Alignments for a candidate for metH in Thermithiobacillus tepidarius DSM 3134

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Thermithiobacillus tepidarius DSM 3134

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_081662708.1 G579_RS16870 methionine synthase

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



>NCBI__GCF_000423825.1:WP_081662708.1
          Length = 849

 Score =  863 bits (2230), Expect = 0.0
 Identities = 462/873 (52%), Positives = 604/873 (69%), Gaps = 35/873 (4%)

Query: 16  SEFLDALANHVLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFE 75
           S F++ L   VLI DG MGT L  FDLD++KD+  LE C+E+L  +RPDV+  +H+++F+
Sbjct: 2   SAFMERLRERVLIADGGMGTSLHTFDLDLDKDYWGLENCSEVLVLSRPDVVAAVHKSFFD 61

Query: 76  AGADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSL 135
           AG+D VET+TFG N   LA++ +++R  E+  K   +AR VAD +        RFV+GS+
Sbjct: 62  AGSDCVETDTFGANKVVLAEFGLSERTFEINEKAAQIARGVADALSTPE--WPRFVIGSI 119

Query: 136 GPGTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAE 195
           GPGTKLPSLGH  Y  L   Y E A G+I GG D  LIETAQD+LQVKAAV+G + A AE
Sbjct: 120 GPGTKLPSLGHTSYDVLEDSYAEQARGLIAGGVDLLLIETAQDILQVKAAVNGCKIARAE 179

Query: 196 LDTFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSK 255
               +PI   VT+ETTGTML+G++I AA TA+  LG+D +G+NCATGP EMSEH+R+L +
Sbjct: 180 AGMDVPIFAQVTIETTGTMLVGTDIAAAATAIHALGVDGMGMNCATGPAEMSEHVRWLGE 239

Query: 256 HADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRA 315
           +    +SVMPNAGLP+L +    YPL   +LA  +  +V E G+++VGGCCGTTPEHIRA
Sbjct: 240 NWPHLISVMPNAGLPMLVEGQTVYPLGPRELADWMLRYVEEDGVNLVGGCCGTTPEHIRA 299

Query: 316 VRDAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTN 375
           +R+A +G   +                +R  E   +V+SLY+ VPL QE  +  +GER N
Sbjct: 300 LREA-IGFDRR--------------PRARSPEWVPAVSSLYSQVPLRQENAVLAVGERAN 344

Query: 376 SNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSS 435
           +NGSK FRE + + DW+  V +A+ Q ++G+H+LD+C  YVGR   ADM  +        
Sbjct: 345 ANGSKKFRELLAAEDWDAMVGVARDQVKEGSHVLDVCTAYVGRPEVADMQEVVNRYRGQV 404

Query: 436 TLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALT 495
           T+P+MIDSTE  V+   L+ LGG+SI+NS+NFEDG   E + +R++   +++GAAVVALT
Sbjct: 405 TVPLMIDSTEVPVLEAALKLLGGKSIINSINFEDG---EEKAERVLGFARKYGAAVVALT 461

Query: 496 IDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIE 555
           IDEEG A+  E K+ IA RL D     YGL   D++ D LTF I TG EE RR GI T+E
Sbjct: 462 IDEEGMAKEVEQKLAIAHRLYDFAVKRYGLPASDLIYDPLTFTICTGVEEDRRHGINTLE 521

Query: 556 AIRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMN 615
           AI  +++  PE    LGLSNISFGL PAAR VLNSVFL+   + GL +AI H + I P++
Sbjct: 522 AIERIRRELPECQIMLGLSNISFGLKPAARHVLNSVFLHHAQKRGLTAAIIHVAAIKPLH 581

Query: 616 RIDDRQREVALDMVYDRRTEDYDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQR 675
           +I     E A D+++DRR + +DPL  F++LF+ V+ A AK A     A   + ERL QR
Sbjct: 582 QIPPEHVEAAEDLIFDRRDKGFDPLLRFVELFKDVTVASAKKA-----APATVEERLTQR 636

Query: 676 IIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKT 735
           I+DGDK GLEDDL+A +++  P+ IIN  LL+GMK VGELFGSGQMQLPFVLQSAETMK 
Sbjct: 637 IVDGDKQGLEDDLKAALEQYPPLEIINTFLLDGMKVVGELFGSGQMQLPFVLQSAETMKA 696

Query: 736 AVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGI 795
           AVA+LEPFME+        + E KG +V+ATVKGDVHDIGKNLVDIIL+NNGY VVNLGI
Sbjct: 697 AVAFLEPFMEK-------VEGEEKGILVLATVKGDVHDIGKNLVDIILTNNGYKVVNLGI 749

