GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Marinobacter adhaerens HP15

Align Ornithine aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase

Query= SwissProt::Q6CWC1
         (437 letters)



>FitnessBrowser__Marino:GFF3915
          Length = 422

 Score =  172 bits (436), Expect = 2e-47
 Identities = 135/412 (32%), Positives = 214/412 (51%), Gaps = 29/412 (7%)

Query: 30  PVVFSRASGAHVWDPEGKEYLDFLSAYSAVNQGHCHPHIIQALVD--QASKLTLSSRAFS 87
           PV+F+RA  AH++  +GKEYLDFL+   ++N GH +  + +AL++  +A  ++     F+
Sbjct: 19  PVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQGLDMFT 78

Query: 88  ---NDCFASFSKFVTEFFG--YESVLPMNTGAEAVESALKLARRWGYMVKKIQPNEAIIL 142
              +D   S+ K + +  G  Y+      TG   VE+ALKLAR       K++    II 
Sbjct: 79  TAKHDFMESYKKHILDPRGLDYKMQFTGPTGTNCVEAALKLAR-------KVKGRSGIIS 131

Query: 143 GARGNFHGRTFGAISLSTDEEDSRMNFGPFLENVTAKIPGGSDDEFIRYGEIDDYKRAFE 202
              G FHG T GA++ +T  +  R   G  L NV      G   + +    I D   +  
Sbjct: 132 FTNG-FHGVTMGAVA-TTGNKHHRGGVGTPLGNVDFMFYDGYLGDDVDTLAIMDKLLSDG 189

Query: 203 SHGDKI-CAVIVEPIQGEAGIVVPRADFLTDLQELCKKHQVLLICDEIQTGIARTGKLLC 261
           S G ++  AVIVE +QGE G+   RA++L  L ELCKKH +LLI D+IQ G  RTG+   
Sbjct: 190 SSGFELPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEFFS 249

Query: 262 YEHSPNCKPDIILLGKAISGGVLPVSCVLSSREIMDCFTPGSHGSTYGGNPLASRVAIAA 321
           +E +   KPDI+ + K++SG  LP++ VL   E +D + PG H  T+ GN +A   A AA
Sbjct: 250 FEFA-GIKPDIVTVSKSLSGYGLPMALVLFKPE-LDVWDPGEHNGTFRGNNMAFITARAA 307

Query: 322 LEVVQNENLVERSARL-GKFLQDELVKLQHESNGVISEVRGKGLLTAIVINPEKANG--- 377
           +E    ++      +   + L D L  +  +  G   +++G+GL+  I        G   
Sbjct: 308 VENYWKDDAFANEVKAKTEVLGDALQSICDKYPGQF-KMKGRGLMRGIEAKHADITGPIT 366

Query: 378 RTAWDLCLLMKDQGVLAKPTHEHIIRLAPPLVISEEDLLKGVDSIRVSLSKL 429
           + A++  L+++  G      ++ +I+   PL  SEEDL KG   +  S+ ++
Sbjct: 367 KRAFEHGLIIETSG-----PNDEVIKCLMPLTTSEEDLKKGAALLAKSVDEI 413


Lambda     K      H
   0.318    0.136    0.400 

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: 467
Number of extensions: 17
Number of successful extensions: 5
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: 437
Length of database: 422
Length adjustment: 32
Effective length of query: 405
Effective length of database: 390
Effective search space:   157950
Effective search space used:   157950
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 (21.7 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