GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Methylocella silvestris BL2

Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012592503.1 MSIL_RS18005 methionine synthase

Query= CharProtDB::CH_090726
         (1227 letters)



>NCBI__GCF_000021745.1:WP_012592503.1
          Length = 1245

 Score = 1483 bits (3838), Expect = 0.0
 Identities = 763/1221 (62%), Positives = 922/1221 (75%), Gaps = 15/1221 (1%)

Query: 14   ERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAYFE 73
            +RILVLDG MGTMIQ ++  E  FRGERFADWP DL+GNNDLL L++P+ I  IH AY +
Sbjct: 20   KRILVLDGAMGTMIQQHKFTEEQFRGERFADWPSDLRGNNDLLSLTQPKAIEQIHRAYID 79

Query: 74   AGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAGVL 133
            AGADII TNTFNST+I+ ADY M+ L  E+N  +A+L R  AD    +   K R+VAG L
Sbjct: 80   AGADIIATNTFNSTSISQADYGMQELVFELNRESARLCRVAADA-AEKHDGKRRFVAGAL 138

Query: 134  GPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKAAV 193
            GPT+RTASISPDVN+P FR ++FD L  AY E+ +AL+EGGADL++IET+FDTLNAKAA+
Sbjct: 139  GPTSRTASISPDVNNPGFRAVSFDELRDAYDEAARALIEGGADLLIIETIFDTLNAKAAL 198

Query: 194  FAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGPDE 253
              V+  F  LGVE P+MISGTITD SGRTLSGQT  AF++SLRHA+ LT GLNCALG  E
Sbjct: 199  AGVRDAFAKLGVEAPVMISGTITDLSGRTLSGQTPTAFWHSLRHADPLTIGLNCALGARE 258

Query: 254  LRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCCGT 313
            +R ++ ELSRIA+  V A+PNAGLPN FG YD   + MA  + E+A +G +N+VGGCCGT
Sbjct: 259  MRAHLAELSRIADTLVCAYPNAGLPNEFGLYDESPEYMASLVGEFADSGLVNVVGGCCGT 318

Query: 314  TPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKR 373
            TP HI A+++ +EG+APR++PEI    RLSGLEP  +  +  FVNVGERTNVTGSAKF++
Sbjct: 319  TPAHIHAIAKRIEGVAPREIPEIAPLLRLSGLEPFVLAPEIPFVNVGERTNVTGSAKFRK 378

Query: 374  LIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMI 433
            LIK+  ++ ALDVAR QV  GAQIID+NMDEG+LD+E AMV FLNLIA EPDIARVP+MI
Sbjct: 379  LIKQGDFAAALDVARDQVAAGAQIIDVNMDEGLLDSEKAMVEFLNLIAAEPDIARVPVMI 438

Query: 434  DSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADT 493
            DSSK+ VIE GLKC+QGK +VNSISMKEGV+ FI  A+ +R YGAAVVVMAFDE+GQADT
Sbjct: 439  DSSKFSVIEAGLKCVQGKSVVNSISMKEGVEKFIADARTVRAYGAAVVVMAFDEKGQADT 498

Query: 494  RARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKREL 553
              RK+EIC +AY+ILT+E GFPPEDIIFDPNIFA+ATGIEEHNNY  DFI A  +I++  
Sbjct: 499  FERKVEICAKAYQILTQEAGFPPEDIIFDPNIFAIATGIEEHNNYGVDFIEATREIRKRF 558

Query: 554  PHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELR 613
            P   ISGGVSN+SFSFRGN+PVREA+HAVFLY+AI+ GMDMGIVNAGQLA+Y ++   LR
Sbjct: 559  PLVHISGGVSNLSFSFRGNEPVREAMHAVFLYHAIQAGMDMGIVNAGQLAVYAEIEPGLR 618

