GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7025360
          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 (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