Alignments for a candidate for metH in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Dinoroseobacter shibae DFL-12

Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate 3608273 Dshi_1677 Methionine synthase (RefSeq)

Query= reanno::DvH:207036
         (804 letters)



>FitnessBrowser__Dino:3608273
          Length = 329

 Score =  167 bits (422), Expect = 1e-45
 Identities = 111/316 (35%), Positives = 162/316 (51%), Gaps = 28/316 (8%)

Query: 302 VLTTRSHLVRVGGDAPVRIIGERINPTGKKQLIAELQAGDFSLALRFSDEQVEAGAPILD 361
           V+ +++  V +G D P  +IGERINPTG+K+L AEL+AGDFS   + + EQV  GA +LD
Sbjct: 5   VIESKTKTVTIGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALEQVACGAMVLD 64

Query: 362 VNVGAPMVD--------------EEVLLPDLVQRLITRHGVPLSIDSSNAAAIERALPYC 407
           VN GA   +              E +L+ +LV R+     +PL IDSS   A+E  L   
Sbjct: 65  VNSGAVFTNKMAEDPRYADNNFVEPMLMKELVARVQALVDIPLCIDSSVPGALENGLEMA 124

Query: 408 PGSTLVNSISGEPGRMERLGPLCRDHGAPFILLPLKGRKLPVAATERIAIIEELLVQAEG 467
            G  L+NS++GE  R+E + PL + +  P + +      +      R A+ ++++ +A  
Sbjct: 125 EGRPLLNSVTGEEDRLETILPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAAD 184

Query: 468 LGIPRRLVMVDVLALAVSSKAEAARQCLETI-RWCTANGFATTIGLSNISFGLPARELLN 526
            GIP   ++VD L + V + A A RQ    + R     G  TT G SN+SFGLP R  L 
Sbjct: 185 FGIPAHDIVVDPLVMPVGAMATAGRQVFTLVARLREELGVNTTCGASNVSFGLPNRHGLG 244

Query: 527 GTFLAMAAGAGLSSCIAHPGNGRIRETVACADVLLARDANA------ERFIDAYAAWTP- 579
             FL MA  +G++S I +P   +  E V  A+ L+  D N        R ++A+ A  P 
Sbjct: 245 AAFLPMAIASGMTSAIMNPIRPQEMEAVHAANFLMNHDPNGATWINFARVMEAHKAGMPF 304

Query: 580 ------ATQGGPVASG 589
                  T GG   SG
Sbjct: 305 PEAAKAGTSGGGGRSG 320


Lambda     K      H
   0.320    0.137    0.392 

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: 625
Number of extensions: 27
Number of successful extensions: 4
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: 804
Length of database: 329
Length adjustment: 35
Effective length of query: 769
Effective length of database: 294
Effective search space:   226086
Effective search space used:   226086
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: 52 (24.6 bits)

Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate 3607665 Dshi_1074 homocysteine S-methyltransferase (RefSeq)

Query= reanno::DvH:207036
         (804 letters)



>FitnessBrowser__Dino:3607665
          Length = 341

 Score =  162 bits (411), Expect = 2e-44
 Identities = 107/288 (37%), Positives = 148/288 (51%), Gaps = 12/288 (4%)

Query: 14  LLFDGGLGTMLQARGLPAGVSPEQFCLDRPDVLRGIHADYVRAGADILTTNTFGG--SRF 71
           LL DG  GT L   GL +G +PE +  D PD +  ++   V AG+D+  TN+FGG  SR 
Sbjct: 16  LLTDGATGTTLFNMGLSSGDAPELWNTDHPDRIAALYQGAVDAGSDLFLTNSFGGNASRL 75

Query: 72  KLGDGFDVV-DFNRRMAAIAREAADASGRQAFVAGSIGPTGHFVKPLGEVEPAALVAAFR 130
           KL    D V + NR  A I R  AD + R+  VAGS+GPTG  + P+G +     V  F 
Sbjct: 76  KLHAAQDRVRELNRLAAEIGRGVADKADRKVLVAGSMGPTGEIMAPMGPLTHDIAVEMFH 135

Query: 131 EQVRGLVAGGADLLMIETQFDLAEARAAVVAARAECSLPIAVSMTFEN-GVSLTGSTPEV 189
           EQ  GL  GGAD+L +ET     E  AA   A A   +P   +M+F+  G ++ G+T   
Sbjct: 136 EQAEGLKEGGADILWVET-ISAPEEYAAAAEAAARADMPWCGTMSFDTAGRTMMGTTSAT 194

Query: 190 FVATMLNLGVD--LLGTNCSAG-PDQMHDVVASLLASASVPVLVEPNAGLPELIDGKTVF 246
               +  L       G NC  G  D +  V+    A    P++ + NAG+P+ +DG   +
Sbjct: 195 MARMVEKLAHPPVAFGANCGVGASDLLRTVLGFAAAGTERPIIAKGNAGIPKYVDGHIHY 254

Query: 247 RLPPAPFAEKTAAFAAMGARVLGGCCGTTPDHI----AALRQAVADIP 290
              P   A+      A GA V+GGCCGTT +H+    AAL  + AD+P
Sbjct: 255 DGTPDLMAQYAILARASGASVIGGCCGTTFEHLRHMRAALDASAADMP 302


Lambda     K      H
   0.320    0.137    0.392 

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: 660
Number of extensions: 37
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 1
Length of query: 804
Length of database: 341
Length adjustment: 35
Effective length of query: 769
Effective length of database: 306
Effective search space:   235314
Effective search space used:   235314
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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