GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metH in Synechococcus elongatus PCC 7942

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate Synpcc7942_1372 Synpcc7942_1372 methionine synthase (B12-dependent)

Query= metacyc::G18NG-11090-MONOMER
         (1221 letters)



>FitnessBrowser__SynE:Synpcc7942_1372
          Length = 1190

 Score =  998 bits (2580), Expect = 0.0
 Identities = 561/1223 (45%), Positives = 765/1223 (62%), Gaps = 54/1223 (4%)

Query: 16   SEFLDALANH---VLIGDGAMGTQLQGFDLDVEKDF--LDLEGCNEILNDTRPDVLRQIH 70
            S FLD L +    VL+ DG MGT LQ  +L  E DF   + EGCNE L  T+P+ +  +H
Sbjct: 3    SLFLDRLHSPERPVLVFDGGMGTTLQFQNLTAE-DFGGPETEGCNEWLIRTKPEAIATVH 61

Query: 71   RAYFEAGADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRF 130
            R + EAGAD++ET+TFG     LA+Y + D    L  +   +A+ +A E         RF
Sbjct: 62   RQFLEAGADVIETDTFGATSIVLAEYGLEDHAYALNVEAAKLAKAIAAEFSTPEKP--RF 119

Query: 131  VVGSLGPGTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQ 190
            V GS+GP TKLP+LGH  Y +++  + E A G+ +GG D F++ET QD+LQ+KAA++G+ 
Sbjct: 120  VAGSMGPTTKLPTLGHIGYDEMKASFAEQARGLWEGGVDLFIVETCQDVLQIKAALNGIA 179

Query: 191  DAMAELDTFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHL 250
            +  +E     P++  VT+ETTGTML+GS++ A L  L+P  ID++GLNCATGPD M EH+
Sbjct: 180  EIFSEKGDRRPLMVSVTMETTGTMLVGSDVAAMLAILEPYPIDILGLNCATGPDRMVEHI 239

Query: 251  RYLSKHADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTP 310
            +YLS+H+   +S +PNAG+P      A Y L   +L  AL  FV + G+ ++GGCCGT P
Sbjct: 240  KYLSEHSPFVISCIPNAGIPENVGGHAHYRLTPMELRMALHRFVEDLGVQVIGGCCGTKP 299

Query: 311  EHIRAVRDAVVGVPEQETSTLTKIPAGPVEQASREVEKE-----DSVASLYTSVPLSQET 365
            EHI  +          E +T  +    PV +     +++      S AS+Y + P  Q+ 
Sbjct: 300  EHIAQL---------AEVATQLQAKDRPVRRDRDHQQRQPFNYVPSAASIYGTTPYIQDN 350

Query: 366  GISMIGERTNSNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMA 425
               +IGER N++GSK  RE +   DW+  V IA+ Q ++GAH+LD+ VDYVGRDG  DM 
Sbjct: 351  SFLIIGERLNASGSKKVRELLNEEDWDGLVAIARSQVKEGAHVLDVNVDYVGRDGERDMG 410

Query: 426  TLAALLATSSTLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVK 485
             L + L T+  LP+M+DSTE + +  GL+  GG+ I+NS N+EDGD    R+ ++++L K
Sbjct: 411  ELVSRLVTNVNLPLMLDSTEWQKMEAGLKKAGGKCILNSTNYEDGD---ERFFKVLELAK 467

Query: 486  QHGAAVVALTIDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEE 545
            Q+GA +V  TIDEEG ARTAE K  IA+R   D    +G+   +I  D L  PISTG EE
Sbjct: 468  QYGAGIVVGTIDEEGMARTAEKKFAIAQRAYRDAL-EFGIPAHEIFYDPLALPISTGIEE 526

Query: 546  TRRDGIETIEAIRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAI 605
             R +G ETIE+IR +++  P +H  LG+SNISFGLNPAAR VLNSVFL++  EAG+D AI
Sbjct: 527  DRGNGRETIESIRLIRENLPGVHILLGVSNISFGLNPAARIVLNSVFLHDACEAGMDGAI 586

