GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Phyllobacterium brassicacearum STM 196

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_106713177.1 CU102_RS21440 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_003010955.1:WP_106713177.1
          Length = 1262

 Score = 1506 bits (3898), Expect = 0.0
 Identities = 765/1220 (62%), Positives = 926/1220 (75%), Gaps = 11/1220 (0%)

Query: 14   ERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAYFE 73
            ERIL+LDG MGT IQ   LNE  FRG+RFAD  C L+GNNDLL+L++P+ I  IH AY  
Sbjct: 35   ERILILDGAMGTQIQGLNLNEESFRGDRFADCSCHLQGNNDLLILTQPQAIEDIHYAYAM 94

Query: 74   AGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAGVL 133
            AGADI+ETNTF+STTIA ADY ME +  E+N   A+LAR  A +   +   K R+VAG L
Sbjct: 95   AGADILETNTFSSTTIAQADYSMEEVVYELNRDGARLARRAAIK-AEQKDGKRRFVAGAL 153

Query: 134  GPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKAAV 193
            GPTNRTASISPDVN+P +R +TFD L  AY E  + L++GGAD+ILIET+FDTLNAKAA+
Sbjct: 154  GPTNRTASISPDVNNPGYRAVTFDDLRIAYAEQVRGLIDGGADIILIETIFDTLNAKAAI 213

Query: 194  FAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGPDE 253
            FA +  FE  G+ LPIMISGTITD SGRTLSGQT  AF+ S+RHA+  T GLNCALG + 
Sbjct: 214  FATQEVFEEKGITLPIMISGTITDRSGRTLSGQTPTAFWYSVRHAKPFTIGLNCALGANA 273

Query: 254  LRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCCGT 313
            +R ++ E++ +A+ +V A+PNAGLPN FG+YD   + MA Q+ E+A+ G LNIVGGCCG+
Sbjct: 274  MRDHLAEIASVADAFVCAYPNAGLPNEFGQYDESPEAMAAQLEEFAREGLLNIVGGCCGS 333

Query: 314  TPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKR 373
            TP+HI A++ AV    PR++PE  +  RLSGLEP  + +D  FVNVGERTN+TGSAKF++
Sbjct: 334  TPEHIKAIAEAVGKYGPREIPETEIHMRLSGLEPFTLTKDIAFVNVGERTNITGSAKFRK 393

Query: 374  LIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMI 433
            LI    ++ ALDVAR QV NGAQIIDINMDEG++D+E AMV FLNLIA EPDIARVP+MI
Sbjct: 394  LITSGDFATALDVARDQVANGAQIIDINMDEGLIDSEKAMVEFLNLIAAEPDIARVPVMI 453

Query: 434  DSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADT 493
            DSSKWDVIE GLKC+QGK +VNSISMKEG  AFI HAK +R YGAAVVVMAFD QGQADT
Sbjct: 454  DSSKWDVIEAGLKCVQGKPLVNSISMKEGEQAFIDHAKRVRAYGAAVVVMAFDTQGQADT 513

Query: 494  RARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKREL 553
              RK+ I  RAY++LT E GFPPEDI+FDPN+FAVATGIEEHN Y   FI A   I   L
Sbjct: 514  LERKVAISTRAYELLTREAGFPPEDIVFDPNVFAVATGIEEHNGYGVAFIEATRQITETL 573

Query: 554  PHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELR 613
            PH  ISGG+SN+SFSFRGN+PVREA+HAVFLY+AI+ GMDMGIVNAGQLA+Y+ +  ELR
Sbjct: 574  PHVHISGGISNLSFSFRGNEPVREAMHAVFLYHAIQVGMDMGIVNAGQLAVYESIDPELR 633

Query: 614  DAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITE 673
            +A EDV+LNRRDD TERLL+LAE+Y+G+   + A  +   WR W V KR+E++LV GITE
Sbjct: 634  EACEDVVLNRRDDATERLLDLAERYKGAAGKE-ARERDLAWREWSVEKRIEHALVNGITE 692

Query: 674  FIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLE 733
            FIE DTEEAR +A RP+ VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMKQAVA L 
Sbjct: 693  FIEADTEEARLEAERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAVLL 752

Query: 734  PFIEASK------EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAE 787
            P++EA K       Q ++ GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+DLGVMVP+ 
Sbjct: 753  PYMEAEKLANGGSGQRESAGKVLMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPSA 812

Query: 788  KILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIE 847
            KIL+TA++   D+IGLSGLITPSLDEMV+VA EMER+GF IPLLIGGATTS+ HTAVKI 
Sbjct: 813  KILQTARDEKVDIIGLSGLITPSLDEMVHVAAEMEREGFDIPLLIGGATTSRVHTAVKIN 872

Query: 848  QNY-SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTL 906
              Y  G TVYV +ASR VGVV+ LLS   +  +V   R EY  V   H R +     ++L
Sbjct: 873  PRYHKGQTVYVTDASRAVGVVSNLLSLEAKPGYVDGVRAEYTKVAEAHARNEADKQRLSL 932

