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:

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