Alignments for a candidate for lysJ in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysJ in Dyella japonica UNC79MFTsu3.2

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= curated2:Q9YBY6
         (388 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1751
          Length = 467

 Score =  151 bits (382), Expect = 3e-41
 Identities = 136/420 (32%), Positives = 192/420 (45%), Gaps = 55/420 (13%)

Query: 16  LRIVKGSMQYVWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQAREL--VAASSSFST 73
           L IV+G   ++ D  GR+YLD  +       GH+NP I  A+ +Q   L  V  +     
Sbjct: 48  LPIVRGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFTHE 107

Query: 74  PSLEEALTEFSRIAPPWAEEIVFLNTGTEAVEAALKAA---WLATG---KRGIVALKNSF 127
           P++E A    ++I P   E +   + G+ A+E ALK +   WL  G   K   +AL  S+
Sbjct: 108 PAIELA-ERLAQITPAGLERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGSY 166

Query: 128 HGRTLASLSVTWNPRYRRG-VPVLDTRFLSPSTDP-----------------GEVEKLVP 169
           HG TL +LSV+    YR+   P+L T  L+PS D                  GE+  L+ 
Sbjct: 167 HGETLGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLLE 226

Query: 170 E---DTAAIIVEP-IQGEGGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWA 225
           +   +T A+IVEP +Q  GG+   +      LR   D  G   I DEI  GFGRTG ++A
Sbjct: 227 QHAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGTLFA 286

Query: 226 HESLGVEPDIMTAGKSIAGG-LPASAVLSR----EGVLATLASGR---HGSTHAANPLSM 277
            E  GV PD M   K + GG LP SAVL+     E   A   +G+   H  ++  NPL+ 
Sbjct: 287 CEQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNPLAC 346

Query: 278 AAVAAASRFLREEGVPDKARAAGALLEGLLRDRIEGLRLVRGVRGEGLMLGVELRLDPGP 337
            A  A     R+E V ++ R   A L   L    E  + V  VR  G++  VEL  D   
Sbjct: 347 RAALATLDIFRDEPVLERNRELAAHLARRLAPLREHPQ-VADVRQTGMIAAVELVRDKAT 405

Query: 338 VLRCLQESERVL-----------ALRSGATVVRLLPPYSISRED----AEMVVYGLERCI 382
                 E  R L            LR    VV  +PPY +S ++     ++ + G+ER I
Sbjct: 406 RAPYPSEERRGLRVYLHGLEHGALLRPLGNVVYFMPPYVVSTDELDHLVDVAIAGIERAI 465


Lambda     K      H
   0.319    0.136    0.398 

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: 387
Number of extensions: 14
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: 388
Length of database: 467
Length adjustment: 32
Effective length of query: 356
Effective length of database: 435
Effective search space:   154860
Effective search space used:   154860
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for Amino acid biosynthesis