Query: 796 KQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTRTY 855
           KQP+ ++++AA +  A  IGMSGLLVKSTV+MKENLEEM   G  + PV+LGGAALTR +
Sbjct: 750 KQPIDSIVQAACDCGAHAIGMSGLLVKSTVIMKENLEEMRRRGL-DIPVLLGGAALTRRF 808

Query: 856 VENDLNEVY--TGEVYYARDAFEGLRLMDEVMA 886
           VEND    Y     V+YA+DAFEGL+LM+++MA
Sbjct: 809 VENDCRAAYGHPERVHYAKDAFEGLKLMEQIMA 841


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: 2436
Number of extensions: 112
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: 1221
Length of database: 849
Length adjustment: 45
Effective length of query: 1176
Effective length of database: 804
Effective search space:   945504
Effective search space used:   945504
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: 57 (26.6 bits)

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_081662709.1 G579_RS18665 hypothetical protein

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



>NCBI__GCF_000423825.1:WP_081662709.1
          Length = 289

 Score =  217 bits (552), Expect = 1e-60
 Identities = 122/288 (42%), Positives = 169/288 (58%), Gaps = 14/288 (4%)

Query: 935  ERSD-VSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERALFMGQWGLKSTRGNEGPSYED 993
            E SD V  D P   PPFWG R+++ + L   +  ++   L+  QWG K+   +    Y+ 
Sbjct: 15   ESSDPVRRDNPIPIPPFWGARVIEHVSLRAIVPYINRNTLYKFQWGFKAPEMSP-QEYKA 73

Query: 994  LVETEGRPRLRYWLDRLKSEGILDHVALVYGYFPAVAEGDDVVILESPDPHAAERMRFSF 1053
               TE  P     +   +++ IL   A VYGYFPA +EGDD+++   P+    ER RF+F
Sbjct: 74   WARTEVDPIFNRLVAASEAQSILQPKA-VYGYFPAQSEGDDLIVYTDPESRQ-ERARFTF 131

Query: 1054 PRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLVTMGNPIADFANELFAANEYREYLEV 1113
            PRQ+  R  CIADF RP    V  G++DV+ FQLVT+G   AD A ELF  ++Y+EYL  
Sbjct: 132  PRQKTARRRCIADFFRP----VDSGEMDVVAFQLVTVGQHAADHARELFHGDQYQEYLYW 187

Query: 1114 HGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFDPEDKTKFFDLDYRGARFSFGYGSCP 1173
            HG+  +  E LAEY H ++R+EL        A  D  D       +YRG+R+SFGY +CP
Sbjct: 188  HGLNAEGAEGLAEYIHKQIRAEL------GFAREDARDIQAMIKQEYRGSRYSFGYPACP 241

Query: 1174 DLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDAFVLYHPEAKYFNV 1221
            +L D+ K+++LL   RIGV + +E QL PE ST A V +HP+AKYF V
Sbjct: 242  NLHDQHKILDLLGAERIGVVMGDEDQLWPEDSTSAIVAHHPQAKYFGV 289


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: 831
Number of extensions: 40
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1221
Length of database: 289
Length adjustment: 36
Effective length of query: 1185
Effective length of database: 253
Effective search space:   299805
Effective search space used:   299805
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: 53 (25.0 bits)

Align candidate WP_081662708.1 G579_RS16870 (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.3374.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 1072.6   0.0          0 1072.4   0.0    1.0  1  lcl|NCBI__GCF_000423825.1:WP_081662708.1  G579_RS16870 methionine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000423825.1:WP_081662708.1  G579_RS16870 methionine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1072.4   0.0         0         0       2     859 ..       9     841 ..       8     848 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1072.4 bits;  conditional E-value: 0
                                 TIGR02082   2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDivetn 70 
                                               ++r+l+ DG+mGt l +++L+ ++  +        l+ + ++L+l++P+v+aa+h+++f+aG+D vet+
  lcl|NCBI__GCF_000423825.1:WP_081662708.1   9 RERVLIADGGMGTSLHTFDLDLDKDYW-------GLENCSEVLVLSRPDVVAAVHKSFFDAGSDCVETD 70 
                                               79*******************986666.......39********************************* PP

                                 TIGR02082  71 tFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefr 139
                                               tF++++++la+++l +++ e+n+kaa++ar vad ++ tpe +Rfv+Gs+GP++kl++l+         
  lcl|NCBI__GCF_000423825.1:WP_081662708.1  71 TFGANKVVLAEFGLSERTFEINEKAAQIARGVADALS-TPEWPRFVIGSIGPGTKLPSLG--------- 129
                                               *************************************.**********************......... PP

