GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Klebsiella michiganensis M5al

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein

Query= curated2:Q4A0N2
         (394 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS26000 BWI76_RS26000 aspartate
           aminotransferase family protein
          Length = 406

 Score =  270 bits (691), Expect = 4e-77
 Identities = 143/385 (37%), Positives = 223/385 (57%), Gaps = 9/385 (2%)

Query: 16  YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75
           Y+P +    KG+G++VWD +   Y+D   G +V   GHCHP ++ AL EQ +++   S  
Sbjct: 21  YAPAEFIPVKGKGSRVWDQQGKEYVDFAGGIAVTALGHCHPALVAALHEQGEKLWHTSNV 80

Query: 76  LYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMN 135
             ++   +   K+      + V+ MN+GTEA ETA K+AR +   +       ++IIA +
Sbjct: 81  FTNEPALRLGRKLVDATFADRVVFMNSGTEANETAFKLARHY--TVTRHSPYKTKIIAFH 138

Query: 136 GNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGE 195
             FHGR+L ++S+  Q  Y  GFGP   +I +  F D+  +K ++++ T A+++EPIQGE
Sbjct: 139 NAFHGRSLFTVSVGGQPKYSDGFGPKPADIVHVPFNDLHAVKAVMDDHTCAVVVEPIQGE 198

Query: 196 GGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLG 255
           GGV      F+Q +R LC+++  LL+ DE+Q G+GRTG +FA       PDI    K+LG
Sbjct: 199 GGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGRTGSLFAYMHYGVTPDILTSAKALG 258

Query: 256 GGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDR 315
           GG +PISA+L   D+ S    G+HGST+GGNPLACAV  AA D++N   ++       + 
Sbjct: 259 GG-FPISAMLTTHDIASAFHAGSHGSTYGGNPLACAVGGAAFDLINTPEVLDGVTAKREL 317

Query: 316 LLKHLQQIES--ELIVEVRGRGLFIGIEL----NVAAQDYCEQMINKGVLCKETQGNIIR 369
            ++HLQQI++  +L  ++RG GL IG EL    +  A+D+       GV+      +++R
Sbjct: 318 FVQHLQQIDARFDLFSDIRGMGLLIGAELKPQYHGKARDFLYAAAEAGVMVLNAGPDVMR 377

Query: 370 IAPPLVIDKDEIDEVIRVITEVLEK 394
             P LVID  +I E +    + +E+
Sbjct: 378 FVPSLVIDDSDIAEGMARFAQAVER 402


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: 341
Number of extensions: 11
Number of successful extensions: 4
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: 406
Length adjustment: 31
Effective length of query: 363
Effective length of database: 375
Effective search space:   136125
Effective search space used:   136125
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