GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Sinorhizobium meliloti 1021

Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate SMc02138 SMc02138 acetylornithine transaminase

Query= SwissProt::P38021
         (401 letters)



>lcl|FitnessBrowser__Smeli:SMc02138 SMc02138 acetylornithine
           transaminase
          Length = 399

 Score =  243 bits (620), Expect = 7e-69
 Identities = 135/366 (36%), Positives = 207/366 (56%), Gaps = 8/366 (2%)

Query: 20  NNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADKITLTS 79
           + Y   P+      G W+   +G  Y+D  +  +  + GH HP +++ALK QADK+   S
Sbjct: 9   DTYLRAPLRFERGEGVWLIAEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQADKVWHLS 68

Query: 80  RAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAEIIA 139
             +          +  ++T  + +   N+GAEA+E A+K ARR+ +  KG  + +  +I 
Sbjct: 69  NLYEIAGQESLARRLTQVTFADRVFFTNSGAEALECAIKTARRYHF-AKGHVE-KFHVIT 126

Query: 140 CVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNTAAFLFEPIQ 199
             G FHGRT+  ++   +++Y  GFGP  PG   +P+GD+ A++ AI   TAA L EPIQ
Sbjct: 127 FEGAFHGRTLATIAAGGQQKYIEGFGPKAPGFYQVPFGDIGAVKNAINEETAAILVEPIQ 186

Query: 200 GEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYILGKA 259
           GE GI    + F+Q    +C E  +L I DE+Q+G+GRTGK FA +W GI PD+  + K 
Sbjct: 187 GEGGIRTASKEFMQGLRELCDEFGLLLILDEVQSGVGRTGKLFAHEWAGIKPDIMAVAKG 246

Query: 260 LGGGVFPI-SCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLEDEKLADRSLEL 318
           +GGG FP+ +C+A +    G+   G+HGST+GGNPLA AV  A L+V+  E   D+  E+
Sbjct: 247 IGGG-FPLGACLATEAAAAGMV-AGTHGSTYGGNPLAMAVGNAVLDVVLAEGFLDQVREV 304

Query: 319 GEYFKSELESIDS---PVIKEVRGRGLFIGVELTEAARPYCERLKEEGLLCKETHDTVIR 375
              F+  L S+      VI+E+RG GL +G++    +    + ++ E LL     + V+R
Sbjct: 305 ALVFRQGLASLKDRFPDVIEEIRGDGLMLGIKAKVPSADLLKAIRAEKLLVVPAGENVLR 364

Query: 376 FAPPLI 381
             PPLI
Sbjct: 365 LLPPLI 370


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: 383
Number of extensions: 14
Number of successful extensions: 4
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: 399
Length adjustment: 31
Effective length of query: 370
Effective length of database: 368
Effective search space:   136160
Effective search space used:   136160
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: 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