GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_2 in Sinorhizobium meliloti 1021

Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate SMc04325 SMc04325 methionine synthase I

Query= reanno::Phaeo:GFF1321
         (338 letters)



>FitnessBrowser__Smeli:SMc04325
          Length = 337

 Score =  343 bits (881), Expect = 3e-99
 Identities = 178/331 (53%), Positives = 223/331 (67%), Gaps = 1/331 (0%)

Query: 3   NTFTTLLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLF 62
           +  + LL  K  LLADGATGT+LF MGL++G+APE+WN  +P  IT L+Q  VDAG+D+ 
Sbjct: 6   HALSDLLAQKGVLLADGATGTSLFAMGLEAGEAPEIWNETKPDNITKLHQDFVDAGADII 65

Query: 63  LTNTFGGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVG 122
           LTN+FGGT  RLKLH A  RV +LN   AE+ R VAD++ RK+  AGSVGPTGE++ P+G
Sbjct: 66  LTNSFGGTRHRLKLHQAEDRVHQLNKRAAEIARAVADKAPRKVITAGSVGPTGELLIPLG 125

Query: 123 ELSHALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFKLADMPWCGTMSFDTA 182
            LS+  AV  F EQ E LK GG +V W+ET+S+P+E RAAAEA     +P+  T SFDTA
Sbjct: 126 ALSYEDAVAAFVEQIEGLKAGGAEVAWIETMSSPDEIRAAAEAAAKVGLPYVYTGSFDTA 185

Query: 183 GRTMMGVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAG 242
           G+TMMG+   D+  +  +    P+A GANCG GASDIL ++L   A      I+ KGN G
Sbjct: 186 GKTMMGLHPKDIHGVAADIGEGPVAVGANCGVGASDILSSLLDMTAASPEATIVVKGNCG 245

Query: 243 IPKYVDGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRPRGEQL 302
           IP++    IHY GTP LM EYA +A D GAKIIGGCCGT  +HL AMR A+D   RGE+ 
Sbjct: 246 IPEFRGSEIHYSGTPPLMAEYARLAVDAGAKIIGGCCGTSCNHLAAMRLAIDNHTRGERP 305

Query: 303 TLERIVEVLGPFTSDSDGTGEDTAPDRRSRR 333
           TLE IVE +GP  + S   G   AP R  RR
Sbjct: 306 TLETIVEKIGPLRNKSANEG-PAAPARERRR 335


Lambda     K      H
   0.317    0.134    0.397 

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: 406
Number of extensions: 17
Number of successful extensions: 1
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: 338
Length of database: 337
Length adjustment: 28
Effective length of query: 310
Effective length of database: 309
Effective search space:    95790
Effective search space used:    95790
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 (21.7 bits)
S2: 49 (23.5 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:

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:

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:

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:

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