Query: 907  EAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYPRILE 965
              AR N    DW +YTPP    LG +  E   +  +  YIDWTPFF TW L G+YP ILE
Sbjct: 933  AKARANAQMVDWVSYTPPKPSFLGTRVFENYDLAEIARYIDWTPFFQTWELKGRYPAILE 992

Query: 966  DEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINV 1025
            DE  G  A++LF DA  ML K+ AEK  NP+ V+GL+PA  VGDDI ++ DE R   +  
Sbjct: 993  DEKQGPAARQLFDDAQAMLKKIIAEKWFNPKAVIGLWPAGAVGDDIRLFTDEARGQELAT 1052

Query: 1026 SHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYN 1084
               LRQQ +++ G  N  L+DFVAP  SGK DY+G F VT G+EE A+A+ FE  +DDY+
Sbjct: 1053 FFTLRQQLSKRDGRPNVALSDFVAPVDSGKEDYVGGFVVTAGIEEVAIAERFERANDDYS 1112

Query: 1085 KIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPE 1144
             I+VKALADR AEAFAE +H+RVRK +WGYAP ENL++++LI E Y+GIRPAPGYPA P+
Sbjct: 1113 SILVKALADRFAEAFAELMHQRVRKEFWGYAPEENLASDDLIGEAYRGIRPAPGYPAQPD 1172

Query: 1145 HTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYA 1204
            HTEK T++ LL+ E    ++LTESFAMWPG+SVSG Y +HPDS Y+ VA+++RDQVEDYA
Sbjct: 1173 HTEKETLFRLLDAEAKIDVRLTESFAMWPGSSVSGIYIAHPDSYYFGVAKVERDQVEDYA 1232

Query: 1205 RRKGMSVTEVERWLAPNLGY 1224
             RK M V +VERWL P L Y
Sbjct: 1233 ARKSMPVADVERWLGPILNY 1252


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: 3669
Number of extensions: 125
Number of successful extensions: 9
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: 1262
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1214
Effective search space:  1431306
Effective search space used:  1431306
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: 59 (27.3 bits)

Align candidate WP_106713177.1 CU102_RS21440 (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.2578274.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 1754.0   0.0          0 1753.8   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106713177.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106713177.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1753.8   0.0         0         0       2    1182 .]      34    1220 ..      33    1220 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1753.8 bits;  conditional E-value: 0
                             TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetnt 71  
                                            ++ril+lDGamGtq+q  nL+e+ Frg+ +ad++++l+GnndlL lt+P++i++ih ay  aGaDi+etnt
  NCBI__GCF_003010955.1:WP_106713177.1   34 RERILILDGAMGTQIQGLNLNEESFRGDrFADCSCHLQGNNDLLILTQPQAIEDIHYAYAMAGADILETNT 104 
                                            68********************************************************************* PP

                             TIGR02082   72 FnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvt 142 
                                            F+st+ia+adY +e+ +yeln+ +a+lar++a + +++  k+RfvaG+lGPtn++a++spdv++p++r vt
  NCBI__GCF_003010955.1:WP_106713177.1  105 FSSTTIAQADYSMEEVVYELNRDGARLARRAAIKAEQKDGKRRFVAGALGPTNRTASISPDVNNPGYRAVT 175 
                                            ************************************999999***************************** PP

                             TIGR02082  143 ydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGq 213 
                                            +d+l+ aY eqv+gl+dGG+D++Liet+fDtlnakaa+fa++evfeekg+ lPi+isg+i+d+sGrtLsGq
  NCBI__GCF_003010955.1:WP_106713177.1  176 FDDLRIAYAEQVRGLIDGGADIILIETIFDTLNAKAAIFATQEVFEEKGITLPIMISGTITDRSGRTLSGQ 246 
                                            *********************************************************************** PP

                             TIGR02082  214 tleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalke 284 
                                            t  af  s++ha+ +++GLnCalGa+ +r+++ e++  a+a+v ++PnaGLPn++g+Yd+ pe +a++l+e
  NCBI__GCF_003010955.1:WP_106713177.1  247 TPTAFWYSVRHAKPFTIGLNCALGANAMRDHLAEIASVADAFVCAYPNAGLPNEFGQYDESPEAMAAQLEE 317 
                                            *********************************************************************** PP

                             TIGR02082  285 faeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGs 355 
                                            fa+egllnivGGCCG+tPehi+aiaeav +  pr+ +e+e +++lsgle+++++++  fvn+GeRtn++Gs
  NCBI__GCF_003010955.1:WP_106713177.1  318 FAREGLLNIVGGCCGSTPEHIKAIAEAVGKYGPREIPETEIHMRLSGLEPFTLTKDIAFVNVGERTNITGS 388 
                                            *********************************************************************** PP

                             TIGR02082  356 kkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefe 426 
                                            +kfrkli+ +d+  al++a++qv +Gaqi+Din+De+l D+e++m+++l+l+a+epdia+vP+m+Dss+++
  NCBI__GCF_003010955.1:WP_106713177.1  389 AKFRKLITSGDFATALDVARDQVANGAQIIDINMDEGLIDSEKAMVEFLNLIAAEPDIARVPVMIDSSKWD 459 
                                            *********************************************************************** PP

