GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metY in Phaeobacter inhibens BS107

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate GFF2323 PGA1_c23540 O-succinylhomoserine sulfhydrylase MetZ

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



>lcl|FitnessBrowser__Phaeo:GFF2323 PGA1_c23540 O-succinylhomoserine
           sulfhydrylase MetZ
          Length = 396

 Score =  367 bits (941), Expect = e-106
 Identities = 187/392 (47%), Positives = 263/392 (67%), Gaps = 6/392 (1%)

Query: 11  ITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARF--SGDQQGMTYSRL 68
           +++ W   T+ + GGT RS++ E SEA++LT G+ YD A  A ARF  +G  +   Y+R 
Sbjct: 1   MSETWNKRTKLVHGGTRRSQYNEVSEAIYLTQGFVYDTAEQAEARFIETGPDE-FIYARY 59

Query: 69  QNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTD 128
            NPTV M E+RIA LEGAE   ATASGMAA+  AL   L AGDH++  +A FGSC ++ +
Sbjct: 60  GNPTVAMFEERIAALEGAEDAFATASGMAAVNGALTSILKAGDHVVSAKALFGSCLYILE 119

Query: 129 TQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIV 188
             L ++G+E T VD  D   +  A+RP+TK  FFE+ +NPT++V+D+ AV  +A   G  
Sbjct: 120 NILTRYGVEVTFVDGTDLDAWRAALRPDTKAVFFESMSNPTLEVIDIAAVAELAHAVGAT 179

Query: 189 TVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNT 248
            VVDN F+TP     ++ GADVV YSATK +DGQGRVL G + GT +FI  T+ P+ ++T
Sbjct: 180 VVVDNVFSTPVFSNAIEQGADVVIYSATKHIDGQGRVLGGVILGTRDFIRGTVEPYMKHT 239

Query: 249 GPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLA 306
           G +LSPFNAW +LKGLET+ LR+  Q+E AL++A+ L G   + R+ +PGL  H QH L 
Sbjct: 240 GGSLSPFNAWTLLKGLETISLRVNAQAETALELAQALSGHPALSRLMYPGLEDHAQHALV 299

Query: 307 MSQMAA-AGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAED 365
             Q+    G + S++L GG+  A   L+AL +  ISNN+GD++S+ THPA+TTH  ++E+
Sbjct: 300 QRQLGGKGGTVLSLDLKGGKDAAFRFLNALTIPVISNNLGDAKSIATHPATTTHQRLSEE 359

Query: 366 QRLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397
            +  +G+  G++R +VGLED  DLIADL QAL
Sbjct: 360 LKSELGITPGLVRFSVGLEDAGDLIADLTQAL 391


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: 412
Number of extensions: 18
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: 396
Length adjustment: 31
Effective length of query: 371
Effective length of database: 365
Effective search space:   135415
Effective search space used:   135415
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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