Query: 614  DAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITE 673
            +A EDV+LNRR D TERLL +AE +RG   +     +   WR   V KRLE++LV GITE
Sbjct: 619  EACEDVVLNRRPDATERLLAIAEGFRGHGVEKA--ERDLVWREQPVIKRLEHALVNGITE 676

Query: 674  FIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLE 733
            F+E D EEAR  + RP++VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMKQAVAYL 
Sbjct: 677  FVELDVEEARAASKRPLDVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAYLL 736

Query: 734  PFIEASKEQG-----KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEK 788
            P+++  K +       T GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+DLGVMVPA K
Sbjct: 737  PYMDEEKRKNGGSERSTAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPAAK 796

Query: 789  ILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQ 848
            IL  A+    D IGLSGLITPSLDEM  VA EMER+GF +PLLIGGATTS+ HTAVKI  
Sbjct: 797  ILSVARAEKVDAIGLSGLITPSLDEMCYVAAEMEREGFDLPLLIGGATTSRVHTAVKIHP 856

Query: 849  NYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVART-RKEYETVRIQHGRKKPRTPPVTL 906
            NY+ G TVYV +ASR VGVV +LL ++ RD   A T R EYE V   H R +     + +
Sbjct: 857  NYTRGQTVYVNDASRAVGVVQSLLGESARD--AAETFRAEYEKVAAAHRRGEAEKLRLPI 914

Query: 907  EAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKYPRILE 965
              AR N    DW  Y PP     G +   +  +  L  YIDWTPFF TW L G+YP IL+
Sbjct: 915  GKARANALKIDWDDYAPPRPTFTGSRVFRSYDVAELIPYIDWTPFFQTWELRGRYPAILD 974

Query: 966  DEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINV 1025
            D   G  A+ LF DA  ML ++  E  L+P+ V+G +PAN VGDDI +Y  E+R+  +  
Sbjct: 975  DPKQGEAARSLFDDAQAMLKRMVEEHWLDPKAVIGFWPANSVGDDIALYTGESRSEKLAA 1034

Query: 1026 SHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYN 1084
             H LRQQ T + G  N  L+DF+AP   GK DYIGAF VT G +E  +AD F   +DDY 
Sbjct: 1035 FHTLRQQLTRRDGKPNIALSDFIAP-AGGKPDYIGAFVVTAGAQEGKIADRFAKANDDYG 1093

Query: 1085 KIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPE 1144
             I+VKALADR+AEA AE +HERVR+ +W YAP+E +S ++ +RE Y+GIRPAPGYPA P+
Sbjct: 1094 SILVKALADRIAEALAERMHERVRREFWAYAPDEAISEDDRLREEYRGIRPAPGYPAQPD 1153

Query: 1145 HTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYA 1204
            HTEKAT++ELL  EK  G+ LTESFAMWPGASVSG YF+HP + Y+ VA+I+RDQVEDYA
Sbjct: 1154 HTEKATLFELLAAEKRIGVSLTESFAMWPGASVSGLYFAHPQAHYFGVAKIERDQVEDYA 1213

Query: 1205 RRKGMSVTEVERWLAPNLGYD 1225
             RKGMSV E+ERWLAP L YD
Sbjct: 1214 LRKGMSVAEMERWLAPILNYD 1234


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: 3661
Number of extensions: 133
Number of successful extensions: 8
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: 1245
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1197
Effective search space:  1411263
Effective search space used:  1411263
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_012592503.1 MSIL_RS18005 (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.3061049.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 1727.5   0.0          0 1727.3   0.0    1.0  1  NCBI__GCF_000021745.1:WP_012592503.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021745.1:WP_012592503.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1727.3   0.0         0         0       2    1182 .]      19    1201 ..      18    1201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1727.3 bits;  conditional E-value: 0
                             TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetnt 71  
                                            +krilvlDGamGt++q+++ te++Frge +ad++++l+GnndlL+lt+P +i++ihray +aGaDi+ tnt
  NCBI__GCF_000021745.1:WP_012592503.1   19 RKRILVLDGAMGTMIQQHKFTEEQFRGErFADWPSDLRGNNDLLSLTQPKAIEQIHRAYIDAGADIIATNT 89  
                                            79********************************************************************* PP

