GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Shewanella sp. ANA-3

Align O-acetylhomoserine sulfhydrylase protein; EC 2.3.1.31 (characterized, see rationale)
to candidate 7023700 Shewana3_0930 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)

Query= uniprot:D8J1Y3_HERSS
         (413 letters)



>FitnessBrowser__ANA3:7023700
          Length = 430

 Score =  234 bits (598), Expect = 3e-66
 Identities = 142/403 (35%), Positives = 224/403 (55%), Gaps = 20/403 (4%)

Query: 30  PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89
           PI+ + ++ ++D +  A++F  K  G  Y R  NPT + LE ++  +E G   +  A+GM
Sbjct: 24  PIYQTTSYTFDDTQHGADLFDLKVAGNIYTRIMNPTSSVLEQRLAAIEGGIGALALASGM 83

Query: 90  AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDATDVKNVEAAITAN 148
           AAI   +Q L + GD++VS++ L+G T +L+  T+  QG +V M    D + ++A I A 
Sbjct: 84  AAITYAIQALTQVGDNIVSTSQLYGGTYNLFAHTLPRQGVEVRMAAFDDFEELDALIDAK 143

Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208
           T+ +F E+I NP   + DLKR+ E+  + G+  +VDNT+ +P L RP   GA +V++SLT
Sbjct: 144 TKALFCESIGNPAGNIVDLKRLAEIAHKHGVPLIVDNTVATPVLCRPFEHGADIVIHSLT 203

Query: 209 KSIGGHGNALGGALTDTGEFDW-TRYPHIAENYKKNPA-------PQWGMA----QIRAK 256
           K IGGHG  +GG + D+G+FDW       A   + +P+         +G A    + R  
Sbjct: 204 KYIGGHGTTIGGVIIDSGKFDWVANKERFALLNQADPSYHGVVYTEAFGAAAFIGRCRVV 263

Query: 257 ALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHP 316
            LR+ G +L P +A  +  G ET++LR ER C NALALA+ L     V+ V Y  L S P
Sbjct: 264 PLRNTGAALSPHSAFLLLQGLETLSLRMERHCSNALALAEYLILHPSVSWVNYGALPSSP 323

Query: 317 -QHALSKALFRSFGSLMSFELKDG------IDCFDYLNRLRLAIPTSNLGDTRTLVIPVA 369
            +    K        ++SF +K        I    +++ L++ +   N+GD ++L    A
Sbjct: 324 YRENCQKITGGKASGIISFGIKAATPEEGKIAGGKFIDALQMILRLVNIGDAKSLACHPA 383

Query: 370 HTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412
            T   ++ A   A  G++E LIR+SVG+E  DD++AD  QAL+
Sbjct: 384 STTHRQLDANELARAGVSEDLIRISVGIEHIDDIIADVAQALE 426


Lambda     K      H
   0.319    0.134    0.391 

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: 480
Number of extensions: 28
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: 413
Length of database: 430
Length adjustment: 32
Effective length of query: 381
Effective length of database: 398
Effective search space:   151638
Effective search space used:   151638
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