GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Halioglobus japonicus S1-36

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_084199387.1 C0029_RS09770 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= curated2:Q4A0N2
         (394 letters)



>NCBI__GCF_002869505.1:WP_084199387.1
          Length = 467

 Score =  153 bits (386), Expect = 1e-41
 Identities = 116/436 (26%), Positives = 206/436 (47%), Gaps = 72/436 (16%)

Query: 8   TDKYSSKNY-SPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQS 66
           + K +SK Y  P +  + +  G  VWD++ N YID  +G++    G+CHP+I++A+ E  
Sbjct: 31  SQKSASKGYVPPAQFIVGRAEGDYVWDLDGNQYIDFQNGWATNPLGNCHPEILEAVHEAQ 90

Query: 67  QRITMVSRALYSDNLGKWEEKI-CKLANK-ENVLPMN---------TGTEAVETAIKMAR 115
           ++              +WE  +   LA +  +++P           +GTEA E+AI +A 
Sbjct: 91  RQYGF-----------QWEHPLRIPLAERLASIMPSGSLPRFSFEVSGTEAAESAIHLAL 139

Query: 116 KWGADIKNIDESSSEIIAMNGNFHGRTLGSLSLSSQDS----YKKGFGPLLNNIHYADFG 171
                          I++    FHG  LG+  +S+ +S    Y +G+      +  A F 
Sbjct: 140 --------CHTQRRYIVSFTSCFHGEGLGTKMVSAYNSDNNLYMEGWA---GGVLKAPFP 188

Query: 172 DIEQLKKLIN-----------------------NQTTAIILEPIQGEGGVNIPPTHFIQE 208
             E++   ++                           AI++EP   EGG  IP   F+Q 
Sbjct: 189 YSEEIPAGMDQAQYTEYCLWYIETHLTEYVVPAENIAAILVEPGLAEGGNWIPSKAFMQG 248

Query: 209 VRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLGGGLYPISAVLANQ 268
           +R++C++++ LLIADE+  GLGRTG M+A+E  +  PDI + GK+L GG+ P + V A  
Sbjct: 249 LRRICDKFDWLLIADEVLTGLGRTGTMWAVEHFDVVPDILVAGKNLSGGIEPCAGVAARD 308

Query: 269 DVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDRLLKHLQQIES--E 326
           +++      T GSTF G P  CA ++  L++   + ++ +   L    ++ +   ES  E
Sbjct: 309 EILGDNPRATAGSTFAGTPGGCAAALKTLEIYERDAVLTHTQHLAGVAMQRMSDWESRYE 368

Query: 327 LIVEVRGRGLFIGIELNVAAQD---------YCEQMINKGVLCKETQGNIIRIAPPLVID 377
           ++ +VRG GL +G+      +D           ++M+ +G+         +R+ P L + 
Sbjct: 369 IVSQVRGLGLLLGVSFRAGREDIEDFHIARSVRDEMLKRGLWAICDNEPQVRMYPALNMA 428

Query: 378 KDEIDEVIRVITEVLE 393
           +D + E +  + E +E
Sbjct: 429 EDVLLEGLSRMEEAIE 444


Lambda     K      H
   0.317    0.136    0.396 

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: 408
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 394
Length of database: 467
Length adjustment: 32
Effective length of query: 362
Effective length of database: 435
Effective search space:   157470
Effective search space used:   157470
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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