIEEDTEE 350 
                                                ************************998887776555438**************************** PP

                                 TIGR02082  669 arkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed..... 730 
                                                ar+++ +pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+avayL+P+le+ek ++     
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  351 ARQQAAKPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAYLQPFLEEEKRASgvdqm 417 
                                                ***********************************************************99899999 PP

                                 TIGR02082  731 kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivks 797 
                                                 ++Gkiv+atvkGDvhDiGkniv+vvL+cn+yev+dlGv+vP++kileaakk+kaD+iglsGLi++s
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  418 PAAGKIVMATVKGDVHDIGKNIVGVVLQCNNYEVIDLGVMVPAAKILEAAKKEKADMIGLSGLITPS 484 
                                                9****************************************************************** PP

                                 TIGR02082  798 ldemvevaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvkdaseavkvvdkllsekkk 863 
                                                ldem +va emer+g++ Pll+GGa++s+ h+avki ++Y kg+ +yv das+av vv+kllse+ +
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  485 LDEMCFVAAEMEREGFDCPLLIGGATTSRVHTAVKISPNYsKGQAIYVLDASRAVGVVSKLLSETDR 551 
                                                ****************************************5589*********************** PP

                                 TIGR02082  864 aeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieel 929 
                                                ++++++i++ey ++re++ +++  ++ ++++aar+++f++d+  ++++p+p+flGt+++e++ ++el
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  552 QDYVAEIQTEYVKVRENHLKNEASKKRIPLSAARENKFNIDWP-NYTPPKPTFLGTRKFENYpLAEL 617 
                                                *******************************************.9********************** PP

                                 TIGR02082  930 lkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg 996 
                                                ++yiDw+++F +Wel+g+yp ilkd+++g+ea+klf+da+e+l  ++a + +ra+gvvG++Pa+ +g
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  618 VPYIDWTPFFQTWELAGRYPAILKDNKVGAEAQKLFNDAQEMLRAMVAGNWVRASGVVGFWPANAIG 684 
                                                ******************************************************************* PP

                                 TIGR02082  997 ddieiytdetvsqetkpiatvrekleqlrqqsdr...ylclaDfiaskesGikDylgallvtaglga 1060
                                                ddi++y+d+++s ++ +  t+r+   q+ ++ +r   +++l+Dfia++ sGi+Dy+g ++vtaglg+
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  685 DDIAVYADDSRSEQIATFHTLRQ---QIARDPKRdraHTALSDFIAPQGSGIADYVGGFAVTAGLGE 748 
                                                *********99766666666654...444433333359***************************** PP

                                 TIGR02082 1061 eelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpa 1127
                                                e+   k  + +ddy+ il+kal+drlaea+ae +h rvR+elwgya++e+l+++dl+ e+Y Girpa
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  749 EDAIAKHVKATDDYSRILLKALSDRLAEAFAECMHARVRRELWGYAADEKLSNDDLILEKYSGIRPA 815 
                                                **99999999********************************************************* PP

                                 TIGR02082 1128 fGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                                +GYpa+Pdhtek t++eL+++e+ iG++ltes+a++P a+v+glyf+hp+++Yf v
  lcl|NCBI__GCF_001541235.1:WP_083509711.1  816 PGYPAQPDHTEKGTIWELMDVENaIGMQLTESYAMWPGAAVAGLYFSHPDSHYFGV 871 
                                                ******************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (913 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: 13.16
//
[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