Alignments for a candidate for metH in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for metH in Sinorhizobium meliloti 1021

Align Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) (characterized)
to candidate SMc04325 SMc04325 methionine synthase I

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



>FitnessBrowser__Smeli:SMc04325
          Length = 337

 Score =  176 bits (447), Expect = 1e-48
 Identities = 115/283 (40%), Positives = 159/283 (56%), Gaps = 14/283 (4%)

Query: 14  LLFDGGLGTMLQARGLPAGVSPEQFCLDRPDVLRGIHADYVRAGADILTTNTFGGSR--F 71
           LL DG  GT L A GL AG +PE +   +PD +  +H D+V AGADI+ TN+FGG+R   
Sbjct: 18  LLADGATGTSLFAMGLEAGEAPEIWNETKPDNITKLHQDFVDAGADIILTNSFGGTRHRL 77

Query: 72  KLGDGFDVV-DFNRRMAAIAREAADASGRQAFVAGSIGPTGHFVKPLGEVEPAALVAAFR 130
           KL    D V   N+R A IAR  AD + R+   AGS+GPTG  + PLG +     VAAF 
Sbjct: 78  KLHQAEDRVHQLNKRAAEIARAVADKAPRKVITAGSVGPTGELLIPLGALSYEDAVAAFV 137

Query: 131 EQVRGLVAGGADLLMIETQFDLAEARAAVVAARAECSLPIAVSMTFEN-GVSLTGSTPEV 189
           EQ+ GL AGGA++  IET     E RAA  AA A+  LP   + +F+  G ++ G  P+ 
Sbjct: 138 EQIEGLKAGGAEVAWIETMSSPDEIRAAAEAA-AKVGLPYVYTGSFDTAGKTMMGLHPKD 196

Query: 190 F--VATMLNLGVDLLGTNCSAGPDQMHDVVASLL----ASASVPVLVEPNAGLPELIDGK 243
              VA  +  G   +G NC  G     D+++SLL    AS    ++V+ N G+PE    +
Sbjct: 197 IHGVAADIGEGPVAVGANCGVGAS---DILSSLLDMTAASPEATIVVKGNCGIPEFRGSE 253

Query: 244 TVFRLPPAPFAEKTAAFAAMGARVLGGCCGTTPDHIAALRQAV 286
             +   P   AE        GA+++GGCCGT+ +H+AA+R A+
Sbjct: 254 IHYSGTPPLMAEYARLAVDAGAKIIGGCCGTSCNHLAAMRLAI 296


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: 659
Number of extensions: 26
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: 804
Length of database: 337
Length adjustment: 35
Effective length of query: 769
Effective length of database: 302
Effective search space:   232238
Effective search space used:   232238
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 SMc04342 SMc04342 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase

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



>FitnessBrowser__Smeli:SMc04342
          Length = 320

 Score =  171 bits (432), Expect = 7e-47
 Identities = 109/292 (37%), Positives = 158/292 (54%), Gaps = 5/292 (1%)

Query: 302 VLTTRSHLVRVGGDAPVRIIGERINPTGKKQLIAELQAGDFSLALRFSDEQVEAGAPILD 361
           ++ + +  + +G D P  +IGERINPTG+K+L AE+  G+F   ++ + EQV AGA +LD
Sbjct: 5   IVASATREIIIGFDQPFCVIGERINPTGRKKLAAEMIEGNFDTVIKDALEQVAAGATMLD 64

Query: 362 VNVGAPMVD-EEVLLPDLVQRLITRHG---VPLSIDSSNAAAIERALPYCPGSTLVNSIS 417
           VN G   VD  E   P LV+ L    G   VPLSIDSS  AAIE  L    G  LVNS++
Sbjct: 65  VNAGVTAVDPNETEPPLLVKTLEIVQGLVDVPLSIDSSVTAAIEAGLRVAKGRPLVNSVT 124

Query: 418 GEPGRMERLGPLCRDHGAPFILLPLKGRKLPVAATERIAIIEELLVQAEGLGIPRRLVMV 477
           GE  ++E + PLC+ +  P + +      + +    R A+ ++++ +A   GI    ++V
Sbjct: 125 GEEEKLEAILPLCKKYDVPVVAISNDETGISMDPDVRFAVAKKIVERAADYGIKPHDIVV 184

Query: 478 DVLALAVSSKAEAARQCLETIRWCTAN-GFATTIGLSNISFGLPARELLNGTFLAMAAGA 536
           D L + + +   A +Q    +R         TT GLSNISFGLP R  +N  F+ M  GA
Sbjct: 185 DPLVMPIGALGSAGQQVFALLRRLREELKVNTTCGLSNISFGLPHRHGINAGFIPMVIGA 244

Query: 537 GLSSCIAHPGNGRIRETVACADVLLARDANAERFIDAYAAWTPATQGGPVAS 588
           G++S I +P   +  E V  A+VL   D N   +I  Y    PA  G  VA+
Sbjct: 245 GMTSAIMNPCRPQEMEAVRAANVLNGTDPNCTNWIMTYRDHKPAEGGHAVAA 296


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: 617
Number of extensions: 43
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: 804
Length of database: 320
Length adjustment: 34
Effective length of query: 770
Effective length of database: 286
Effective search space:   220220
Effective search space used:   220220
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.

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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