Alignments for a candidate for metH in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Desulfobulbus mediterraneus DSM 13871

Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_028583363.1 G494_RS0103145 5-methyltetrahydrofolate--homocysteine methyltransferase

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



>NCBI__GCF_000429965.1:WP_028583363.1
          Length = 816

 Score =  626 bits (1615), Expect = 0.0
 Identities = 367/872 (42%), Positives = 511/872 (58%), Gaps = 60/872 (6%)

Query: 351  SVASLYTSVPLSQETGISMIGERTNSNGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLD 410
            SV+SLY +V L QE    +IGER NSNGSK FRE +L+ D+E C+ IA++Q   GAH++D
Sbjct: 4    SVSSLYQAVELQQEIPPLLIGERANSNGSKKFRELLLADDFEACLKIAQEQESKGAHIID 63

Query: 411  LCVDYVGRDGTADMATLAALLATSSTLPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDG 470
            LC  Y GRD  AD+  L  +  +S   PIMIDST PE I   L    GR ++NS+N EDG
Sbjct: 64   LCTAYAGRDELADLTRLVKMCVSSLKAPIMIDSTTPECIEACLRLYPGRCVINSINLEDG 123

Query: 471  DGPESRYQRIMKLVKQHGAAVVALTIDEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDI 530
                   +RI +  K++GAAVVALTIDE+G A TAE K+RIAK +       + L   D+
Sbjct: 124  G---HNIRRICQAAKRYGAAVVALTIDEQGMAMTAEDKLRIAKAIYAIAVDEFKLRPSDL 180

Query: 531  VVDCLTFPISTGQEETRRDGIETIEAIRELKKLYPEIHTTLGLSNISFGLNPAARQVLNS 590
            + DCLTF + +G E+ R   I+T+E IR +K+  P   T LGLSNISFGL P AR++LNS
Sbjct: 181  LFDCLTFTVGSGDEKLRDAAIQTLEGIRLIKRELPGCLTVLGLSNISFGLAPKARRILNS 240

Query: 591  VFLNECIEAGLDSAIAHSSKILPMNRIDDRQREVALDMVYDRRTE-DYDPLQEFMQLFEG 649
            VFL++ +EAGLD+AI  ++KILP+ RI    REV LD++YDR  E +  PL  F+  F  
Sbjct: 241  VFLHQAVEAGLDAAIVDAAKILPLARISQEDREVCLDLLYDRDGEGEGKPLMRFIDYFSD 300

Query: 650  VSAADAKDARAEQLAAMPLFERLAQRIIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGM 709
             +  +  +A A +       E+L  ++++G+K+ + D L   M+  +P+ IIN+ L+  M
Sbjct: 301  RNVGEEDEAEAVKRTPE---EQLFLQVVNGNKDEVGDVLPVLMERFAPLDIINQILVPAM 357

Query: 710  KTVGELFGSGQMQLPFVLQSAETMKTAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKG 769
            + VGELFG G++ LPFVLQSAE MK AV++LEPFME         + E   +I++ATV+G
Sbjct: 358  RHVGELFGKGEILLPFVLQSAEVMKRAVSFLEPFMER-------IEDEHTTRILLATVQG 410

Query: 770  DVHDIGKNLVDIILSNNGYDVVNLGIKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKE 829
            DVHDIGKNLVDIILSNNGY V N+GIK     ++E A E K D+IG+SGLLVKS +VM+E
Sbjct: 411  DVHDIGKNLVDIILSNNGYTVYNIGIKVGAETIIEKARELKPDLIGLSGLLVKSAIVMQE 470

Query: 830  NLEEMNNAGASNYPVILGGAALTRTYVENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKR 889
            ++ +   AG  + P++LGGAALT  +V       Y G V Y  DAF GLR + E    + 
Sbjct: 471  SMAQYREAGL-DIPILLGGAALTPKFVAESCVPNYGGPVVYCSDAFAGLRAVRE---HEE 526

Query: 890  GEGLDPNSPEAIEQAKKKAERKARNERSRKIAAERKANAAPVIVPERSDVSTDTPTAAPP 949
            G  +      A+     K  RK R+                        +S   P   PP
Sbjct: 527  GTLVSTVFDPAVVGEPLKPGRKERS------------------------ISRTNPVPEPP 562

