GapMind for catabolism of small carbon sources

 

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

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase

Query= SwissProt::Q8ZPV2
         (408 letters)



>lcl|FitnessBrowser__Cola:Echvi_2919 Echvi_2919
           Ornithine/acetylornithine aminotransferase
          Length = 393

 Score =  218 bits (555), Expect = 2e-61
 Identities = 129/369 (34%), Positives = 203/369 (55%), Gaps = 23/369 (6%)

Query: 27  RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWH--IGNGYTNEPAL 84
           + EG  ++  +G++YID   GI V+ +GH HP + +A+ +Q +++ H  +   Y   P  
Sbjct: 25  KAEGIYMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDKYMHLMVYGEYVQSPQT 84

Query: 85  RLAKKLIDAT--FAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRT 142
           +LAK L D      + V+  NSG+EA E ALKLA++Y   R       I++  NA+HG +
Sbjct: 85  QLAKALTDTLPKKLDNVYLVNSGSEAVEGALKLAKRYTGRRE------ILSCVNAYHGSS 138

Query: 143 LFTVSAGGQPTYSQDFAPLPPDIRHAAYNDLNSASALIDDNTCAVIVEPVQGEGGVIPAT 202
              +S GG   + + + PL P IRH  +N+ +    + ++ T A++VE VQGE G+   T
Sbjct: 139 HGALSVGGNEIFKRAYRPLLPGIRHLDFNEPDQLDQITEE-TAAIMVETVQGEAGIRVGT 197

Query: 203 KAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTTAKALGGGFPIGA 262
           K + + LR  CD    LLI DE+Q G GRTG+ +A+ HY + PDI+  AK +GGG PIGA
Sbjct: 198 KEYFKALRHRCDETGTLLILDEIQAGFGRTGKFWAFQHYDIVPDIVVCAKGMGGGMPIGA 257

Query: 263 MLTTQDYASVMTPGT---HGTTYGGNPLATAVAGKVLDIINTPEMQNGVRQRHDAFIERL 319
            +  Q   SV        H TT+GG+P++ A A   +DI+   ++   V ++ + F + L
Sbjct: 258 FIAPQSIMSVFKNNPLLGHITTFGGHPVSCAAALATIDILRDEKLIQHVERKANLFKKHL 317

Query: 320 NTLNVRFGMFSEIRGLGLLLGCVLQTEFAGKAKLIAQEAAKAGVMV--LIAGGDVVRFAP 377
           N   ++     EIR  GL++   ++ E     K I   A + G++    +   D +R AP
Sbjct: 318 NHPKIQ-----EIRNKGLMM--AVKFEAFEVLKPIIDRAIELGIITDWFLFCEDSMRIAP 370

Query: 378 ALNVSDEEI 386
            L ++DEEI
Sbjct: 371 PLTITDEEI 379


Lambda     K      H
   0.320    0.137    0.413 

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: 402
Number of extensions: 22
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: 408
Length of database: 393
Length adjustment: 31
Effective length of query: 377
Effective length of database: 362
Effective search space:   136474
Effective search space used:   136474
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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