GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Shewanella sp. ANA-3

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate 7025360 Shewana3_2520 aminotransferase (RefSeq)

Query= BRENDA::P31893
         (426 letters)



>lcl|FitnessBrowser__ANA3:7025360 Shewana3_2520 aminotransferase
           (RefSeq)
          Length = 452

 Score =  104 bits (260), Expect = 5e-27
 Identities = 85/286 (29%), Positives = 136/286 (47%), Gaps = 42/286 (14%)

Query: 52  YGAHNYHHCSAYRAKGVSLDM-EGKRYFDFLSAYSAVNQGHCHPKIVNTMVEQAQRLT-- 108
           YG H+        A+G  L++ +G++  D  S++ A   G+ HP I+  M  Q  +L+  
Sbjct: 28  YGVHS--------AQGCELELVDGRKLIDGTSSWWACVHGYGHPAILTAMERQLHQLSHV 79

Query: 109 ----LTSRAFYT---DVLGEYEEFLTKLFNYDKVLPMNTGVEGGETACKIA-RCWAYMKK 160
               +T     T    +L    E LTK+F  D      +G    E A K+A + W     
Sbjct: 80  MFGGITHEPAITLCKKLLAMTCEPLTKVFLCD------SGSIAVEVAIKMALQYWQGQDL 133

Query: 161 KVPENQAK--IIFAENNFWGRTLSAISASTDPMSYDEL------------RPYMPGFEIV 206
            + +   K  I+  +  + G T +A+S          +             P  P  E +
Sbjct: 134 PLAQKAQKQRILTVKKGYHGDTFAAMSVCDPEGGMHTMFGEAVTKQCFVDAPQTPFGEPL 193

Query: 207 KYNDTAALEKAF--QDPNVCAYMVEPI-QGEAGVVALDAGYLTEVRELCTKYNVLFIADE 263
           + +D A +++    Q P + A ++EPI QG  G+    + YL  +R LC +YNVL I DE
Sbjct: 194 RQDDLAPMQRILREQHPEIAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNVLLILDE 253

Query: 264 VQTGLARTGRMLAVDHEDVKPDLLILGKALSGGLYPVSAVLRDDHI 309
           + TG  RTG++ A +H D+ PD+L LGKAL+GG   ++A L  D++
Sbjct: 254 IATGFGRTGKLFAYEHADITPDILCLGKALTGGYISLAATLCTDNV 299


Lambda     K      H
   0.322    0.137    0.424 

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: 424
Number of extensions: 21
Number of successful extensions: 2
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: 426
Length of database: 452
Length adjustment: 32
Effective length of query: 394
Effective length of database: 420
Effective search space:   165480
Effective search space used:   165480
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 (21.9 bits)
S2: 51 (24.3 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, 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