GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Pseudomonas putida KT2440

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate PP_1308 PP_1308 methionine gamma-lyase

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



>FitnessBrowser__Putida:PP_1308
          Length = 398

 Score =  277 bits (709), Expect = 3e-79
 Identities = 159/384 (41%), Positives = 229/384 (59%), Gaps = 4/384 (1%)

Query: 18  ATQAIRGG-TARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEML 76
           +T+AI  G    S  G     ++ T+ YA+      AA F+G++ G  YSR+ NPT+ +L
Sbjct: 11  STRAIHHGYDPLSHGGALVPPVYQTATYAFPTVEYGAACFAGEEPGHFYSRISNPTLALL 70

Query: 77  EQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGI 136
           EQR+A LEG EA  A ASGM A+T+ L   L  GD LI GR  +G         + +FG+
Sbjct: 71  EQRMASLEGGEAGLALASGMGAITSTLWTLLRPGDELIVGRTLYGCTFAFLHHGIGEFGV 130

Query: 137 ETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFA 196
           +   VD  D +    AI   T++ +FETPANP M +VD+ AV    R   +  VVDN + 
Sbjct: 131 KVRHVDLNDAKALKAAISSKTRMIYFETPANPNMQLVDIAAVVEAVRGHDVHVVVDNTYC 190

Query: 197 TPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRN-TGPTLSPF 255
           TP LQRP++ GAD+V +SATK + G G + AG V G +  ++   L   ++ TG  LSP 
Sbjct: 191 TPYLQRPLELGADLVVHSATKYLSGHGDITAGLVVGRKVLVDRIRLEGLKDMTGAVLSPH 250

Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFL--EGRVPRVNFPGLPSHPQHNLAMSQMAAA 313
           +A ++++G++TL LR+ R   NA +VA FL  + +V  +++PGLPS  Q+ LA  QM   
Sbjct: 251 DAALLMRGIKTLALRMDRHCANAQQVAEFLVRQPQVELIHYPGLPSFAQYALAQRQMRLP 310

Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373
           G + + EL GG       ++AL L   + ++GD+ SL  HPAS THS     +R   G+ 
Sbjct: 311 GGMIAFELKGGIEAGRRFMNALQLFARAVSLGDAESLAQHPASMTHSSYTPQERAHHGIS 370

Query: 374 EGMLRLNVGLEDPEDLIADLDQAL 397
           EG++RL+VGLED EDL+AD++QAL
Sbjct: 371 EGLVRLSVGLEDVEDLLADVEQAL 394


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: 358
Number of extensions: 9
Number of successful extensions: 2
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: 398
Length adjustment: 31
Effective length of query: 371
Effective length of database: 367
Effective search space:   136157
Effective search space used:   136157
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