Query: 606  AHSSKILPMNRIDDRQREVALDMVYDRRTED-----YDPLQEFMQLFEGVSAADAKDARA 660
              ++KILP+++ID++  +V  D++ DRR  +     YDPL E   LFEGVSA +A+ A  
Sbjct: 587  VSAAKILPLSKIDEKPLQVCRDLIGDRRRFENGICVYDPLTELTTLFEGVSAKEAR-ASG 645

Query: 661  EQLAAMPLFERLAQRIIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQ 720
              LA +PL ERL Q IIDG++ GL+  L   +++  P+ IIN  LL+GMK VG+LFGSGQ
Sbjct: 646  PSLADLPLEERLKQHIIDGERIGLDQALATALEQYPPLEIINTFLLDGMKVVGDLFGSGQ 705

Query: 721  MQLPFVLQSAETMKTAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVD 780
            MQLPFVLQSAETMK+AVAYLEPFM++E          GKG  ++ATVKGDVHDIGKNLVD
Sbjct: 706  MQLPFVLQSAETMKSAVAYLEPFMDKE-----ETNDSGKGTFLIATVKGDVHDIGKNLVD 760

Query: 781  IILSNNGYDVVNLGIKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGAS 840
            IIL+NNGY VVN+GIKQP+  +++A  +  AD I MSGLLVKST  MKENL   N  G S
Sbjct: 761  IILTNNGYKVVNIGIKQPVENIIQAYRDCNADCIAMSGLLVKSTAFMKENLATFNEEGIS 820

Query: 841  NYPVILGGAALTRTYVENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEA 900
              PVILGGAALT  +V  D  + Y G+V Y +DAF  L  MD++MA K  +  D      
Sbjct: 821  -VPVILGGAALTPKFVYEDCQQTYKGQVIYGKDAFADLHFMDQLMAAKSKDQWDDQLGFL 879

Query: 901  IEQAKKKAERKARNERSRKIAAERKANAAPVIVPERSD-VSTDTPTAAPPFWGTRIV--K 957
             EQ +        +E +      R++ A  VI  ERS+ V+ D     PPFWG++I+   
Sbjct: 880  DEQGQPLQVAAIASEAAEP-TESRESVAEVVIDLERSEAVAVDIDRPTPPFWGSKILGPD 938

Query: 958  GLPLAEFLGNLDERALFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILD 1017
             +P AE    LD +ALF+GQW  +  +      Y+  +  +  P L+ W  R+ +E +L+
Sbjct: 939  EIPFAEVFSYLDRQALFVGQWQFRKPKEQSREEYDAFIAEKVEPILQQWTTRILAEDLLE 998

Query: 1018 HVALVYGYFPAVAEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKD 1077
               +VYGYFP VA G+ + + + P+       RF FPRQ+  R LCIADF  P E  ++ 
Sbjct: 999  -PQVVYGYFPCVAVGNSLQLFD-PNDRDRPTARFDFPRQRSLRRLCIADFFAPEELGIQ- 1055

Query: 1078 GQVDVMPFQLVTMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELK 1137
               DV P Q VT+G+   +FA +LFA ++Y +YL  HG+ VQL EALAE+ H+R+R EL 
Sbjct: 1056 ---DVFPMQAVTVGHKATEFAAQLFAGDQYSDYLYFHGLAVQLAEALAEWTHARIRREL- 1111

Query: 1138 LNDGGSVADFDPEDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEE 1197
                      +PE         Y+G+R+SFGY +CP++ D    +ELLE  RIG+ + E 
Sbjct: 1112 -----GYGSLEPESLRDILAQRYQGSRYSFGYPACPNVADSRIQLELLEADRIGMSMDES 1166

Query: 1198 LQLHPEQSTDAFVLYHPEAKYFN 1220
             QL+PEQST A V YHP AKYF+
Sbjct: 1167 EQLYPEQSTTAIVAYHPAAKYFS 1189


Lambda     K      H
   0.316    0.135    0.386 

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: 3401
Number of extensions: 173
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: 1221
Length of database: 1190
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1143
Effective search space:  1341882
Effective search space used:  1341882
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 Synpcc7942_1372 Synpcc7942_1372 (methionine synthase (B12-dependent))
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.1810.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 1521.6   0.0          0 1521.4   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1372  Synpcc7942_1372 methionine synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1372  Synpcc7942_1372 methionine synthase (B12-dependent)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1521.4   0.0         0         0       2    1181 ..      13    1189 ..      12    1190 .] 0.97

