GapMind for Amino acid biosynthesis

 

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

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= SwissProt::P38021
         (401 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1751
          Length = 467

 Score =  169 bits (427), Expect = 2e-46
 Identities = 127/422 (30%), Positives = 198/422 (46%), Gaps = 50/422 (11%)

Query: 16  HYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADKI 75
           H  A     LPIV  E  G W+ D +G  Y+D +S++     GH +P+I  ALK Q D +
Sbjct: 39  HDHAGTVPMLPIVRGE--GPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTL 96

Query: 76  T-LTSRAFHNDQLGPFYEKTAKLT--GKEMILPMNTGAEAVESAVKAARRWAYEVKGVAD 132
             +    F ++      E+ A++T  G E +   + G+ A+E A+K +  + Y +   A 
Sbjct: 97  EHVIFAGFTHEPAIELAERLAQITPAGLERVFLADNGSAAIEVALKMS--FHYWLNQGAG 154

Query: 133 NQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIP----------------- 175
            +   IA  G++HG T+ A+S+S    Y++ + P+L    L P                 
Sbjct: 155 QKTRFIALTGSYHGETLGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACA 214

Query: 176 ---YGDVEALRQAITPNTAAFLFEP-IQGEAGIVIPPEGFLQEAAAICKEENVLFIADEI 231
               G++  L +     T A + EP +Q   G+ +    +L    A+C E  V FIADEI
Sbjct: 215 ARRLGELRVLLEQHAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEI 274

Query: 232 QTGLGRTGKTFACDWDGIVPDMYILGKALGGGVFPISCIAADREILGVF----NPGS--- 284
             G GRTG  FAC+  G+ PD   L K L GG  P+S +     +   F    N G    
Sbjct: 275 AVGFGRTGTLFACEQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFL 334

Query: 285 HGSTFGGNPLACAVSIASLEVLEDEKLADRSLELGEYFKSELESI-DSPVIKEVRGRGLF 343
           H  ++ GNPLAC  ++A+L++  DE + +R+ EL  +    L  + + P + +VR  G+ 
Sbjct: 335 HSHSYTGNPLACRAALATLDIFRDEPVLERNRELAAHLARRLAPLREHPQVADVRQTGMI 394

Query: 344 IGVEL-----TEAARPYCERL--------KEEGLLCKETHDTVIRFAPPLIISKEDLDWA 390
             VEL     T A  P  ER          E G L +     V+ F PP ++S ++LD  
Sbjct: 395 AAVELVRDKATRAPYPSEERRGLRVYLHGLEHGALLRPL-GNVVYFMPPYVVSTDELDHL 453

Query: 391 IE 392
           ++
Sbjct: 454 VD 455


Lambda     K      H
   0.318    0.136    0.401 

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: 456
Number of extensions: 26
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: 401
Length of database: 467
Length adjustment: 32
Effective length of query: 369
Effective length of database: 435
Effective search space:   160515
Effective search space used:   160515
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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