GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Bacillus alkalinitrilicus DSM 22532

Align Methionine synthase; EC 2.1.1.13; 5-methyltetrahydrofolate--homocysteine methyltransferase; Methionine synthase, vitamin-B12 dependent; MS (uncharacterized)
to candidate WP_078430828.1 BK574_RS10060 methionine synthase

Query= curated2:Q5E814
         (1226 letters)



>NCBI__GCF_002019605.1:WP_078430828.1
          Length = 1148

 Score =  810 bits (2093), Expect = 0.0
 Identities = 471/1194 (39%), Positives = 724/1194 (60%), Gaps = 57/1194 (4%)

Query: 7    KVQIEKQLSERILLIDGGMGTMIQGYKFEEEDYRGERFNKWHCDLKGNNDLLVLSQPQII 66
            K + E+QL ++IL++DG MGTM+Q      ED+ GE +       +G N+ L ++ P +I
Sbjct: 3    KNKFEQQLEKKILVLDGAMGTMLQDANLTAEDFGGEEY-------EGCNEYLNITAPHVI 55

Query: 67   RDIHEAYLEAGADILETNTFNATTIAMADYDMESLSEEINFEAAKLAREVADKWTEKTPN 126
              IH AY EAGADI+ETNTF AT I + DYD++ L+EE+N +AA++A++VA++++  T  
Sbjct: 56   EYIHRAYFEAGADIVETNTFGATDIVLEDYDLQHLAEELNIKAAQIAKKVAEEFS--TSE 113

Query: 127  KPRYVAGVLGPTNRTCSISPDVNDPGFRNVSFDELVEAYSESTRALIRGGSDLILIETIF 186
             PR+VAG +GPT ++ S++          V+FD+L++AY +    LI+GG D++L+ET  
Sbjct: 114  HPRFVAGAMGPTTKSLSVTG--------GVTFDQLIKAYEQQVIGLIKGGVDVLLLETSQ 165

Query: 187  DTLNAKACSFAVESVFEELDITLPVMISGTITDASGRTLSGQTTEAFYNALRHVKPISFG 246
            DT N KA    +E  F++L++ +P+++SGTI +  G TL+GQ  EAFY ++ H+ P   G
Sbjct: 166  DTRNVKAAYLGIERAFKQLNVKMPILVSGTI-EPMGTTLAGQNIEAFYLSIEHMTPTVVG 224

Query: 247  LNCALGPDELREYVSDLSRISECYVSAHPNAGLPNAFGEYDLSPEDMAEHVAEWASSGFL 306
            LNCA GP+ +++++  LS ++  YVS +PNAGLP+  G+Y  +PE + + +  +A  G+L
Sbjct: 225  LNCATGPEFMQDHIRSLSDLATSYVSCYPNAGLPDEDGKYHETPESLTKKLTAFAEKGWL 284

Query: 307  NLIGGCCGTTPEHIRQMALVVEGVKPRQLPE-LPVACRLSGLEPLTIEKDSLFINVGERT 365
            NL+GGCCGTTP HI+ M+  ++  +PR+L E  P A  +SG+EPL  ++    + VGERT
Sbjct: 285  NLVGGCCGTTPAHIKAMSEAMKSYQPRKLNEGHPHA--VSGIEPLVYDESMRPLFVGERT 342

Query: 366  NVTGSARFKRLIKEELYDEALSVAQEQVENGAQIIDINMDEGMLDAEACMVRFLNLCASE 425
            NV GS +FK LI + LY+EA  +A+ QV+ GA IIDI + +   + +  M  FL    ++
Sbjct: 343  NVIGSRKFKNLIADGLYEEASEIARSQVKKGAHIIDICLADPDREEKEDMEHFLKYVVNK 402

Query: 426  PEISKVPVMVDSSKWEVIEAGLKCIQGKGIVNSISLKEGKEKFVHQAKLIRRYGAAVIVM 485
                KVP+M+DS+  EV+E  L   QGK I+NSI+L++G+E+F     L+ RYGAAV+V 
Sbjct: 403  V---KVPLMIDSTDEEVLELALTYSQGKAIINSINLEDGEERFEKVIPLVHRYGAAVVVG 459

Query: 486  AFDEVGQADTRERKIEICTNAYNILVDEVGFPPEDIIFDPNIFAVATGIDEHNNYAVDFI 545
              DE G A T +RK+E+   +Y++LV++ G  P DIIFDP +F V TG +++   A + +
Sbjct: 460  TIDEEGMAVTAKRKLEVAKRSYDLLVNKYGLQPSDIIFDPLVFPVGTGDEQYIGSAKETV 519