                                 TIGR02082 140 nvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGr 208
                                               ++ yd l d+Y eq++gl+ GGvDllLiet +D+l++kaa+++ + + +e+g ++Pi+++ v+++++G+
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 130 HTSYDVLEDSYAEQARGLIAGGVDLLLIETAQDILQVKAAVNGCKIARAEAGMDVPIFAQ-VTIETTGT 197
                                               ************************************************************.******** PP

                                 TIGR02082 209 tLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg...eYdlt 274
                                               +L+G++++a++++++  +++ +G+nCa+G++e++e+v+ l+e+ + l+sv+PnaGLP  +     Y+l 
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 198 MLVGTDIAAAATAIHALGVDGMGMNCATGPAEMSEHVRWLGENWPHLISVMPNAGLPMLVEgqtVYPLG 266
                                               *********************************************************99977889**** PP

                                 TIGR02082 275 peelakalkefaeegllnivGGCCGttPehiraiaeavk.dikprkrqeleeksvlsglealkiaqess 342
                                               p ela  +  ++ee ++n+vGGCCGttPehira+ ea+  d +pr r     + v+s+++++++ qe+ 
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 267 PRELADWMLRYVEEDGVNLVGGCCGTTPEHIRALREAIGfDRRPRARSPEWVPAVSSLYSQVPLRQENA 335
                                               ***********************************9985489999999999****************** PP

                                 TIGR02082 343 fvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasep 411
                                               ++ +GeR n++Gskkfr+l+ aed+++++ +a++qv+eG+++lD++  +v++  +adm++++++  ++ 
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 336 VLAVGERANANGSKKFRELLAAEDWDAMVGVARDQVKEGSHVLDVCTAYVGRPEVADMQEVVNRYRGQ- 403
                                               *******************************************************************9. PP

                                 TIGR02082 412 diakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqart 480
                                                + +vPlm+Ds+e+ vlea Lk ++Gk+i+nsi+++dGee+  + + ++++yGaavv++++DeeG+a++
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 404 -V-TVPLMIDSTEVPVLEAALKLLGGKSIINSINFEDGEEKAERVLGFARKYGAAVVALTIDEEGMAKE 470
                                               .6.9***************************************************************** PP

                                 TIGR02082 481 adkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGv 549
                                                ++k+ ia+R+y+ +++++g+p++d+i+Dp+++ti tG+ee++r++i+++eai++i++elP+++i +G+
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 471 VEQKLAIAHRLYDFAVKRYGLPASDLIYDPLTFTICTGVEEDRRHGINTLEAIERIRRELPECQIMLGL 539
                                               ********************************************************************* PP

                                 TIGR02082 550 snvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekL 618
                                               sn+sF+l+  +a+R++l+svFL++a+k Gl ++i++ + ++++++i++e  e++edli+drr++  ++L
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 540 SNISFGLK--PAARHVLNSVFLHHAQKRGLTAAIIHVAAIKPLHQIPPEHVEAAEDLIFDRRDKGFDPL 606
                                               ********..*********************************************************** PP

                                 TIGR02082 619 lelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldG 687
                                               l+++el+k+++ +s+k     + +   veeRL++++v+G ++g+e+dl++a+ ++++pleii++ LldG
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 607 LRFVELFKDVTVASAK-----KAAPATVEERLTQRIVDGDKQGLEDDLKAAL-EQYPPLEIINTFLLDG 669
                                               ***********99555.....567789*************************.999************* PP

                                 TIGR02082 688 mkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvv 756
                                               mkvvG+LFGsG+m+LP+v++sa++mk+ava+LeP++ek +   + kG +vlatvkGDvhDiGkn+vd++
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 670 MKVVGELFGSGQMQLPFVLQSAETMKAAVAFLEPFMEKVE--GEEKGILVLATVKGDVHDIGKNLVDII 736
                                               ************************************9876..8899*********************** PP

                                 TIGR02082 757 LscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaals 825
                                               L++ngy+vv+lG+k+P++ i++aa +  a  ig+sGL+vks++ m+e++eem+rrg++iP+llGGaal+
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 737 LTNNGYKVVNLGIKQPIDSIVQAACDCGAHAIGMSGLLVKSTVIMKENLEEMRRRGLDIPVLLGGAALT 805
                                               ********************************************************************* PP

                                 TIGR02082 826 kahvavkiaekYkg..evvyvkdaseavkvvdklls 859
                                               + +v++++  +Y    +v+y+kda+e++k++++++ 
  lcl|NCBI__GCF_000423825.1:WP_081662708.1 806 RRFVENDCRAAYGHpeRVHYAKDAFEGLKLMEQIMA 841
                                               ************75226*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1182 nodes)
Target sequences:                          1  (849 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 0.02s 00:00:00.09 Elapsed: 00:00:00.09
# Mc/sec: 11.11
//
[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