  Alignments for each domain:
  == domain 1  score: 1521.4 bits;  conditional E-value: 0
                                 TIGR02082    2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDive 68  
                                                ++++lv+DG+mGt+lq +nLt++dF g       e +G+n+ L  tkPe+ia++hr+++eaGaD++e
  lcl|FitnessBrowser__SynE:Synpcc7942_1372   13 ERPVLVFDGGMGTTLQFQNLTAEDFGGP------ETEGCNEWLIRTKPEAIATVHRQFLEAGADVIE 73  
                                                689************************5......99******************************* PP

                                 TIGR02082   69 tntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdver 135 
                                                t+tF++t+i+la+Y+led+ay+ln +aakla+++a+ef+ tpek+RfvaGs+GPt+kl+tl+     
  lcl|FitnessBrowser__SynE:Synpcc7942_1372   74 TDTFGATSIVLAEYGLEDHAYALNVEAAKLAKAIAAEFS-TPEKPRFVAGSMGPTTKLPTLG----- 134 
                                                ***************************************.**********************..... PP

                                 TIGR02082  136 pefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvi 202 
                                                    ++ yde+++++ eq++gl +GGvDl+++et++D+l++kaal+++ e+f+ekg+++P+++s v+
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  135 ----HIGYDEMKASFAEQARGLWEGGVDLFIVETCQDVLQIKAALNGIAEIFSEKGDRRPLMVS-VT 196 
                                                ....************************************************************.** PP

                                 TIGR02082  203 vdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg 269 
                                                ++++G++L+G++++a+la+le+++i+ilGLnCa+G+d + e++k+lse++++++s+iPnaG+P+++g
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  197 METTGTMLVGSDVAAMLAILEPYPIDILGLNCATGPDRMVEHIKYLSEHSPFVISCIPNAGIPENVG 263 
                                                ******************************************************************9 PP

                                 TIGR02082  270 ...eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqe........... 322 
                                                   +Y+ltp+el +al+ f+e+++++++GGCCGt+Pehi+++ae++ +++ ++r+            
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  264 ghaHYRLTPMELRMALHRFVEDLGVQVIGGCCGTKPEHIAQLAEVATQLQAKDRPVrrdrdhqqrqp 330 
                                                999*********************************************9987665433444444455 PP

                                 TIGR02082  323 .leeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDin 388 
                                                  + +s++s++ + ++ q++sf++iGeR+n++Gskk+r+l+++ed++ ++ ia++qv+eGa++lD+n
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  331 fNYVPSAASIYGTTPYIQDNSFLIIGERLNASGSKKVRELLNEEDWDGLVAIARSQVKEGAHVLDVN 397 
                                                567899************************************************************* PP

                                 TIGR02082  389 vDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFle 455 
                                                vD+v++Dge+dm +l+s+l+++  + ++PlmlDs+e++++eaGLk+++Gk+i+ns++++dG+erF++
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  398 VDYVGRDGERDMGELVSRLVTN--V-NLPLMLDSTEWQKMEAGLKKAGGKCILNSTNYEDGDERFFK 461 
                                                **********************..6.99*************************************** PP

                                 TIGR02082  456 kaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieeh 522 
                                                 ++l+k+yGa++vv ++DeeG+arta+kk+ ia+Ray+++ e +g+p+++i++Dp++l+i+tGiee+
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  462 VLELAKQYGAGIVVGTIDEEGMARTAEKKFAIAQRAYRDALE-FGIPAHEIFYDPLALPISTGIEED 527 
                                                *****************************************9.************************ PP

                                 TIGR02082  523 dryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagkl 589 
                                                + ++ ++ie+ir i+e+lP ++i++Gvsn+sF+l+  +a+R +l+svFL++a +aG+D +iv+a+k+
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  528 RGNGRETIESIRLIRENLPGVHILLGVSNISFGLN--PAARIVLNSVFLHDACEAGMDGAIVSAAKI 592 
                                                ***********************************..****************************** PP

