GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc02138
          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:

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