Alignments for a candidate for metH in Geobacter metallireducens GS-15

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Geobacter metallireducens GS-15

Align vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (characterized)
to candidate WP_004512200.1 GMET_RS02515 bifunctional homocysteine S-methyltransferase/methylenetetrahydrofolate reductase

Query= reanno::Miya:8499710
         (818 letters)



>NCBI__GCF_000012925.1:WP_004512200.1
          Length = 605

 Score =  189 bits (481), Expect = 3e-52
 Identities = 143/427 (33%), Positives = 208/427 (48%), Gaps = 27/427 (6%)

Query: 14  LVFDGGMGTMLQSRGLPPGVSPELFCLARPDVLVGIHADYLRAGADVLTTNTFGGCIHKL 73
           LV DG +GTML ++G+    + E   L RP++++ +H +YL AGA V+ TNTFG    KL
Sbjct: 12  LVGDGAIGTMLYAKGVSLDANVEHLNLVRPELVLELHREYLGAGAKVIETNTFGANWTKL 71

Query: 74  GTGPGAPDVVEFNRAMARAAREAVLASGREAFVAGSVGPSGHFMRPLGDLDPAELVAAFR 133
                     E     AR AREA  A G +AFVAGS+GP         +L PAE    FR
Sbjct: 72  SAIGLDKREREIILRGARLAREA--AEGTDAFVAGSMGPLARVKGDERELSPAETTEIFR 129

Query: 134 AQIRGLVQGGVDLILAETQFDLAEARAIVLAARAECDLPVGVSMTF-ENGVSLTGTRPEV 192
            Q   L +GGVDL++ ET  DLA+    + AAR E  LPV  +M F ENG    G   E 
Sbjct: 130 RQALALAEGGVDLLILETFTDLAQILCALSAAR-ETGLPVVANMAFLENGRLAGGADVER 188

Query: 193 FVQSMLNMGVDLVGTNCSAGPEQMAEVADELLAISEVPVLVEPNAGLPELVDGKTVFRLG 252
             + +   G  +VG NC AGP ++      +   + +P+   PN+G PE V+G+ V+R  
Sbjct: 189 AARELTAAGASVVGANCGAGPLEVLGTIRRMAGATALPIAAYPNSGFPEYVNGRHVYRTT 248

Query: 253 PDDFARHTARFAASGVRMLGGCCGTTPDHI-------AALRGALDNLSGGLVPDPARRDG 305
           PD FA   A   A+G  ++GGCCGTTP+HI       A LR A+ N++   V    RR  
Sbjct: 249 PDYFAERAAEMVAAGAALVGGCCGTTPEHILRLAERLAGLRPAVRNVAVPAVSVEERRGE 308

Query: 306 IVLTTRAQAVHIGAGSPIRIIGERINP----TGKKLLTAELQAGEFAQALRFADEQVEAG 361
              +T A+      G    +  E   P     GK +  + +  G  A A+  A+      
Sbjct: 309 ---STEAEGFLARWGEEPVVTVELDPPKGFDCGKVIEGSRVLKGAGADAINIAEN----- 360

Query: 362 APLLDVNVGAPMVDEAVLLPALVERLVARHSLPLSLDSSNADAIAAALPFHPGSPLVNSI 421
            PL  + +G   +   +     +E +V       +L    +D + A+L    G   + ++
Sbjct: 361 -PLARIRMGNIALGHLIQQEVGIEVIVHVTCRDRNLLGLQSDLMGASL---LGIRSILAV 416

Query: 422 SGEPGRM 428
           +G+P R+
Sbjct: 417 TGDPARI 423


Lambda     K      H
   0.320    0.137    0.395 

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: 1214
Number of extensions: 61
Number of successful extensions: 5
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: 818
Length of database: 605
Length adjustment: 39
Effective length of query: 779
Effective length of database: 566
Effective search space:   440914
Effective search space used:   440914
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 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