GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Escherichia coli BW25113

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate 17148 b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq)

Query= curated2:Q4A0N2
         (394 letters)



>FitnessBrowser__Keio:17148
          Length = 459

 Score =  253 bits (645), Expect = 1e-71
 Identities = 144/377 (38%), Positives = 220/377 (58%), Gaps = 22/377 (5%)

Query: 33  DIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRALYSDNLGKWEEKICKLA 92
           D +   +IDC+ GF + N GH +P ++ A+Q Q  +  + S+ L         + +  L 
Sbjct: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137

Query: 93  NKENVLPM--NTGTEAVETAIKMARKWGADIKNIDESSSEIIAMNGNFHGRTLGSLSLSS 150
             +       N+GTE+VE A+K+A+ + +            IA +G FHG++LG+LS ++
Sbjct: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSP-----RGKFTFIATSGAFHGKSLGALSATA 192

Query: 151 QDSYKKGFGPLLNNIHYADFGDIEQLKKLIN------NQTTAIILEPIQGEGGVNIPPTH 204
           + +++K F PLL    +  FG+IE ++  +N      +   A+ILEPIQGEGGV +PP  
Sbjct: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252

Query: 205 FIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLGGGLYPISAV 264
           ++  VR+LC+E+  L+I DE+Q G+GRTGKMFA E EN +PDI  L K+LGGG+ PI A 
Sbjct: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312

Query: 265 LANQDVMSVL--TPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDRLLKHLQQ 322
           +A ++V SVL   P  H +TFGGNPLACA ++A ++VL E++L   A   GD LL   +Q
Sbjct: 313 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQ 372

Query: 323 IESE---LIVEVRGRGLFIGIEL--NVAAQDYCEQMINKGVLCKETQGN--IIRIAPPLV 375
           +  E   L+ E RG+G+ + IE   N    ++  +M  + VL   T  N   IRI PPL 
Sbjct: 373 LAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLT 432

Query: 376 IDKDEIDEVIRVITEVL 392
           +  ++ + VI+   + L
Sbjct: 433 LTIEQCELVIKAARKAL 449


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: 401
Number of extensions: 24
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: 459
Length adjustment: 32
Effective length of query: 362
Effective length of database: 427
Effective search space:   154574
Effective search space used:   154574
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: 51 (24.3 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