GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B 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)



>FitnessBrowser__Cola:Echvi_2919
          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 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