Query: 546  EAVGDIKRTLPHAMISGGVSNVSFSFRGNNYVREAIHAVFLYHCFKNGMDMGIVNAGQLE 605
            E +  IK  LP  +   GVSNVSF        RE ++AV+LYHC + G+D  IVN  +LE
Sbjct: 520  EGIRLIKEALPECLTILGVSNVSFGL--PQVGREVLNAVYLYHCTQAGLDYAIVNTEKLE 577

Query: 606  IYDNVPEDLREAVEDVVLNRRDDSTERLLDIATEYLERAVGKVEDKSALEWRDWPVEKRL 665
             Y ++PE+ ++  + ++ +  D   E L +    Y    V KVE K  ++  +  +E+RL
Sbjct: 578  RYASIPENEKQLSDKLLFDTND---ETLAEFTAFY---RVKKVEKK--VQTSNLSLEERL 629

Query: 666  EHSLVKGITEFIVEDTEEARINAEKPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSAR 725
               +V+G  E ++ED ++A     +P+++I GPLM+GM+ VG LF   ++ + +V++SA 
Sbjct: 630  ASYIVEGTKEGLIEDLKQALEKYTEPLDIINGPLMNGMDEVGRLFNNNELIVAEVLQSAE 689

Query: 726  VMKQAVAHLEPFINASKEVGATNGKILLATVKGDVHDIGKNIVGVVLQCNNYEIIDLGVM 785
            VMK +VA LE ++   K      GKILLATVKGDVHDIGKN+V ++L  N ++I++LG+ 
Sbjct: 690  VMKASVAFLEQYME-KKSGDNGKGKILLATVKGDVHDIGKNLVEIILGNNGFKIVNLGIK 748

Query: 786  VSCETILKVAKEENVDIIGLSGLITPSLDEMVHVAKEMERQGFDLPLLIGGATTSKAHTA 845
            V+   +++  K EN D IGLSGL+  S  +MV  A++++ Q   +P+L+GGA  ++  T 
Sbjct: 749  VTSNELIEAVKRENPDAIGLSGLLVKSAQQMVLTAQDLKEQNISIPILVGGAALTRKFTD 808

Query: 846  VKIEQNYSQPVVYVNNASRAVGVCTSLL-SDELKPSFVEKLDIDYERVREQHSRKQPRTK 904
             +I + Y   V+Y  +A   + +   L+  DELK     KL+ D +   +Q   ++   K
Sbjct: 809  NRISREYDGVVLYAKDAMNGLDLANKLVKEDELK-----KLEEDKQTKLQQVGNEETEKK 863

Query: 905  -PVTLEVARANKVAIDWASYTPPVPLKPGVHIFDNFDVSTLRNYIDWTPFF-MTWSLVGK 962
              VT E+ R+    +       P  L+P  HI   + +S L  YI+          L GK
Sbjct: 864  NKVTTELPRSKVSQV--VPIHKPNDLQP--HILKEYKISHLEPYINLQMLLGKHLGLHGK 919

Query: 963  YPKILDHEEVGEEAKRLFKDANDLLDRVEKEGLLKARGMCALFPASSVGDDIEVY-TDES 1021
              ++L   E  E+A  L    + LL   +  GLL+ARGM   FPA S G+DI +Y   + 
Sbjct: 920  VSRLL--AEGDEKAHTLKDKVDSLLYEAKTNGLLQARGMYQFFPAQSKGNDIIIYDPQDE 977

Query: 1022 RTKVAKVLHNLRQQTEKPKGFNYCLSDYIAPKESGKNDWIGGFAVTGGIGERELADEYKA 1081
            +T++ +   +  +Q  +P     CL+DY+   +SG+ D++G  AVT GIG RE A + K 
Sbjct: 978  KTEIER--FSFPRQNHEP---FLCLADYVRSIDSGEMDYVGFLAVTAGIGVREKAMKAKD 1032

Query: 1082 NGDDYNAIMIQAVADRLAEAFAEYLHEKVRKEIWGYSPNETLSNDDLIREKYQGIRPAPG 1141
             GD   + +IQA A  LAE FAE  H+ +R + WG+     L+  D    KYQG+R + G
Sbjct: 1033 EGDYLFSHLIQATALELAEGFAERTHQLIRDQ-WGFPDPVELTMVDRFSAKYQGVRVSFG 1091

