GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS26000
          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 (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