                             TIGR02082   72 FnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvt 142 
                                            Fnst+i++adY++++++ eln+++a+l r +ad  +++  k+RfvaG+lGPt+++a++spdv++p+fr v 
  NCBI__GCF_000021745.1:WP_012592503.1   90 FNSTSISQADYGMQELVFELNRESARLCRVAADAAEKHDGKRRFVAGALGPTSRTASISPDVNNPGFRAVS 160 
                                            ************************************999******************************** PP

                             TIGR02082  143 ydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGq 213 
                                            +del+daY e++++l++GG+Dll+iet+fDtlnakaal +v+++f++ g+e P++isg+i+d sGrtLsGq
  NCBI__GCF_000021745.1:WP_012592503.1  161 FDELRDAYDEAARALIEGGADLLIIETIFDTLNAKAALAGVRDAFAKLGVEAPVMISGTITDLSGRTLSGQ 231 
                                            *********************************************************************** PP

                             TIGR02082  214 tleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalke 284 
                                            t  af +sl+ha+ l++GLnCalGa e+r ++ els++a++lv ++PnaGLPn++g Yd+ pe +a+ + e
  NCBI__GCF_000021745.1:WP_012592503.1  232 TPTAFWHSLRHADPLTIGLNCALGAREMRAHLAELSRIADTLVCAYPNAGLPNEFGLYDESPEYMASLVGE 302 
                                            *********************************************************************** PP

                             TIGR02082  285 faeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGs 355 
                                            fa  gl+n+vGGCCGttP+hi+aia+ +++++pr+ +e+ + ++lsgle++ +a+e  fvn+GeRtnv+Gs
  NCBI__GCF_000021745.1:WP_012592503.1  303 FADSGLVNVVGGCCGTTPAHIHAIAKRIEGVAPREIPEIAPLLRLSGLEPFVLAPEIPFVNVGERTNVTGS 373 
                                            *********************************************************************** PP

                             TIGR02082  356 kkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefe 426 
                                            +kfrklik++d+ +al++a++qv  Gaqi+D+n+De+llD+e++m+++l+l+a+epdia+vP+m+Dss+f 
  NCBI__GCF_000021745.1:WP_012592503.1  374 AKFRKLIKQGDFAAALDVARDQVAAGAQIIDVNMDEGLLDSEKAMVEFLNLIAAEPDIARVPVMIDSSKFS 444 
                                            *********************************************************************** PP

                             TIGR02082  427 vleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykllte 497 
                                            v+eaGLk++qGk++vnsis+k+G+e+F+  a+ ++ yGaavvvmafDe+Gqa+t ++k+ei+ +ay++lt+
  NCBI__GCF_000021745.1:WP_012592503.1  445 VIEAGLKCVQGKSVVNSISMKEGVEKFIADARTVRAYGAAVVVMAFDEKGQADTFERKVEICAKAYQILTQ 515 
                                            *********************************************************************** PP

                             TIGR02082  498 kvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhs 568 
                                            ++gfppediifDpni++iatGieeh++y++dfiea+rei++++P ++isgGvsn+sFs+rgn++vRea+h+
  NCBI__GCF_000021745.1:WP_012592503.1  516 EAGFPPEDIIFDPNIFAIATGIEEHNNYGVDFIEATREIRKRFPLVHISGGVSNLSFSFRGNEPVREAMHA 586 
                                            *********************************************************************** PP

                             TIGR02082  569 vFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqea 639 
                                            vFLy+ai+aG+Dmgivnag+lavy++i++ lre++ed++l+rr++ate+Ll +ae ++g   +  k ++  
  NCBI__GCF_000021745.1:WP_012592503.1  587 VFLYHAIQAGMDMGIVNAGQLAVYAEIEPGLREACEDVVLNRRPDATERLLAIAEGFRGHGVE--KAERDL 655 
                                            *************************************************************99..888999 PP

