GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Dyadobacter tibetensis Y620-1

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= curated2:Q4A0N2
         (394 letters)



>NCBI__GCF_000566685.1:WP_025763135.1
          Length = 384

 Score =  188 bits (477), Expect = 3e-52
 Identities = 115/374 (30%), Positives = 192/374 (51%), Gaps = 21/374 (5%)

Query: 25  KGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRALYSDNLGKW 84
           K +G+ +WD     Y+D   G +V++ GHCHP  +  L EQ  +I+  S ++      + 
Sbjct: 17  KAQGSYLWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISFYSNSVQIPQQEEL 76

Query: 85  EEKICKLANKEN--VLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMNGNFHGRT 142
             K+  L+   +  +   N+G EA E A+K+A        +      +++A    FHGRT
Sbjct: 77  ATKLGTLSGYPDYKLFLCNSGAEANENALKLA--------SFHTGRKKVVAFTKAFHGRT 128

Query: 143 LGSLSLSSQDSYKKGFGPLLNNIH--YADFGDIEQLKKLINNQTTAIILEPIQGEGGVNI 200
            G+++ +   S      P+  N H  +  F DIE L+  I  +  A+I+E IQG GG+ +
Sbjct: 129 AGAVAATDNPSI---VAPVNYNEHVSFLPFNDIEALQAGITEEVAAVIVEGIQGVGGIQV 185

Query: 201 PPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLGGGLYP 260
               F+Q +R+ C+E    LI D +Q G GRTGK F+ ++    PD+  + K +G G +P
Sbjct: 186 CSDEFLQALRKRCDETGAALILDSVQCGYGRTGKFFSHQFSGIHPDMMTMAKGMGNG-FP 244

Query: 261 ISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDRLLKHL 320
           I+ VL      +    G  G+TFGGN LACA  +A LD++ +E L+ NA  +G  L   +
Sbjct: 245 IAGVLIAPQFKASF--GLLGTTFGGNHLACAAGIAVLDIMKDEQLLDNATKIGAYLFHEI 302

Query: 321 QQIESELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQG-NIIRIAPPLVIDKD 379
           +++      ++RGRGL IGIE +   ++   +++ +  +     G   +R+ P L I + 
Sbjct: 303 EELGG--YKDLRGRGLMIGIEFDFPVKELRNKLLFEHHIFTGVAGAYTLRLLPSLAISQK 360

Query: 380 EIDEVIRVITEVLE 393
           E D+ +      L+
Sbjct: 361 EADQFLEAYRSCLK 374


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: 353
Number of extensions: 20
Number of successful extensions: 6
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: 394
Length of database: 384
Length adjustment: 30
Effective length of query: 364
Effective length of database: 354
Effective search space:   128856
Effective search space used:   128856
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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