Query: 950  FWGTRIVKGLPLAEFLGNLDERALFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDR 1009
            F G R V+ L        ++ +ALF G+WG +  +      Y  L+  +  P  +  + R
Sbjct: 563  FLGQRYVEELDPELLFPLVNTQALFRGRWGYRRAKMG-AEEYRQLISEQVEPIYQGLIRR 621

Query: 1010 LKSEGILDHVALVYGYFPAVAEGDDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIR 1069
               EG++    + YGYFP  A+ + V++      H      F+FPRQQ    LCIAD+ +
Sbjct: 622  SLDEGLI-RPKVSYGYFPCYAQEETVMVEVEGSLHP-----FAFPRQQEQPHLCIADYFK 675

Query: 1070 PREQAVKDGQVDVMPFQLVTMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWH 1129
             RE+       D+  F +VT+G  +      L+ A+ Y +YL +HG  V++T+ALAEYWH
Sbjct: 676  TREEG-----GDIAGFFIVTIGERMGQETARLYEADRYHDYLMLHGFSVEVTDALAEYWH 730

Query: 1130 SRVRSELKLNDGGSVADFDPEDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGR 1189
              +RSEL       +A  DP         +Y+G+R+ FGY +CPD+E    L   L+P +
Sbjct: 731  GVMRSEL------GIAGADPTAGGSLVSQNYQGSRYGFGYPACPDMEVHKPLFSFLKPEK 784

Query: 1190 IGVELSEELQLHPEQSTDAFVLYHPEAKYFNV 1221
            IGV L+E +Q+ PEQ+T A V++HP+AKYF V
Sbjct: 785  IGVSLTENMQMVPEQTTSAIVVHHPQAKYFAV 816


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: 2254
Number of extensions: 110
Number of successful extensions: 10
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: 816
Length adjustment: 44
Effective length of query: 1177
Effective length of database: 772
Effective search space:   908644
Effective search space used:   908644
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_028583364.1 G494_RS0103150 5-methyltetrahydrofolate--homocysteine methyltransferase

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



>NCBI__GCF_000429965.1:WP_028583364.1
          Length = 307

 Score =  245 bits (626), Expect = 3e-69
 Identities = 134/298 (44%), Positives = 183/298 (61%), Gaps = 7/298 (2%)

Query: 26  VLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFEAGADLVETNT 85
           +LI DGA GT LQ  ++  E+ +   EGCNE+LN T P+ + Q+HR + EAGA ++ETNT
Sbjct: 8   LLILDGACGTNLQEMEIP-EEAWEGSEGCNELLNSTAPESIIQLHRGFVEAGAMVIETNT 66

Query: 86  FGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGPGTKLPSLG 145
           FG +   L +Y + DR  EL   G A AR   D    G+  +  +V GS+GPGTKLPSLG
Sbjct: 67  FGASRIVLEEYGLEDRVEELNQAGVACARAAID----GKADV--YVGGSVGPGTKLPSLG 120

Query: 146 HAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELDTFLPIICH 205
           H    DL    ++    +++ G D  +IET QDLLQ+K A+      + EL   +P++  
Sbjct: 121 HIEVEDLARAQEQHIRSLVEAGVDLLIIETCQDLLQIKVAMTSCFSILEELGRDIPVMGS 180

Query: 206 VTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHADIPVSVMP 265
           VT+E TGTML+G++I AA    +P  +   GLNCATGP EM  HLRYLS++    +S +P
Sbjct: 181 VTIERTGTMLVGTDIAAAAVTFEPFPLFSFGLNCATGPAEMESHLRYLSRNWPGRISCVP 240

Query: 266 NAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVRDAVVGV 323
           N GLP +      YPL  E   Q +  FV+E+G+S+VGGCCGTTP H R +  A+ GV
Sbjct: 241 NQGLPEVVDGKTCYPLTPEQYGQDMKRFVTEFGVSVVGGCCGTTPAHTRELVRALDGV 298


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: 889
Number of extensions: 48
Number of successful extensions: 3
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: 307
Length adjustment: 37
Effective length of query: 1184
Effective length of database: 270
Effective search space:   319680
Effective search space used:   319680
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)

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