                                 TIGR02082  590 avyddidkelrevvedlildrr.....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLe 651 
                                                +++ +id+  ++v+ dli drr      + +++L+el++l++g+++k ++ a    +++lp+eeRL+
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  593 LPLSKIDEKPLQVCRDLIGDRRrfengICVYDPLTELTTLFEGVSAK-EARASGPSLADLPLEERLK 658 
                                                **********************77776789*****************.55588899*********** PP

                                 TIGR02082  652 ralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavay 718 
                                                +++++Ger g++++l  a+ ++++pleii++ LldGmkvvGdLFGsG+m+LP+v++sa++mk avay
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  659 QHIIDGERIGLDQALATAL-EQYPPLEIINTFLLDGMKVVGDLFGSGQMQLPFVLQSAETMKSAVAY 724 
                                                *******************.999******************************************** PP

                                 TIGR02082  719 LePylekekeedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkka 785 
                                                LeP+++ke+++d+ kG++++atvkGDvhDiGkn+vd++L++ngy+vv++G+k+Pve+i++a+++ +a
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  725 LEPFMDKEETNDSGKGTFLIATVKGDVHDIGKNLVDIILTNNGYKVVNIGIKQPVENIIQAYRDCNA 791 
                                                ******************************************************************* PP

                                 TIGR02082  786 DviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavk 852 
                                                D+i++sGL+vks+++m+e++  ++++g+++P++lGGaal++++v  +++++Ykg+v+y+kda+++++
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  792 DCIAMSGLLVKSTAFMKENLATFNEEGISVPVILGGAALTPKFVYEDCQQTYKGQVIYGKDAFADLH 858 
                                                ******************************************************************* PP

                                 TIGR02082  853 vvdkllsekkk...aeelekikeeyeeirekfgekkeklialsekaarkevfaldrse....dlevp 912 
                                                ++d+l+ +k+k   +++l+ + e+ + ++  +  ++    + s+++  + v++l+rse    d+++p
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  859 FMDQLMAAKSKdqwDDQLGFLDEQGQPLQVAAIASEAAEPTESRESVAEVVIDLERSEavavDIDRP 925 
                                                *********99555556667788888899999999999999999999999********99999**** PP

                                 TIGR02082  913 apkflGtkvleas...ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldkl 975 
                                                +p+f+G+k+l       +e+++y+D +alFv qW++r+ ++ ++++e+  + a+k+ ++++++  ++
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  926 TPPFWGSKILGPDeipFAEVFSYLDRQALFVgQWQFRKPKE-QSREEYDAFIAEKVEPILQQWTTRI 991 
                                                **********7555579************************.9************************ PP

                                 TIGR02082  976 saekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaske 1042
                                                 ae+ll++++v+G+fP+  vg+ +++++++ +      + ++ ++++++rq s r+lc+aDf+a+ e
  lcl|FitnessBrowser__SynE:Synpcc7942_1372  992 LAEDLLEPQVVYGYFPCVAVGNSLQLFDPNDR------DRPT-ARFDFPRQRSLRRLCIADFFAPEE 1051
                                                ****************************8777......2222.4689******************** PP

                                 TIGR02082 1043 sGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeee 1109
                                                 Gi+D++++++vt+g +a+e+a +l+a +++ d++++++la++laealae++h r+R+el  y++ e
  lcl|FitnessBrowser__SynE:Synpcc7942_1372 1052 LGIQDVFPMQAVTVGHKATEFAAQLFAGDQYSDYLYFHGLAVQLAEALAEWTHARIRRELG-YGSLE 1117
                                                ***********************************************************96.669** PP

                                 TIGR02082 1110 nldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpe 1176
                                                +++ +d+l +rY+G+r++fGYpacP++ + + +leLlea+riG+ ++es++l+Pe+s+++++ +hp+
  lcl|FitnessBrowser__SynE:Synpcc7942_1372 1118 PESLRDILAQRYQGSRYSFGYPACPNVADSRIQLELLEADRIGMSMDESEQLYPEQSTTAIVAYHPA 1184
                                                ******************************************************************* PP

                                 TIGR02082 1177 akYfa 1181
                                                akYf+
  lcl|FitnessBrowser__SynE:Synpcc7942_1372 1185 AKYFS 1189
                                                ****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (1190 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: 0.07u 0.04s 00:00:00.11 Elapsed: 00:00:00.11
# Mc/sec: 12.38
//
[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:

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