GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Neptunomonas antarctica S3-22

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_054341133.1 Nant_RS08065 acetyl-CoA C-acyltransferase FadA

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_001305295.1:WP_054341133.1
          Length = 392

 Score =  308 bits (788), Expect = 2e-88
 Identities = 179/406 (44%), Positives = 245/406 (60%), Gaps = 28/406 (6%)

Query: 3   EAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61
           +  I DGIRTP+G+  GG+  +VRA+ L+A  ++ LL RNP ++   I+DV+ GC NQ  
Sbjct: 7   DVVIVDGIRTPMGKSKGGSFRNVRAESLSASIMKGLLARNPNVNPADIEDVVWGCVNQTK 66

Query: 62  EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121
           E   N+AR A +LAGLP +V G TINRLCGS + AL  AA++I  G+GD  I GGVE M 
Sbjct: 67  EQGFNIARNALVLAGLPHTVGGQTINRLCGSSMSALHNAAQSIMTGNGDTFIVGGVEHMG 126

Query: 122 RAPFVMG----KAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKIS 177
               + G       S +  +A M                      M  TAE + ++  IS
Sbjct: 127 HLNILHGIDLNSEMSKYVAKAAMM---------------------MGITAEMLGKMNGIS 165

Query: 178 REDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRG 237
           RE QD F  RS +   +A+ +G    EI+ +   +  G  + ++ DE +RPETT E L+ 
Sbjct: 166 REMQDEFGARSHRLAHEARETGRFDNEIIAIEGHDANGFKSLLEQDEVIRPETTFEVLQS 225

Query: 238 LKAPFRAN-GVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMG 296
           LK  F    G +TAG +S  +DGA+ +++ S   A + GL PRA I +MA AG +P +MG
Sbjct: 226 LKPAFVPKVGTVTAGTSSAFSDGASGMLVMSAAKAQSLGLKPRAVIRSMAVAGCDPSIMG 285

Query: 297 LGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDD-APHVNPNGGAIAL 355
            GPVPAT++ L+RAGL + D+D IELNEAFAAQ L VL+ L L D    +VN NGGAIAL
Sbjct: 286 YGPVPATQKALKRAGLKMDDIDYIELNEAFAAQGLAVLKGLKLLDRMEENVNLNGGAIAL 345

Query: 356 GHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           GHPLG SG R++    + L ++NG + L TMCIG+GQG+A + ER+
Sbjct: 346 GHPLGCSGTRISTTLLNVLEQKNGTFGLATMCIGMGQGVATVFERL 391


Lambda     K      H
   0.319    0.135    0.384 

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: 434
Number of extensions: 23
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: 401
Length of database: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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