GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Pseudomonas fluorescens FW300-N1B4

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate Pf1N1B4_5610 Probable acyl-CoA dehydrogenase (EC 1.3.99.3)

Query= metacyc::MONOMER-20676
         (396 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5610
          Length = 387

 Score =  147 bits (370), Expect = 7e-40
 Identities = 102/315 (32%), Positives = 156/315 (49%), Gaps = 18/315 (5%)

Query: 48  RILNKKGWAVTHWPKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSE 107
           + L   GW     P EYGG+G    +  +  EE+           G       +   GSE
Sbjct: 43  KALTDAGWLAAMIPVEYGGSGLGLAEASVILEEVNRCGGNSGTVHGQMYNMFTLLRHGSE 102

Query: 108 EQKKRFLPRIANVD-DWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHA 166
            QK  +LP++A+ +      G +EP +G+D   +KT A +KGDK++INGQK W +  QH+
Sbjct: 103 AQKSYYLPKLASGELRLQSMGVTEPTTGTDTTKIKTTAVRKGDKYVINGQKVWISRIQHS 162

Query: 167 DWIFCLCRTDPAA---KKQEGISFILVDMKT---KGITVRPIQTIDGGHEVNEVFFDDVE 220
           D +  L RT P A   KK EG+S  LVD++     G+TV+PI  +   HE NE+FFD++E
Sbjct: 163 DLMILLARTTPLANVQKKSEGMSIFLVDLREAIGNGMTVQPIANM-VNHETNELFFDNLE 221

Query: 221 VPLENLVGQENKGWDYAKFLLGNERTGIAR--VGMSKERIRRIKQLAAQVESGGKPVIED 278
           +P ++L+G+E KG+ Y    L  ERT IA   +G  +  I +    A      G+P+ ++
Sbjct: 222 IPADSLIGEEGKGFRYILDGLNAERTLIAAECIGDGRWFIEKASAYARDRVVFGRPIGQN 281

Query: 279 PKFRDKLAAVEIELKALELTQLRVVA--DEGKHGKGKPNPASSVLKIKGSEIQQATTELL 336
              +  +A   IE++A +L + R     D G +     N A    K   ++         
Sbjct: 282 QGVQFPIAEAHIEIEAADLMRWRACEEYDSGINAGASANMA----KYLAAKASWEAANAC 337

Query: 337 MEVIG--PFAAPYDV 349
           ++  G   FA  YDV
Sbjct: 338 LQTHGGFGFACEYDV 352


Lambda     K      H
   0.317    0.135    0.411 

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: 353
Number of extensions: 19
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: 396
Length of database: 387
Length adjustment: 31
Effective length of query: 365
Effective length of database: 356
Effective search space:   129940
Effective search space used:   129940
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.

Links

Downloads

Related tools

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