                             TIGR02082  640 ewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksar 710 
                                             wr++pv +RLe+alv+G++e++e d+eear   k+pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksar
  NCBI__GCF_000021745.1:WP_012592503.1  656 VWREQPVIKRLEHALVNGITEFVELDVEEARAASKRPLDVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSAR 726 
                                            *********************************************************************** PP

                             TIGR02082  711 vmkkavayLePylekekeed.....kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPveki 776 
                                            vmk+avayL Py+++ek ++     +++Gki++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP++ki
  NCBI__GCF_000021745.1:WP_012592503.1  727 VMKQAVAYLLPYMDEEKRKNggserSTAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPAAKI 797 
                                            *****************999999999********************************************* PP

                             TIGR02082  777 leaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkd 846 
                                            l +a+ +k D iglsGLi++sldem +va emer+g+++Pll+GGa++s+ h+avki+++Y  g++vyv+d
  NCBI__GCF_000021745.1:WP_012592503.1  798 LSVARAEKVDAIGLSGLITPSLDEMCYVAAEMEREGFDLPLLIGGATTSRVHTAVKIHPNYTrGQTVYVND 868 
                                            *************************************************************548******* PP

                             TIGR02082  847 aseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkfl 917 
                                            as+av vv++ll e ++++ +e  ++eye++   +++ + ++  l++ +ar + +++d+  d+ +p p+f 
  NCBI__GCF_000021745.1:WP_012592503.1  869 ASRAVGVVQSLLGESARDA-AETFRAEYEKVAAAHRRGEAEKLRLPIGKARANALKIDWD-DYAPPRPTFT 937 
                                            ***************8665.59*************************************9.********** PP

                             TIGR02082  918 Gtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvv 987 
                                            G++v++++ ++el++yiDw+++F +Welrg+yp il+d+++g+ ar lf+da+++l+++++e+ l +++v+
  NCBI__GCF_000021745.1:WP_012592503.1  938 GSRVFRSYdVAELIPYIDWTPFFQTWELRGRYPAILDDPKQGEAARSLFDDAQAMLKRMVEEHWLDPKAVI 1008
                                            *********************************************************************** PP

                             TIGR02082  988 GlfPaqsvgddieiytdetvsqetkpiatvrekleq.lrqqsdrylclaDfiaskesGikDylgallvtag 1057
                                            G++Pa+svgddi++yt+e++s   +++a++++ ++q +r++ + +++l+Dfia+ + G+ Dy+ga++vtag
  NCBI__GCF_000021745.1:WP_012592503.1 1009 GFWPANSVGDDIALYTGESRS---EKLAAFHTLRQQlTRRDGKPNIALSDFIAP-AGGKPDYIGAFVVTAG 1075
                                            ****************99995...45555555445505555555**********.88************** PP

                             TIGR02082 1058 lgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpaf 1128
                                             ++ ++a+++ + +ddy+silvkaladr+aealae +hervR+e+w+ya +e+ + +d l+e+YrGirpa+
  NCBI__GCF_000021745.1:WP_012592503.1 1076 AQEGKIADRFAKANDDYGSILVKALADRIAEALAERMHERVRREFWAYAPDEAISEDDRLREEYRGIRPAP 1146
                                            *********************************************************************** PP

                             TIGR02082 1129 GYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
                                            GYpa+Pdhtekatl+eLl ae+ iG+ ltes+a++P asvsglyfahp+a+Yf v
  NCBI__GCF_000021745.1:WP_012592503.1 1147 GYPAQPDHTEKATLFELLAAEKrIGVSLTESFAMWPGASVSGLYFAHPQAHYFGV 1201
                                            *********************99******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1245 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 30.60
//
[ok]

This GapMind analysis is from Jul 25 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