GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Echinicola vietnamensis KMM 6221, DSM 17526

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase

Query= BRENDA::Q9I6M4
         (426 letters)



>lcl|FitnessBrowser__Cola:Echvi_3848 Echvi_3848
           Ornithine/acetylornithine aminotransferase
          Length = 381

 Score =  186 bits (473), Expect = 8e-52
 Identities = 129/351 (36%), Positives = 188/351 (53%), Gaps = 37/351 (10%)

Query: 17  PRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSH 76
           P  V  +  V   +A  ST+WD +G EY+D  GG AV++ GH HP     ++EQL  ++ 
Sbjct: 3   PFDVYPLIDVTPVKASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAF 62

Query: 77  TCFQVLAYEPYIELAEEIAKRVP--GDFPKKTL-LVTSGSEAVENAVKIARAATGRAGVI 133
               V      I + +E+A ++     +P   L L  SG+EA ENA+K+A   TG+ G I
Sbjct: 63  YSNSV-----QIPIQKELATKLGQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFI 117

Query: 134 AFTGAYHGRTMMTLGLTGK---VVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIER 190
           AFT  +HGRT   + LT     + P++A  G+              H +  +D    +E 
Sbjct: 118 AFTKGFHGRTSGAVALTDNPKIIAPFNAHEGV--------------HILPFND----LEA 159

Query: 191 IFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTG 250
           + K  A    IA +I+E +QG GG  V   +F+  L AL  Q+G  LI DEVQ+G  R+G
Sbjct: 160 VEKQLATGT-IAGVIVEGIQGVGGIQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSG 218

Query: 251 TFFATEQL-GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAA 309
            FFA + + G+ PDL T AK +G GFPI GV    E     + G LG T+ G+ +ACAAA
Sbjct: 219 KFFAHQWVEGLKPDLITVAKGMGNGFPIGGVLISPEF--KASHGLLGTTFGGNHLACAAA 276

Query: 310 LAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIEL 360
           LAVL+V +EE L+  +   G+ + A L ++      + +VRG G M+  +L
Sbjct: 277 LAVLEVIDEENLITAAAENGKAIMAALEKVAG----VTEVRGKGLMIGFDL 323


Lambda     K      H
   0.319    0.137    0.393 

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: 372
Number of extensions: 22
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 426
Length of database: 381
Length adjustment: 31
Effective length of query: 395
Effective length of database: 350
Effective search space:   138250
Effective search space used:   138250
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 Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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