Query: 1142 YPACPEHTEKGALWELMNVEESIGMSLTSSYAMWPGASVSGMYFSHPDSRYFAI 1195
            YPACP   ++  L++L+   E IG+ LT  + M P ASV+ M FSHP+ RYF +
Sbjct: 1092 YPACPNLEDQAKLFKLLQ-PEKIGIKLTEEFMMEPEASVTAMVFSHPEGRYFNV 1144


Lambda     K      H
   0.317    0.135    0.394 

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: 3211
Number of extensions: 169
Number of successful extensions: 16
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: 1226
Length of database: 1148
Length adjustment: 47
Effective length of query: 1179
Effective length of database: 1101
Effective search space:  1298079
Effective search space used:  1298079
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 (21.6 bits)
S2: 59 (27.3 bits)

Align candidate WP_078430828.1 BK574_RS10060 (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.15418.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 1295.1   3.9          0 1294.9   3.9    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078430828.1  BK574_RS10060 methionine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078430828.1  BK574_RS10060 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1294.9   3.9         0         0       1    1182 []      10    1144 ..      10    1144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1294.9 bits;  conditional E-value: 0
                                 TIGR02082    1 lnkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67  
                                                l+k+ilvlDGamGt+lq anLt++dF ge      e++G+n++Ln+t P vi+ ihrayfeaGaDiv
  lcl|NCBI__GCF_002019605.1:WP_078430828.1   10 LEKKILVLDGAMGTMLQDANLTAEDFGGE------EYEGCNEYLNITAPHVIEYIHRAYFEAGADIV 70  
                                                579*************************7......9******************************* PP

                                 TIGR02082   68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134 
                                                etntF++t i+l+dYdl+++a eln kaa++a++va+ef+ t+e++RfvaG++GPt+k  +++    
  lcl|NCBI__GCF_002019605.1:WP_078430828.1   71 ETNTFGATDIVLEDYDLQHLAEELNIKAAQIAKKVAEEFS-TSEHPRFVAGAMGPTTKSLSVT---- 132 
                                                ****************************************.*******************999.... PP

                                 TIGR02082  135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201 
                                                      vt+d+l +aY++qv gl+ GGvD+lL+et +Dt n+kaa +++e++f++ ++++Pil+sg+
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  133 ----GGVTFDQLIKAYEQQVIGLIKGGVDVLLLETSQDTRNVKAAYLGIERAFKQLNVKMPILVSGT 195 
                                                ....789**********************************************************87 PP

                                 TIGR02082  202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268 
                                                i + +G+tL Gq++eaf+ s+eh+   ++GLnCa+G++ ++++++ ls  a+ +vs++PnaGLP++ 
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  196 I-EPMGTTLAGQNIEAFYLSIEHMTPTVVGLNCATGPEFMQDHIRSLSDLATSYVSCYPNAGLPDED 261 
                                                5.99*************************************************************** PP

                                 TIGR02082  269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335 
                                                g+Y++tpe+l k+l+ fae+g ln+vGGCCGttP+hi+a++ea+k  +prk +e +++ ++sg+e+l
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  262 GKYHETPESLTKKLTAFAEKGWLNLVGGCCGTTPAHIKAMSEAMKSYQPRKLNEGHPH-AVSGIEPL 327 
                                                ***************************************************9987665.679***** PP

                                 TIGR02082  336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402 
                                                 +++    + +GeRtnv Gs+kf++li ++ yeea +ia++qv++Ga+i+Di++ +  ++ ++dm++
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  328 VYDESMRPLFVGERTNVIGSRKFKNLIADGLYEEASEIARSQVKKGAHIIDICLADPDREEKEDMEH 394 
                                                ******************************************************************* PP

                                 TIGR02082  403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469 
                                                +l+ ++++  + kvPlm+Ds++ evle  L   qGkai+nsi+l+dGeerF + + l+++yGaavvv
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  395 FLKYVVNK--V-KVPLMIDSTDEEVLELALTYSQGKAIINSINLEDGEERFEKVIPLVHRYGAAVVV 458 
                                                ********..6.******************************************************* PP

                                 TIGR02082  470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536 
                                                 ++DeeG+a ta++k+e+akR y+ll++k+g++p+diifDp++++++tG e     a++++e ir i
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  459 GTIDEEGMAVTAKRKLEVAKRSYDLLVNKYGLQPSDIIFDPLVFPVGTGDEQYIGSAKETVEGIRLI 525 
                                                ******************************************************************* PP

