GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2323
          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:

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