GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Pseudomonas putida KT2440

Align Ornithine aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate PP_4108 PP_4108 putative 4-aminobutyrate aminotransferase

Query= SwissProt::Q6CWC1
         (437 letters)



>FitnessBrowser__Putida:PP_4108
          Length = 416

 Score =  167 bits (422), Expect = 7e-46
 Identities = 127/419 (30%), Positives = 209/419 (49%), Gaps = 37/419 (8%)

Query: 30  PVVFSRASGAHVWDPEGKEYLDFLSAYSAVNQGHCHPHIIQALVDQASKLT-LSSRAFSN 88
           P+  S    A VWD +GK Y+DF+     +N GHC+P +++A+  QA++LT  +  A  +
Sbjct: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74

Query: 89  DCFASFSKFVTEFFGYESVLP---MNTGAEAVESALKLARRWGYMVKKIQPNEAIILGAR 145
             + +  + +++F      L     N+GAEA E+ALK+AR            +  I+   
Sbjct: 75  GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG--------ATGKRAIIAFD 126

Query: 146 GNFHGRTFGAISLSTDEEDSRMNFGPFLENVTAKIPGGSDDEFIRYGE-IDDYKRAF--E 202
           G FHGRT   ++L+      +   G  L      +P  S D  +   + +    R F  E
Sbjct: 127 GGFHGRTLATLNLNGKVAPYKQRVGE-LPGPVYHLPYPSADTGVTCEQALKAMDRLFSVE 185

Query: 203 SHGDKICAVIVEPIQGEAGIVVPRADFLTDLQELCKKHQVLLICDEIQTGIARTGKLLCY 262
              + + A I EP+QGE G +     F   L+  C +  +L+I DEIQ+G  RTG+   +
Sbjct: 186 LAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAF 245

Query: 263 EHSPNCKPDIILLGKAISGGVLPVSCVLSSREIMDCFTPGSHGSTYGGNPLASRVAIAAL 322
                 +PD++LL K+I+GG +P+  V+  +E+M     G  G TY GNP++   A+A+L
Sbjct: 246 PRL-GIEPDLLLLAKSIAGG-MPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303

Query: 323 EVVQNENLVERSARLGKFLQDELVKLQHE---SNGV---ISEVRGKGLLTAIVINPEKAN 376
             + +ENL     R     Q++ +  ++E   ++G+   I  + G G +  I      A+
Sbjct: 304 AQMTDENLATWGER-----QEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEF--ANAD 356

Query: 377 GRTA-WDLCLLM---KDQGVLAKPTHE--HIIRLAPPLVISEEDLLKGVDSIRVSLSKL 429
           G  A   L  +M   + +G+L  P+ +  HIIRL  PL I  E L +G+D +   L++L
Sbjct: 357 GSPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415


Lambda     K      H
   0.318    0.136    0.400 

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: 387
Number of extensions: 14
Number of successful extensions: 7
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: 437
Length of database: 416
Length adjustment: 32
Effective length of query: 405
Effective length of database: 384
Effective search space:   155520
Effective search space used:   155520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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