                                 TIGR02082  537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603 
                                                ke lP++ + +GvsnvsF+l   +  Re+l++v+Ly++ +aGlD +ivn+ kl+ y+ i+++ +++ 
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  526 KEALPECLTILGVSNVSFGLP--QVGREVLNAVYLYHCTQAGLDYAIVNTEKLERYASIPENEKQLS 590 
                                                ********************9..999***************************************** PP

                                 TIGR02082  604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670 
                                                  l++d ++   e L e++  y+ +k +     ++ +  nl++eeRL+  +v+G++eg+ edl++a+
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  591 DKLLFDTND---ETLAEFTAFYRVKKVE-----KKVQTSNLSLEERLASYIVEGTKEGLIEDLKQAL 649 
                                                *****9876...5688899888877777.....34567899************************** PP

                                 TIGR02082  671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkiv 737 
                                                +k+++pl+ii+gpL++Gm+ vG LF + ++ +  v++sa+vmk++va+Le y+ek+   d+ kGki+
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  650 EKYTEPLDIINGPLMNGMDEVGRLFNNNELIVAEVLQSAEVMKASVAFLEQYMEKKS-GDNGKGKIL 715 
                                                ******************************************************976.999****** PP

                                 TIGR02082  738 latvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvev 804 
                                                latvkGDvhDiGkn+v+++L++ng+++v+lG+kv  ++++ea k++++D iglsGL+vks ++mv  
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  716 LATVKGDVHDIGKNLVEIILGNNGFKIVNLGIKVTSNELIEAVKRENPDAIGLSGLLVKSAQQMVLT 782 
                                                ******************************************************************* PP

                                 TIGR02082  805 aeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekik 871 
                                                a+++++++++iP+l+GGaal+++++++ i ++Y+g v+y+kda++++ +++kl++e++ ++  e  +
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  783 AQDLKEQNISIPILVGGAALTRKFTDNRISREYDGVVLYAKDAMNGLDLANKLVKEDELKKLEEDKQ 849 
                                                ******************************************************9997555434333 PP

                                 TIGR02082  872 eeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwka 937 
                                                +   ++++  +e+ ek+++++++  r++v ++     + + +p++l  ++l+++ i +l +yi++++
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  850 T---KLQQVGNEETEKKNKVTTELPRSKVSQV-----VPIHKPNDLQPHILKEYkISHLEPYINLQM 908 
                                                3...4444445555666777777777544443.....456789999999****************** PP

                                 TIGR02082  938 lFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiyt 1003
                                                l   + +l+gk  + l +   +++a+ l +++++ll + ++++ll+arg++ +fPaqs+g+di iy+
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  909 LLGkHLGLHGKVSRLLAEG--DEKAHTLKDKVDSLLYEAKTNGLLQARGMYQFFPAQSKGNDIIIYD 973 
                                                *99799*******888775..667899999************************************* PP

                                 TIGR02082 1004 detvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelakkleak 1070
                                                ++          t +e++ ++rq+ + +lclaD+++s +sG+ Dy+g+l+vtag+g++e a k +++
  lcl|NCBI__GCF_002019605.1:WP_078430828.1  974 PQ-------DEKTEIERFSFPRQNHEPFLCLADYVRSIDSGEMDYVGFLAVTAGIGVREKAMKAKDE 1033
                                                44.......446778899************************************************* PP

                                 TIGR02082 1071 eddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdht 1137
                                                 d+  s l++a a  lae +ae +h+ +R ++ +  +  +l + d +  +Y+G+r +fGYpacP+++
  lcl|NCBI__GCF_002019605.1:WP_078430828.1 1034 GDYLFSHLIQATALELAEGFAERTHQLIRDQWGFP-DPVELTMVDRFSAKYQGVRVSFGYPACPNLE 1099
                                                *****************************987777.77778999*********************** PP

                                 TIGR02082 1138 ekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
                                                ++a+l++Ll++e+iG+klte+++++Peasv++++f+hpe +Yf+v
  lcl|NCBI__GCF_002019605.1:WP_078430828.1 1100 DQAKLFKLLQPEKIGIKLTEEFMMEPEASVTAMVFSHPEGRYFNV 1144
                                                *******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1148 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: 0.12u 0.04s 00:00:00.16 Elapsed: 00:00:00.15
# Mc/sec: 8.97
//
[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:

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