GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Shewanella loihica PV-4

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate 5209311 Shew_1789 cystathionine beta-lyase (RefSeq)

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



>FitnessBrowser__PV4:5209311
          Length = 395

 Score =  149 bits (375), Expect = 2e-40
 Identities = 117/375 (31%), Positives = 171/375 (45%), Gaps = 25/375 (6%)

Query: 32  GETSEALFLTSGYAYDCAGDAAARFSGDQQG-MTYSRLQNPTVEMLEQRIALLEGAEACR 90
           G  +  +F  S   +D   D          G M Y R   PT    +  IA LEG     
Sbjct: 19  GVINPPVFRASTVVFDTIEDMRHATKNRANGAMFYGRRGTPTHFAFQAAIAELEGGVGTA 78

Query: 91  ATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDARDPQQFI 150
              SG AA++ ALL  L AGDHL+    A+   R L D  L  FGIETT  D        
Sbjct: 79  LYPSGSAAISGALLSFLKAGDHLLMVDTAYEPTRDLCDKLLKGFGIETTYYDPLIGDGIE 138

Query: 151 DAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATPALQRPMDFGADV 210
             IRPNTKV F E+P + T++V D+  + AIA    +V ++DN +A+P   RP + G D+
Sbjct: 139 ALIRPNTKVLFLESPGSITLEVQDVPTLSAIAHRHNLVVMLDNTWASPINCRPFELGVDI 198

Query: 211 VAYSATKMMDGQGRVLAGAVCGT----EEFINNTLLPFHRNTGPTLSPFNAWVVLKGLET 266
              +ATK + G   V+ G         ++   N+ L      G   S  + ++  +GL T
Sbjct: 199 SIQAATKYIVGHSDVMLGTATANQAHWDQLRENSYL-----MGQCTSADDIYLASRGLRT 253

Query: 267 LDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAAGPIFSIELDGG 324
           L +R+ +  +N L+VA  L  R  V  +  P   S P H       +A+  +FS  L  G
Sbjct: 254 LGVRMAQHEKNGLEVANLLATRPEVDHLRHPAFASCPGHEFFKRDFSASNGLFSFVLKRG 313

Query: 325 RTQA-HGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGV----GEGMLRL 379
             +A    ++ +    +  + G   SL+         GV    +L         + ++RL
Sbjct: 314 NIKAITAFVEGMDHFKMGFSWGGYESLIL--------GVFGIDKLRTATQWDSSKPLIRL 365

Query: 380 NVGLEDPEDLIADLD 394
           +VGLE+PEDLI DL+
Sbjct: 366 HVGLENPEDLIKDLE 380


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: 335
Number of extensions: 19
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: 402
Length of database: 395
Length adjustment: 31
Effective length of query: 371
Effective length of database: 364
Effective search space:   135044
Effective search space used:   135044
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 Jul 25 2024. The underlying query database was built on Jul 25 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