GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Magnetospirillum magneticum AMB-1

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_043745532.1 AMB_RS21365 O-succinylhomoserine sulfhydrylase

Query= reanno::Korea:Ga0059261_3194
         (402 letters)



>NCBI__GCF_000009985.1:WP_043745532.1
          Length = 403

 Score =  434 bits (1116), Expect = e-126
 Identities = 220/397 (55%), Positives = 284/397 (71%), Gaps = 7/397 (1%)

Query: 8   DRSITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSR 67
           D   ++ W+P T+A+RGG +R+ + ETSEA+F+ SGY YD A +A A F G    M YSR
Sbjct: 5   DSKPSRTWRPRTRAVRGGLSRTNFCETSEAVFMNSGYVYDSAEEAEASFDGTLDRMVYSR 64

Query: 68  LQNPTVEMLEQRIALLEGAE-----ACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGS 122
            +NPTV + EQR+A +EGA      A RATASGMAA+ AALLCQL AGD ++   A FGS
Sbjct: 65  FKNPTVAVFEQRLAEMEGAPPGMAVAARATASGMAAVHAALLCQLRAGDRVVASTALFGS 124

Query: 123 CRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIA 182
           C W+ +  LP++G+E   VD  D + +  A+   T   F ETP+NPT++++DL AVC +A
Sbjct: 125 CHWIINELLPRYGVERVFVDGTDLKSWEAALSRPTACVFLETPSNPTLEIIDLAAVCELA 184

Query: 183 RERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLL 242
            + G   VVDN FATP LQ P++ GAD+V YSATK MDGQGR L GAV G+ EF  + L 
Sbjct: 185 HKAGAKVVVDNVFATPILQSPLELGADIVVYSATKHMDGQGRCLGGAVLGSPEFCADILG 244

Query: 243 PFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSH 300
           PF RNTGP LSPFNAWV+LKGLETLDLR++R   NALKVARFLE R  V RV +PGL SH
Sbjct: 245 PFLRNTGPALSPFNAWVLLKGLETLDLRMERHCANALKVARFLEARPEVARVLYPGLESH 304

Query: 301 PQHNLAMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHS 360
           PQH+LA  QM   G I ++EL GG+  A+ LL+ + LIDISNN+GD++SL+THP +TTH 
Sbjct: 305 PQHDLAKRQMRGWGSIVALELKGGKPAAYKLLNGVELIDISNNLGDAKSLITHPWTTTHQ 364

Query: 361 GVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397
            ++ + +L MG+ EG+LRL+VGLED +DL+ DL +AL
Sbjct: 365 RLSPEDKLSMGITEGLLRLSVGLEDGDDLVEDLGRAL 401


Lambda     K      H
   0.319    0.134    0.396 

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: 454
Number of extensions: 19
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: 402
Length of database: 403
Length adjustment: 31
Effective length of query: 371
Effective length of database: 372
Effective search space:   138012
Effective search space used:   138012
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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