GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Burkholderia phytofirmans PsJN

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase

Query= curated2:Q4A0N2
         (394 letters)



>FitnessBrowser__BFirm:BPHYT_RS07695
          Length = 411

 Score =  239 bits (609), Expect = 1e-67
 Identities = 129/384 (33%), Positives = 213/384 (55%), Gaps = 9/384 (2%)

Query: 16  YSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRA 75
           +SP      +G G++VWD +   YID   G +V   GH HP+++  L EQ  ++  +   
Sbjct: 19  FSPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVLHEQGGKLWHIGNG 78

Query: 76  LYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMN 135
             ++ + +  +++  L   +     N+G EA E A+K+AR+   D    D+   EII+  
Sbjct: 79  YTNEPVLRLAKRLEDLTFADRAFFANSGAEANEAALKLARRVAFDRHGADKY--EIISFT 136

Query: 136 GNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGE 195
            +FHGRT  ++S+  Q  Y +GFGP+   I +  + DIE +KK I  QT A+I+EPIQGE
Sbjct: 137 QSFHGRTFFTVSVGGQPKYSEGFGPVPAGITHLPYNDIEAVKKAIGAQTCAVIVEPIQGE 196

Query: 196 GGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLG 255
           GGV      F++ +R+ C+++  LLI DE+Q G+GR+G  +A +     PDI    K+LG
Sbjct: 197 GGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGVTPDILTTAKALG 256

Query: 256 GGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDR 315
            G +PI A+L   ++ +    G HG+T+GGNPL  A++   ++++++  L++      + 
Sbjct: 257 NG-FPIGAMLTTNELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPKLLEGVRSRSEA 315

Query: 316 LLKHLQQIESE--LIVEVRGRGLFIGIELNVA----AQDYCEQMINKGVLCKETQGNIIR 369
           L  HL ++     L  EVRGRGL IG ELN A    A+D+       GV+      +++R
Sbjct: 316 LKGHLAKLNERFGLFTEVRGRGLLIGAELNEAFKGRAKDFVTAAGQHGVIMLMAGPDVLR 375

Query: 370 IAPPLVIDKDEIDEVIRVITEVLE 393
             P L++  D+++E    + + +E
Sbjct: 376 FVPSLIMPLDDMNEGFERLAKAIE 399


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: 350
Number of extensions: 12
Number of successful extensions: 5
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: 411
Length adjustment: 31
Effective length of query: 363
Effective length of database: 380
Effective search space:   137940
Effective search space used:   137940
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