                             TIGR02082  427 vleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykllte 497 
                                            v+eaGLk++qGk +vnsis+k+Ge++F+++ak ++ yGaavvvmafD +Gqa+t ++k+ i +Ray+llt 
  NCBI__GCF_003010955.1:WP_106713177.1  460 VIEAGLKCVQGKPLVNSISMKEGEQAFIDHAKRVRAYGAAVVVMAFDTQGQADTLERKVAISTRAYELLTR 530 
                                            *********************************************************************** PP

                             TIGR02082  498 kvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhs 568 
                                            ++gfppedi+fDpn++++atGieeh+ y+++fiea+r+i e+lP+++isgG+sn+sFs+rgn++vRea+h+
  NCBI__GCF_003010955.1:WP_106713177.1  531 EAGFPPEDIVFDPNVFAVATGIEEHNGYGVAFIEATRQITETLPHVHISGGISNLSFSFRGNEPVREAMHA 601 
                                            *********************************************************************** PP

                             TIGR02082  569 vFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqea 639 
                                            vFLy+ai++G+Dmgivnag+lavy+ id+elre++ed++l+rr++ate+Ll+lae+ykg   k ++ ++  
  NCBI__GCF_003010955.1:WP_106713177.1  602 VFLYHAIQVGMDMGIVNAGQLAVYESIDPELREACEDVVLNRRDDATERLLDLAERYKGAAGK-EARERDL 671 
                                            **************************************************************9.5558899 PP

                             TIGR02082  640 ewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksar 710 
                                            +wr+++ve+R+e+alv+G++e+ie+d+eear ++++pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksar
  NCBI__GCF_003010955.1:WP_106713177.1  672 AWREWSVEKRIEHALVNGITEFIEADTEEARLEAERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSAR 742 
                                            9********************************************************************** PP

                             TIGR02082  711 vmkkavayLePylekekeed......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvek 775 
                                            vmk+ava+L Py+e+ek ++      +s+Gk+++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP +k
  NCBI__GCF_003010955.1:WP_106713177.1  743 VMKQAVAVLLPYMEAEKLANggsgqrESAGKVLMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPSAK 813 
                                            *****************9999999999******************************************** PP

                             TIGR02082  776 ileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvk 845 
                                            il++a+++k D+iglsGLi++sldemv+va emer+g++iPll+GGa++s+ h+avki+++Y kg++vyv+
  NCBI__GCF_003010955.1:WP_106713177.1  814 ILQTARDEKVDIIGLSGLITPSLDEMVHVAAEMEREGFDIPLLIGGATTSRVHTAVKINPRYhKGQTVYVT 884 
                                            *************************************************************9669****** PP

                             TIGR02082  846 daseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkf 916 
                                            das+av vv++lls ++k  +++ +++ey ++ e + +++  ++ ls+++ar +   +d+   +++p+p f
  NCBI__GCF_003010955.1:WP_106713177.1  885 DASRAVGVVSNLLSLEAKPGYVDGVRAEYTKVAEAHARNEADKQRLSLAKARANAQMVDWV-SYTPPKPSF 954 
                                            *************************************************************.9******** PP

                             TIGR02082  917 lGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargv 986 
                                            lGt+v+e++ ++e+  yiDw+++F +Wel+g+yp il+de++g  ar+lf+da+++l+k++aek  ++++v
  NCBI__GCF_003010955.1:WP_106713177.1  955 LGTRVFENYdLAEIARYIDWTPFFQTWELKGRYPAILEDEKQGPAARQLFDDAQAMLKKIIAEKWFNPKAV 1025
                                            *********************************************************************** PP

                             TIGR02082  987 vGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvta 1056
                                            +Gl+Pa  vgddi ++tde++    +++at+ + ++ql +  +r +++l+Df+a+ +sG++Dy+g ++vta
  NCBI__GCF_003010955.1:WP_106713177.1 1026 IGLWPAGAVGDDIRLFTDEAR---GQELATFFTLRQQLSKRDGRpNVALSDFVAPVDSGKEDYVGGFVVTA 1093
                                            ********************9...556677777778888888888************************** PP

                             TIGR02082 1057 glgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpa 1127
                                            g+++ ++a+++e  +ddy+silvkaladr+aea+ael+h+rvRke+wgya eenl+ +dl+ e YrGirpa
  NCBI__GCF_003010955.1:WP_106713177.1 1094 GIEEVAIAERFERANDDYSSILVKALADRFAEAFAELMHQRVRKEFWGYAPEENLASDDLIGEAYRGIRPA 1164
                                            *********************************************************************** PP

                             TIGR02082 1128 fGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                            +GYpa+Pdhtek tl++Ll+ae  i ++ltes+a++P +svsg+y+ahp++ Yf v
  NCBI__GCF_003010955.1:WP_106713177.1 1165 PGYPAQPDHTEKETLFRLLDAEAkIDVRLTESFAMWPGSSVSGIYIAHPDSYYFGV 1220
                                            **********************99******************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1262 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 43.67
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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