GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Marinobacter adhaerens HP15

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein

Query= curated2:Q4A0N2
         (394 letters)



>FitnessBrowser__Marino:GFF3099
          Length = 404

 Score =  257 bits (656), Expect = 5e-73
 Identities = 141/393 (35%), Positives = 227/393 (57%), Gaps = 10/393 (2%)

Query: 9   DKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQR 68
           D+    NY+P  +   +G G+++WD E   +ID   G +V   GH HP ++ AL +Q+++
Sbjct: 12  DEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEK 71

Query: 69  ITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESS 128
           I  +S  + ++   +  + +C L   E V   N+G EA E A K+AR++  +  +  +  
Sbjct: 72  IWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRYAWE--HHGKEK 129

Query: 129 SEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTT-AI 187
           +EII+   +FHGRTL ++S+  Q  Y +GF P    IH+A+F D+E +KKLI+ + T AI
Sbjct: 130 NEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEKTCAI 189

Query: 188 ILEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDI 247
           ++EPIQGEGGV      F+Q +R LC+E + LL+ DE+Q G+GR+G  +A +     PDI
Sbjct: 190 VVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPDI 249

Query: 248 YLLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQ 307
               K LGGG +P++A+L    V + L  GTHGST+GGN LACAV+   +D +++  +++
Sbjct: 250 LSSAKGLGGG-FPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILK 308

Query: 308 NALDLGDRLLKHLQQIESE--LIVEVRGRGLFIGIELNV----AAQDYCEQMINKGVLCK 361
                 D+L K +  I     +  EVRG GL +G  L       A+D+    + +GV+  
Sbjct: 309 GVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMVL 368

Query: 362 ETQGNIIRIAPPLVIDKDEIDEVIRVITEVLEK 394
               N+IR+AP L+I + +I+  +      ++K
Sbjct: 369 VAGANVIRLAPSLIIPEPDIELALERFEAAVKK 401


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: 374
Number of extensions: 15
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: 404
Length adjustment: 31
Effective length of query: 363
Effective length of database: 373
Effective search space:   135399
Effective search space used:   135399
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