GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Pedobacter sp. GW460-11-11-14-LB5

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein

Query= curated2:Q4A0N2
         (394 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS15205 CA265_RS15205 aspartate
           aminotransferase family protein
          Length = 378

 Score =  228 bits (580), Expect = 3e-64
 Identities = 140/386 (36%), Positives = 215/386 (55%), Gaps = 38/386 (9%)

Query: 21  LALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRALYSDN 80
           L   + +G  ++D ++  +ID I+G  V N GHCHP ++KA+QEQ++  T +   +Y + 
Sbjct: 2   LEFVRAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAE--TYMHLMVYGEY 59

Query: 81  LGKWEEKICKLANKENVLP--------MNTGTEAVETAIKMARKWGADIKNIDESSSEII 132
           +   +    K     ++LP        +N+GTEAVE A+K+A+++              I
Sbjct: 60  VQTPQVNFAKAL--ADILPESLSCTYFLNSGTEAVEGAMKLAKRY--------TGRKGFI 109

Query: 133 AMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPI 192
           A    +HG T G+ SL   D Y  G+GP L ++ + +  ++  L+K I N+  A+ +EPI
Sbjct: 110 ACKNAYHGSTQGAESLMESDFYSSGYGPFLPHVSFIEHNNLADLEK-ITNEIAAVFIEPI 168

Query: 193 QGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGK 252
           QGE G+ +    ++Q +R  C E   LLI DEIQ G GR+GKMFA E  N  PD+ LL K
Sbjct: 169 QGEAGIRVSDLSYMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLLLAK 228

Query: 253 SLGGGLYPISAVLANQDVMSVLTPGT---HGSTFGGNPLACAVSMAALDVLNEEHLVQNA 309
            +GGG+ PI A +++ ++MSVL+      H +TFGG+P+ CA  +A L  L ++H+V   
Sbjct: 229 GIGGGM-PIGAFISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVDEV 287

Query: 310 LDLGDRLLKHLQQIESELIVEVRGRGLFIGI-----ELNVAAQDYCEQMINKGVLCKETQ 364
            + G +L K L  ++   I E+RG+GL + +     E+N    D C   I  GVL     
Sbjct: 288 EEKG-QLFKQL--LQHPAIKEIRGKGLMLAVEFENFEINKKIIDAC---ILDGVLSDWFL 341

Query: 365 --GNIIRIAPPLVIDKDEIDEVIRVI 388
              N +RIAPPL+I K+EI E   +I
Sbjct: 342 HCSNSMRIAPPLIITKEEIAEACTII 367


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: 327
Number of extensions: 17
Number of successful extensions: 8
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: 378
Length adjustment: 30
Effective length of query: 364
Effective length of database: 348
Effective search space:   126672
Effective search space used:   126672
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 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