GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Klebsiella michiganensis M5al

Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein

Query= SwissProt::Q88FI7
         (416 letters)



>FitnessBrowser__Koxy:BWI76_RS14020
          Length = 461

 Score =  198 bits (504), Expect = 2e-55
 Identities = 142/426 (33%), Positives = 216/426 (50%), Gaps = 42/426 (9%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR--LTHYAFNAA 72
           P+ ++      + D D K+Y+D + G G L LGH +P V+++IQ+  T     H      
Sbjct: 42  PLAITKAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDVLQSIQSVITSGLPLHTLDLTT 101

Query: 73  PHGPYLALMEQLSQFVPVSYPLAG------MLTNSGAEAAENALKVARGATGKRAIIAFD 126
           P      L ++ S+++    P  G          SGA+A E ALK+A+  TG+ ++I+F 
Sbjct: 102 P------LKDRFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALKLAKKYTGRSSVISFS 155

Query: 127 GGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPS---ADTGVTCEQALKAMDRLFS 183
           GG+HG T   L++ G ++P     G +P  V  +PYP       G+  E  +KA+   F 
Sbjct: 156 GGYHGMTHGALSVTGNLSPKAAVNGMMP-EVQFMPYPHQYRCPLGIGGEAGVKALTYYFE 214

Query: 184 -----VELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGR 238
                VE  V   AA I E VQGEGG       + Q +R+   E GIL+IIDE+Q+GF R
Sbjct: 215 NLINDVESGVRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVTQEHGILLIIDEVQAGFAR 274

Query: 239 TGQRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAA 298
           TG+ FAF   GIEPD+++++K++ GG+PL AV+G K+   A   G   GT+ GN ++ A 
Sbjct: 275 TGKFFAFEHAGIEPDIIVMSKAVGGGLPL-AVLGIKKQFDAWEPGHHTGTFRGNQLAMAT 333

Query: 299 ALASLAQMTDENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFAN 354
            L +L  + D  +    A  GE  +  +    +R+      P IG + G+G M GIE   
Sbjct: 334 GLTTLRHLKDNKIADKTAAQGEWLKGKLAEMQKRY------PVIGHVRGLGLMIGIEIVK 387

Query: 355 ADGS-------PAPAQLAKVME-AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLD 406
            + +       PA  +L+ +++      GL+L   G+   ++RLL  L I    LE   D
Sbjct: 388 PNEAPDHMGCYPADGELSALLQKKCFEAGLILERGGRHGCVLRLLPSLLISNAELEIFFD 447

Query: 407 ILEQCL 412
             EQ L
Sbjct: 448 KFEQAL 453


Lambda     K      H
   0.320    0.137    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: 502
Number of extensions: 22
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: 416
Length of database: 461
Length adjustment: 32
Effective length of query: 384
Effective length of database: 429
Effective search space:   164736
Effective search space used:   164736
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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