GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Azospirillum brasilense Sp245

Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase

Query= SwissProt::Q88FI7
         (416 letters)



>FitnessBrowser__azobra:AZOBR_RS19025
          Length = 389

 Score =  185 bits (470), Expect = 2e-51
 Identities = 139/407 (34%), Positives = 202/407 (49%), Gaps = 39/407 (9%)

Query: 16  ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75
           I    G    ++ TDG+R++DF  G+ V  LGH NP +VEA+ AQA +L H + N     
Sbjct: 14  IVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTS-NLFRVA 72

Query: 76  PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGF 129
              +L ++L++    ++      TNSGAEA E   K+ R      G   +  II F+  F
Sbjct: 73  GQESLAKRLTE---ATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQAF 129

Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVE 189
           HGRTLA ++     A  ++++ +  GP+                 L     L +V  AV 
Sbjct: 130 HGRTLAAVS-----AAQQEKLIKGFGPLLD------------GFDLVPFGDLEAVRNAVT 172

Query: 190 DVAAFI-FEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248
           D  A I  EP+QGEGG  A    F + LR  CDE G+L+ +DEIQ G GRTG+ FA    
Sbjct: 173 DETAGICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWA 232

Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308
           GI PD++ +AK I GG PLGA +  ++  + +  G  G TY GNP++ A   A L ++ +
Sbjct: 233 GITPDVMAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLE 292

Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368
                  +R    +  R     A   + + G + G G M G+    A G         V+
Sbjct: 293 PGFLDHVQRIGGLLQDRLAGLVAENPAVFKG-VRGKGLMLGLACGPAVGD--------VV 343

Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
            A RA GLL +P+G   +++RLL PL I    +EE + IL +   EL
Sbjct: 344 VALRANGLLSVPAGD--NVVRLLPPLNIGEAEVEEAVAILAKTAKEL 388


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: 454
Number of extensions: 20
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 416
Length of database: 389
Length adjustment: 31
Effective length of query: 385
Effective length of database: 358
Effective search space:   137830
Effective search space used:   137830
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: 50 (23.9 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