GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Dyella japonica UNC79MFTsu3.2

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= SwissProt::Q8ZPV2
         (408 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1751
          Length = 467

 Score =  169 bits (428), Expect = 2e-46
 Identities = 139/421 (33%), Positives = 200/421 (47%), Gaps = 46/421 (10%)

Query: 22  PFIP-VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWH-IGNGYT 79
           P +P VRGEG  L D  G+ Y+D       N  GHA+P +  AL +Q +   H I  G+T
Sbjct: 46  PMLPIVRGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFT 105

Query: 80  NEPALRLAKKLIDATFA--ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNA 137
           +EPA+ LA++L   T A  ERVF  ++G+ A E ALK++  Y  ++    K+  +A   +
Sbjct: 106 HEPAIELAERLAQITPAGLERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGS 165

Query: 138 FHGRTLFTVSAGGQPTYSQDFAPL--------PPDIRHA---------AYNDLNSASALI 180
           +HG TL  +S      Y + +APL         PD   A         A   L     L+
Sbjct: 166 YHGETLGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLL 225

Query: 181 DDN---TCAVIVEP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELY 236
           + +   TCAVIVEP VQ  GG+     ++L GLR LCD      I DE+  G GRTG L+
Sbjct: 226 EQHAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGTLF 285

Query: 237 AYMHYGVTPDILTTAKALGGGF-PIGAMLTT----QDYASVMTPG---THGTTYGGNPLA 288
           A    GV+PD +  +K L GGF P+ A+LTT    + + +    G    H  +Y GNPLA
Sbjct: 286 ACEQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNPLA 345

Query: 289 TAVAGKVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQTEFA 348
              A   LDI     +    R+       RL  L       +++R  G++    L  + A
Sbjct: 346 CRAALATLDIFRDEPVLERNRELAAHLARRLAPLR-EHPQVADVRQTGMIAAVELVRDKA 404

Query: 349 GKAKLIAQEAAKAGVMVLIAG----------GDVVRFAPALNVSDEEIATGLDRFALACE 398
            +A   ++E  + G+ V + G          G+VV F P   VS +E+   +D      E
Sbjct: 405 TRAPYPSEE--RRGLRVYLHGLEHGALLRPLGNVVYFMPPYVVSTDELDHLVDVAIAGIE 462

Query: 399 R 399
           R
Sbjct: 463 R 463


Lambda     K      H
   0.320    0.137    0.413 

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: 492
Number of extensions: 26
Number of successful extensions: 6
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: 408
Length of database: 467
Length adjustment: 32
Effective length of query: 376
Effective length of database: 435
Effective search space:   163560
Effective search space used:   163560
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: 51 (24.3 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