GapMind for Amino acid biosynthesis

 

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

Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate N515DRAFT_1410 N515DRAFT_1410 methionine aminotransferase

Query= BRENDA::Q71RI9
         (455 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1410
          Length = 381

 Score =  223 bits (569), Expect = 6e-63
 Identities = 136/401 (33%), Positives = 211/401 (52%), Gaps = 30/401 (7%)

Query: 45  RIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGH 104
           ++  + + ++   ++LA +   VNLGQGFPD  PP  ++E +++A   +  NQY  G G 
Sbjct: 6   KLPKVGTTIFSVMSQLAVEHQAVNLGQGFPDFEPPQALREAIARA-MAEGRNQYAPGIGL 64

Query: 105 PALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYE 164
           P L + ++    ++Y R+ID   E+ V  GA  +LF +I  +V  GDEVI+  P YD YE
Sbjct: 65  PTLREQIALKTERMYGRRIDAAGEVTVTSGATEALFAAIAAVVRAGDEVIVFDPAYDSYE 124

Query: 165 PMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKV 224
           P++ + GA  V IPL + P+ G+ W         + +    + +T+ I++N+PHNP G V
Sbjct: 125 PVIELQGAKAVHIPL-TVPSFGVDW---------QRVRDAVTPRTRMILINSPHNPSGAV 174

Query: 225 YTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFS 284
            +  +L  +A +    + + +SDEVYE +V+ G  H  +     +  R+I + S GKT+ 
Sbjct: 175 LSAADLDQLAAIVRDTEIVVLSDEVYEHIVFDGALHQSVLRHAELAARSIVVSSFGKTYH 234

Query: 285 VTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLP 344
            TGWKLG+++ PA L    + V Q   +    P Q A AE           PE Y   LP
Sbjct: 235 CTGWKLGYAVAPAALSAEFRKVHQYLTFCTFHPAQVAFAEFM------ASTPEHYL-ELP 287

Query: 345 KELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTK 404
              + KRDR   L+     K +   GGYF + D S++         DEP D  F +W+ K
Sbjct: 288 AFYQAKRDRFRALIAPSRFKLLDVPGGYFQLVDYSAI--------RDEP-DVTFCEWLVK 338

Query: 405 HKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEE 445
              + AIP++ F ++       +LVR CF K D+T+DAA E
Sbjct: 339 QGGVAAIPLAPFYETAPD---TRLVRLCFAKSDATMDAAAE 376


Lambda     K      H
   0.320    0.136    0.419 

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: 384
Number of extensions: 18
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: 455
Length of database: 381
Length adjustment: 31
Effective length of query: 424
Effective length of database: 350
Effective search space:   148400
Effective search space used:   148400
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 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