GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Shewanella amazonensis SB2B

Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.- (uncharacterized)
to candidate 6936059 Sama_0256 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)

Query= curated2:Q9YBY8
         (355 letters)



>FitnessBrowser__SB2B:6936059
          Length = 331

 Score =  158 bits (399), Expect = 2e-43
 Identities = 111/342 (32%), Positives = 169/342 (49%), Gaps = 25/342 (7%)

Query: 6   RAGILGASGMTGGELLRILASHPGVEVEWATSREYA---GKPVHTAHP---HLRGFYTGL 59
           +  I+GASG TG +L  ++ + P ++V+     E +   GKP+ + +P   HL+   + L
Sbjct: 8   KIAIIGASGYTGAQLTALIDAEPHLQVQGLYVSEGSADKGKPLSSLYPVYSHLKYCLSPL 67

Query: 60  KYTSIDKIDIGEVDVVFNALPHGVGASIVAEAYENGVRVVDLSADYRLRDQSLYPKLYGF 119
              + D I + E D V  A  H V   + A  YE G+ V DLS  YR  D + YPK YGF
Sbjct: 68  TDEAKDAI-VAEADAVALATEHSVSLELAAYFYEKGLAVFDLSGAYRFADTAQYPKWYGF 126

Query: 120 KHPRPDLLEEAIYALPEIYGEKLRGARLAAVPGCNATAAILAAAPLVASKIIDMDVGIIV 179
           +H  P++L +A+Y L E   + +   R+ AVPGC  TA++ A  PL   K +  +   ++
Sbjct: 127 EHSHPEVLAKAVYGLAEWNADAVAATRMIAVPGCYPTASLTALKPL---KAMLTEARPVI 183

Query: 180 DVKAASSEAGSKPSRHSIHPLREGSARPYTPWGHRHAAEAVQVLRDLVGRGIRLSLVPHA 239
           +  +  + AG K   H+     E S  PY   GHRH  E    L      G  +   PH 
Sbjct: 184 NAVSGVTGAGRKAQLHT--SFCEVSLTPYGVLGHRHQPEIATQL------GQEVIFTPHL 235

Query: 240 VSMTRGVLASAHALLRDNIGFSEAVRAYASFYKDSQIVRVKPMAPGLPVDPPDVKNVIGS 299
            +  RG+LA+    L+      +  +AY S Y  S IV VK          P V +V+ +
Sbjct: 236 GNFKRGILATITVQLKPGTSREDVAKAY-SVYDQSPIVTVK------EGQFPKVDDVVFT 288

Query: 300 MFAEVGFAVEEESGRITGFAAIDNLVRGAAGQAVYAMNAMLG 341
               +G+  +E+SG +   +AIDNL++GAA QA+  +    G
Sbjct: 289 PNCHLGWKFDEDSGYLVVASAIDNLMKGAASQALQCIKIHFG 330


Lambda     K      H
   0.319    0.136    0.402 

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: 284
Number of extensions: 19
Number of successful extensions: 5
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: 355
Length of database: 331
Length adjustment: 29
Effective length of query: 326
Effective length of database: 302
Effective search space:    98452
Effective search space used:    98452
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: 49 (23.5 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