GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Ruegeria conchae TW15

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase

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



>NCBI__GCF_000192475.1:WP_010441027.1
          Length = 385

 Score =  110 bits (276), Expect = 5e-29
 Identities = 101/337 (29%), Positives = 173/337 (51%), Gaps = 31/337 (9%)

Query: 65  GGTGWSSVQHYIFNEELQAAPAPQPLAFGV-SMVGPVIYTFGSEEQKKRFLPRIANVDDW 123
           GG G+ SV  Y      Q A       +G+ S+V   I T+GSE+QK ++LP++A+ +  
Sbjct: 70  GGMGFDSVTLYE-----QTARGDAGWGYGIQSIVTHYITTYGSEDQKHKWLPKLASGEMI 124

Query: 124 WCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAKKQE 183
                +EPG+GSD+ ++KT AEK G+ + + G K + T  Q AD +    +TD +    +
Sbjct: 125 GALAMTEPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSL-GAK 183

Query: 184 GISFILVDMK-TKGI-TVRPIQTID-GGHEVNEVFFDDVEVPLENLVG-QENKGWDYAKF 239
           G+S I V+ + T+G    R ++ +   G++  E+FF+DV+VP+ NL+G +E +G+     
Sbjct: 184 GVSLIAVETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQLMK 243

Query: 240 LLGNER--TGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALEL 297
            L  ER   GI  +G     I    +   + ++ G+ V++    R KLA  E + KA E+
Sbjct: 244 QLPWERLTIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLA--ECKTKA-EV 300

Query: 298 TQLRVVADEGKHGKGKPNPA-SSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSN 356
            +  V    GK   G+ + A +S++K  GSE+Q       +++ G +    +        
Sbjct: 301 LRSFVNDCIGKLEAGELDAATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEY------- 353

Query: 357 ETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAV 393
                   IA  Y + R   IYGG+NE+ + +I +++
Sbjct: 354 -------PIARLYADARVQMIYGGTNEVMKELIARSL 383


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: 337
Number of extensions: 13
Number of successful extensions: 2
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: 385
Length adjustment: 31
Effective length of query: 365
Effective length of database: 354
Effective search space:   129210
Effective search space used:   129210
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 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